From f8f6309b66758dbbea46963723a885450643e4cf Mon Sep 17 00:00:00 2001 From: jennydaman Date: Mon, 12 Feb 2024 02:26:57 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20FNNDSC/a?= =?UTF-8?q?iochris@2ff1cae8445126840ef68838f42eb90083cefae5=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- v0.5.0a3/aiochris.html | 1871 +++++++++++++++++ v0.5.0a3/aiochris/client.html | 244 +++ v0.5.0a3/aiochris/client/admin.html | 804 +++++++ v0.5.0a3/aiochris/client/anon.html | 445 ++++ v0.5.0a3/aiochris/client/authed.html | 1537 ++++++++++++++ v0.5.0a3/aiochris/client/base.html | 648 ++++++ v0.5.0a3/aiochris/client/from_chrs.html | 824 ++++++++ v0.5.0a3/aiochris/client/normal.html | 434 ++++ v0.5.0a3/aiochris/errors.html | 560 +++++ v0.5.0a3/aiochris/models.html | 249 +++ .../aiochris/models/collection_links.html | 674 ++++++ v0.5.0a3/aiochris/models/data.html | 719 +++++++ v0.5.0a3/aiochris/models/logged_in.html | 1525 ++++++++++++++ v0.5.0a3/aiochris/models/public.html | 630 ++++++ v0.5.0a3/aiochris/types.html | 555 +++++ v0.5.0a3/aiochris/util.html | 262 +++ v0.5.0a3/aiochris/util/search.html | 1047 +++++++++ v0.5.0a3/index.html | 7 + v0.5.0a3/search.js | 46 + 19 files changed, 13081 insertions(+) create mode 100644 v0.5.0a3/aiochris.html create mode 100644 v0.5.0a3/aiochris/client.html create mode 100644 v0.5.0a3/aiochris/client/admin.html create mode 100644 v0.5.0a3/aiochris/client/anon.html create mode 100644 v0.5.0a3/aiochris/client/authed.html create mode 100644 v0.5.0a3/aiochris/client/base.html create mode 100644 v0.5.0a3/aiochris/client/from_chrs.html create mode 100644 v0.5.0a3/aiochris/client/normal.html create mode 100644 v0.5.0a3/aiochris/errors.html create mode 100644 v0.5.0a3/aiochris/models.html create mode 100644 v0.5.0a3/aiochris/models/collection_links.html create mode 100644 v0.5.0a3/aiochris/models/data.html create mode 100644 v0.5.0a3/aiochris/models/logged_in.html create mode 100644 v0.5.0a3/aiochris/models/public.html create mode 100644 v0.5.0a3/aiochris/types.html create mode 100644 v0.5.0a3/aiochris/util.html create mode 100644 v0.5.0a3/aiochris/util/search.html create mode 100644 v0.5.0a3/index.html create mode 100644 v0.5.0a3/search.js diff --git a/v0.5.0a3/aiochris.html b/v0.5.0a3/aiochris.html new file mode 100644 index 0000000..a02f2b2 --- /dev/null +++ b/v0.5.0a3/aiochris.html @@ -0,0 +1,1871 @@ + + + + + + + aiochris API documentation + + + + + + + + + +
+
+

+aiochris

+ +

ChRIS Python client library built on +aiohttp (async HTTP client) and +pyserde +(dataclasses deserializer).

+ +

Installation

+ +

Requires Python 3.10 or 3.11.

+ +
+
pip install aiochris
+# or
+poetry add aiochris
+
+
+ +

Brief Example

+ +
+
from aiochris import ChrisClient
+
+chris = await ChrisClient.from_login(
+    username='chris',
+    password='chris1234',
+    url='https://cube.chrisproject.org/api/v1/'
+)
+dircopy = await chris.search_plugins(name_exact='pl-brainmgz', version='2.0.3').get_only()
+plinst = await dircopy.create_instance(compute_resource_name='host')
+await plinst.set(title="copies brain image files into feed")
+
+
+ +

Introduction

+ +

aiochris provides three core classes: AnonChrisClient, ChrisClient, and ChrisAdminClient. +These clients differ in permissions.

+ +

+Methods are only defined for what the client has permission to see or do.

+ +
+
anon_client = await AnonChrisClient.from_url('https://cube.chrisproject.org/api/v1/')
+# ok: can search for plugins without logging in...
+plugin = await anon_client.search_plugins(name_exact='pl-mri10yr06mo01da_normal').first()
+# IMPOSSIBLE! AnonChrisClient.create_instance not defined...
+await plugin.create_instance()
+
+# IMPOSSIBLE! authentication required for ChrisClient
+authed_client = await ChrisClient.from_url('https://cube.chrisproject.org/api/v1/')
+authed_client = await ChrisClient.from_login(
+    url='https://cube.chrisproject.org/api/v1/',
+    username='chris',
+    password='chris1234'
+)
+# authenticated client can also search for plugins
+plugin = await authed_client.search_plugins(name_exact='pl-mri10yr06mo01da_normal').first()
+await plugin.create_instance()  # works!
+
+
+ +

+ +

Client Constructors

+ + + +

aiochris in Jupyter Notebook

+ +

Jupyter and IPython support top-level await. This, in conjunction with ChrisClient.from_chrs, +make aiochris a great way to use _ChRIS_ interactively with code.

+ +

For a walkthrough, see https://github.com/FNNDSC/aiochris/blob/master/examples/aiochris_as_a_shell.ipynb

+ +

Working with aiohttp

+ +

aiochris hides the implementation detail that it is built upon aiohttp, +however one thing is important to keep in mind: +be sure to call ChrisClient.close at the end of your program.

+ +
+
chris = await ChrisClient.from_login(...)
+# -- snip --
+await chris.close()
+
+
+ +

You can also use an +asynchronous context manager.

+ +
+
async with (await ChrisClient.from_login(...)) as chris:
+    await chris.upload_file('./something.dat', 'something.dat')
+    ...
+
+
+ +

Efficiency with Multiple Clients

+ +

If using more than one aiohttp client in an application, it's more efficient +to use the same +connector. +One connector instance should be shared among every client object, +including all aiochris clients and other aiohttp clients.

+ +

+Example: efficiently using multiple aiohttp clients

+ +
+
import aiohttp
+from aiochris import ChrisClient
+
+with aiohttp.TCPConnector() as connector:
+    chris_client1 = await ChrisClient.from_login(
+        url='https://example.com/cube/api/v1/',
+        username='user1',
+        password='user1234',
+        connector=connector,
+        connector_owner=False
+    )
+    chris_client2 = await ChrisClient.from_login(
+        url='https://example.com/cube/api/v1/',
+        username='user2',
+        password='user4321',
+        connector=connector,
+        connector_owner=False
+    )
+    plain_http_client = aiohttp.ClientSession(connector=connector, connector_owner=False)
+
+
+ +

+ +

Advice for Getting Started

+ +

Searching for things (plugins, plugin instances, files) in CUBE is a common task, +and CUBE often returns multiple items per response. +Hence, it is important to understand how the Search helper class works. +It simplifies how we interact with paginated collection responses from CUBE.

+ +

When performing batch operations, use +asyncio.gather +to run async functions concurrently.

+ +

aiochris uses many generic types, so it is recommended you use an IDE +with good support for type hints, such as +PyCharm +or VSCodium with +Pylance configured.

+ +

Examples

+ +

Create a client given username and password

+ +
+
from aiochris import ChrisClient
+
+chris = await ChrisClient.from_login(
+    url='https://cube.chrisproject.org/api/v1/',
+    username='chris',
+    password='chris1234'
+)
+
+
+ +

Search for a plugin

+ +
+
# it's recommended to specify plugin version
+plugin = await chris.search_plugins(name_exact="pl-dcm2niix", version="0.1.0").get_only()
+
+# but if you don't care about plugin version...
+plugin = await chris.search_plugins(name_exact="pl-dcm2niix").first()
+
+
+ +

Create a feed by uploading a file

+ +
+
uploaded_file = await chris.upload_file('./brain.nii', 'my_experiment/brain.nii')
+dircopy = await chris.search_plugins(name_exact='pl-dircopy', version="2.1.1").get_only()
+plinst = await dircopy.create_instance(dir=uploaded_file.parent)
+feed = await plinst.get_feed()
+await feed.set(name="An experiment on uploaded file brain.nii")
+
+
+ +

Run a ds-type ChRIS plugin

+ +
+
# search for plugin to run
+plugin = await chris.search_plugins(name_exact="pl-dcm2niix", version="0.1.0").get_only()
+
+# search for parent node 
+previous = await chris.plugin_instances(id=44).get_only()
+
+await plugin.create_instance(
+    previous=previous,               # required. alternatively, specify previous_id
+    title="convert DICOM to NIFTI",  # optional
+    compute_resource_name="galena",  # optional
+    memory_limit="2000Mi",           # optional
+    d=9,                             # optional parameter of pl-dcm2niix
+)
+
+
+ +

Search for plugin instances

+ +
+
finished_freesurfers = chris.plugin_instances(
+    plugin_name_exact='pl-fshack',
+    status='finishedSuccessfully'
+)
+async for p in finished_freesurfers:
+    print(f'"{p.title}" finished on date: {p.end_date}')
+
+
+ +

Delete all plugin instances with a given title, in parallel

+ +
+
import asyncio
+from aiochris import ChrisClient, acollect
+
+chris = ChrisClient.from_login(...)
+search = chris.plugin_instances(title="delete me")
+plugin_instances = await acollect(search)
+await asyncio.gather(*(p.delete() for p in plugin_instances))
+
+
+ +

Enable Debug Logging

+ +

A log message will be printed to stderr before every HTTP request is sent.

+ +
+
import logging
+
+logging.basicConfig(level=logging.DEBUG)
+
+
+
+ + + + + + 
 1"""
+ 2.. include:: ./home.md
+ 3
+ 4.. include:: ./examples.md
+ 5"""
+ 6
+ 7import aiochris.client
+ 8import aiochris.models
+ 9import aiochris.util
+10from aiochris.util.search import Search, acollect
+11from aiochris.client.normal import ChrisClient
+12from aiochris.client.anon import AnonChrisClient
+13from aiochris.client.admin import ChrisAdminClient
+14from aiochris.enums import Status, ParameterTypeName
+15
+16__all__ = [
+17    "AnonChrisClient",
+18    "ChrisClient",
+19    "ChrisAdminClient",
+20    "Search",
+21    "acollect",
+22    "Status",
+23    "ParameterTypeName",
+24    "client",
+25    "models",
+26    "util",
+27    "errors",
+28    "types",
+29]
+
+ + +
+
+ +
+ + class + AnonChrisClient(aiochris.client.base.BaseChrisClient[aiochris.models.collection_links.AnonymousCollectionLinks, 'AnonChrisClient']): + + + +
+ + 
13class AnonChrisClient(BaseChrisClient[AnonymousCollectionLinks, "AnonChrisClient"]):
+14    """
+15    An anonymous ChRIS client. It has access to read-only GET resources,
+16    such as being able to search for plugins.
+17    """
+18
+19    @classmethod
+20    async def from_url(
+21        cls,
+22        url: str,
+23        max_search_requests: int = 100,
+24        connector: Optional[aiohttp.BaseConnector] = None,
+25        connector_owner: bool = True,
+26    ) -> "AnonChrisClient":
+27        """
+28        Create an anonymous client.
+29
+30        See `aiochris.client.base.BaseChrisClient.new` for parameter documentation.
+31        """
+32        return await cls.new(
+33            url=url,
+34            max_search_requests=max_search_requests,
+35            connector=connector,
+36            connector_owner=connector_owner,
+37        )
+38
+39    @http.search("plugins")
+40    def search_plugins(self, **query) -> Search[PublicPlugin]:
+41        """
+42        Search for plugins.
+43
+44        Since this client is not logged in, you cannot create plugin instances using this client.
+45        """
+46        ...
+
+ + +

An anonymous ChRIS client. It has access to read-only GET resources, +such as being able to search for plugins.

+
+ + +
+ +
+
@classmethod
+ + async def + from_url( cls, url: str, max_search_requests: int = 100, connector: Optional[aiohttp.connector.BaseConnector] = None, connector_owner: bool = True) -> aiochris.AnonChrisClient: + + + +
+ + 
19    @classmethod
+20    async def from_url(
+21        cls,
+22        url: str,
+23        max_search_requests: int = 100,
+24        connector: Optional[aiohttp.BaseConnector] = None,
+25        connector_owner: bool = True,
+26    ) -> "AnonChrisClient":
+27        """
+28        Create an anonymous client.
+29
+30        See `aiochris.client.base.BaseChrisClient.new` for parameter documentation.
+31        """
+32        return await cls.new(
+33            url=url,
+34            max_search_requests=max_search_requests,
+35            connector=connector,
+36            connector_owner=connector_owner,
+37        )
+
+ + +

Create an anonymous client.

+ +

See aiochris.client.base.BaseChrisClient.new for parameter documentation.

+
+ + +
+
+ +
+
@http.search('plugins')
+ + def + search_plugins( self, **query) -> aiochris.Search[aiochris.models.public.PublicPlugin]: + + + +
+ + 
39    @http.search("plugins")
+40    def search_plugins(self, **query) -> Search[PublicPlugin]:
+41        """
+42        Search for plugins.
+43
+44        Since this client is not logged in, you cannot create plugin instances using this client.
+45        """
+46        ...
+
+ + +

Search for plugins.

+ +

Since this client is not logged in, you cannot create plugin instances using this client.

+
+ + +
+
+
Inherited Members
+
+
aiochris.link.collection_client.CollectionJsonApiClient
+
CollectionJsonApiClient
+
url
+ + +
+ +
aiochris.link.linked.Linked
+
max_search_requests
+ +
+
+
+
+
+ +
+ + class + ChrisClient(aiochris.client.authed.AuthenticatedClient[aiochris.models.collection_links.CollectionLinks, 'ChrisClient']): + + + +
+ + 
15class ChrisClient(AuthenticatedClient[CollectionLinks, "ChrisClient"]):
+16    """
+17    A normal user *ChRIS* client, who may upload files and create plugin instances.
+18    """
+19
+20    @classmethod
+21    async def create_user(
+22        cls,
+23        url: ChrisURL | str,
+24        username: Username | str,
+25        password: Password | str,
+26        email: str,
+27        session: Optional[aiohttp.ClientSession] = None,
+28    ) -> UserData:
+29        payload = {
+30            "template": {
+31                "data": [
+32                    {"name": "email", "value": email},
+33                    {"name": "username", "value": username},
+34                    {"name": "password", "value": password},
+35                ]
+36            }
+37        }
+38        headers = {
+39            "Content-Type": "application/vnd.collection+json",
+40            "Accept": "application/json",
+41        }
+42        async with _optional_session(session) as session:
+43            res = await session.post(url + "users/", json=payload, headers=headers)
+44            await raise_for_status(res)
+45            return from_json(UserData, await res.text())
+
+ + +

A normal user ChRIS client, who may upload files and create plugin instances.

+
+ + +
+ +
+
@classmethod
+ + async def + create_user( cls, url: Union[aiochris.types.ChrisURL, str], username: Union[aiochris.types.Username, str], password: Union[aiochris.types.Password, str], email: str, session: Optional[aiohttp.client.ClientSession] = None) -> aiochris.models.data.UserData: + + + +
+ + 
20    @classmethod
+21    async def create_user(
+22        cls,
+23        url: ChrisURL | str,
+24        username: Username | str,
+25        password: Password | str,
+26        email: str,
+27        session: Optional[aiohttp.ClientSession] = None,
+28    ) -> UserData:
+29        payload = {
+30            "template": {
+31                "data": [
+32                    {"name": "email", "value": email},
+33                    {"name": "username", "value": username},
+34                    {"name": "password", "value": password},
+35                ]
+36            }
+37        }
+38        headers = {
+39            "Content-Type": "application/vnd.collection+json",
+40            "Accept": "application/json",
+41        }
+42        async with _optional_session(session) as session:
+43            res = await session.post(url + "users/", json=payload, headers=headers)
+44            await raise_for_status(res)
+45            return from_json(UserData, await res.text())
+
+ + + + +
+
+
Inherited Members
+
+
aiochris.link.collection_client.CollectionJsonApiClient
+
CollectionJsonApiClient
+
url
+ + +
+ + +
aiochris.link.linked.Linked
+
max_search_requests
+ +
+
+
+
+
+ +
+ + class + ChrisAdminClient(aiochris.client.authed.AuthenticatedClient[aiochris.models.collection_links.AdminCollectionLinks, 'ChrisAdminClient']): + + + +
+ + 
 34class ChrisAdminClient(AuthenticatedClient[AdminCollectionLinks, "ChrisAdminClient"]):
+ 35    """
+ 36    A client who has access to `/chris-admin/`. Admins can register new plugins and
+ 37    add new compute resources.
+ 38    """
+ 39
+ 40    @http.post("admin")
+ 41    async def _register_plugin_from_store_raw(
+ 42        self, plugin_store_url: str, compute_names: str
+ 43    ) -> Plugin:
+ 44        ...
+ 45
+ 46    async def register_plugin_from_store(
+ 47        self, plugin_store_url: PluginUrl, compute_names: Iterable[ComputeResourceName]
+ 48    ) -> Plugin:
+ 49        """
+ 50        Register a plugin from a ChRIS Store.
+ 51        """
+ 52        return await self._register_plugin_from_store_raw(
+ 53            plugin_store_url=plugin_store_url, compute_names=",".join(compute_names)
+ 54        )
+ 55
+ 56    async def add_plugin(
+ 57        self,
+ 58        plugin_description: str | dict,
+ 59        compute_resources: str
+ 60        | ComputeResource
+ 61        | Iterable[ComputeResource | ComputeResourceName],
+ 62    ) -> Plugin:
+ 63        """
+ 64        Add a plugin to *CUBE*.
+ 65
+ 66        Examples
+ 67        --------
+ 68
+ 69        ```python
+ 70        cmd = ['docker', 'run', '--rm', 'fnndsc/pl-mri-preview', 'chris_plugin_info']
+ 71        output = subprocess.check_output(cmd, text=True)
+ 72        desc = json.loads(output)
+ 73        desc['name'] = 'pl-mri-preview'
+ 74        desc['public_repo'] = 'https://github.com/FNNDSC/pl-mri-preview'
+ 75        desc['dock_image'] = 'fnndsc/pl-mri-preview'
+ 76
+ 77        await chris_admin.add_plugin(plugin_description=desc, compute_resources='host')
+ 78        ```
+ 79
+ 80        The example above is just for show. It's not a good example for several reasons:
+ 81
+ 82        - Calls blocking function `subprocess.check_output` in asynchronous context
+ 83        - It is preferred to use a versioned string for `dock_image`
+ 84        - `host` compute environment is not guaranteed to exist. Instead, you could
+ 85          call `aiochris.client.authed.AuthenticatedClient.search_compute_resources`
+ 86          or `aiochris.client.authed.AuthenticatedClient.get_all_compute_resources`:
+ 87
+ 88        ```python
+ 89        all_computes = await chris_admin.get_all_compute_resources()
+ 90        await chris_admin.add_plugin(plugin_description=desc, compute_resources=all_computes)
+ 91        ```
+ 92
+ 93        Parameters
+ 94        ----------
+ 95        plugin_description: str | dict
+ 96            JSON description of a plugin.
+ 97            [spec](https://github.com/FNNDSC/CHRIS_docs/blob/5078aaf934bdbe313e85367f88aff7c14730a1d4/specs/ChRIS_Plugins.adoc#descriptor_file)
+ 98        compute_resources
+ 99            Compute resources to register the plugin to. Value can be either a comma-separated `str` of names,
+100            a `aiochris.models.public.ComputeResource`, a sequence of `aiochris.models.public.ComputeResource`,
+101            or a sequence of compute resource names as `str`.
+102        """
+103        compute_names = _serialize_crs(compute_resources)
+104        if not isinstance(plugin_description, str):
+105            plugin_description = json.dumps(plugin_description)
+106        data = aiohttp.FormData()
+107        data.add_field(
+108            "fname",
+109            io.StringIO(plugin_description),
+110            filename="aiochris_add_plugin.json",
+111        )
+112        data.add_field("compute_names", compute_names)
+113        async with self.s.post(self.collection_links.admin, data=data) as res:
+114            await raise_for_status(res)
+115            return deserialize_linked(self, Plugin, await res.json())
+116
+117    async def create_compute_resource(
+118        self,
+119        name: str | ComputeResourceName,
+120        compute_url: str | PfconUrl,
+121        compute_user: str,
+122        compute_password: str,
+123        compute_innetwork: bool = None,
+124        description: str = None,
+125        compute_auth_url: str = None,
+126        compute_auth_token: str = None,
+127        max_job_exec_seconds: str = None,
+128    ) -> ComputeResource:
+129        """
+130        Define a new compute resource.
+131        """
+132        return await (await self._admin).create_compute_resource(
+133            name=name,
+134            compute_url=compute_url,
+135            compute_user=compute_user,
+136            compute_password=compute_password,
+137            compute_innetwork=compute_innetwork,
+138            description=description,
+139            compute_auth_url=compute_auth_url,
+140            compute_auth_token=compute_auth_token,
+141            max_job_exec_seconds=max_job_exec_seconds,
+142        )
+143
+144    @async_cached_property
+145    async def _admin(self) -> _AdminApiClient:
+146        """
+147        Get a (sub-)client for `/chris-admin/api/v1/`
+148        """
+149        res = await self.s.get(self.collection_links.admin)
+150        body = await res.json()
+151        links = from_dict(AdminApiCollectionLinks, body["collection_links"])
+152        return _AdminApiClient(
+153            url=self.collection_links.admin,
+154            s=self.s,
+155            collection_links=links,
+156            max_search_requests=self.max_search_requests,
+157        )
+
+ + +

A client who has access to /chris-admin/. Admins can register new plugins and +add new compute resources.

+
+ + +
+ +
+ + async def + register_plugin_from_store( self, plugin_store_url: aiochris.types.PluginUrl, compute_names: Iterable[aiochris.types.ComputeResourceName]) -> aiochris.models.logged_in.Plugin: + + + +
+ + 
46    async def register_plugin_from_store(
+47        self, plugin_store_url: PluginUrl, compute_names: Iterable[ComputeResourceName]
+48    ) -> Plugin:
+49        """
+50        Register a plugin from a ChRIS Store.
+51        """
+52        return await self._register_plugin_from_store_raw(
+53            plugin_store_url=plugin_store_url, compute_names=",".join(compute_names)
+54        )
+
+ + +

Register a plugin from a ChRIS Store.

+
+ + +
+
+ +
+ + async def + add_plugin( self, plugin_description: str | dict, compute_resources: Union[str, aiochris.models.public.ComputeResource, Iterable[Union[aiochris.models.public.ComputeResource, aiochris.types.ComputeResourceName]]]) -> aiochris.models.logged_in.Plugin: + + + +
+ + 
 56    async def add_plugin(
+ 57        self,
+ 58        plugin_description: str | dict,
+ 59        compute_resources: str
+ 60        | ComputeResource
+ 61        | Iterable[ComputeResource | ComputeResourceName],
+ 62    ) -> Plugin:
+ 63        """
+ 64        Add a plugin to *CUBE*.
+ 65
+ 66        Examples
+ 67        --------
+ 68
+ 69        ```python
+ 70        cmd = ['docker', 'run', '--rm', 'fnndsc/pl-mri-preview', 'chris_plugin_info']
+ 71        output = subprocess.check_output(cmd, text=True)
+ 72        desc = json.loads(output)
+ 73        desc['name'] = 'pl-mri-preview'
+ 74        desc['public_repo'] = 'https://github.com/FNNDSC/pl-mri-preview'
+ 75        desc['dock_image'] = 'fnndsc/pl-mri-preview'
+ 76
+ 77        await chris_admin.add_plugin(plugin_description=desc, compute_resources='host')
+ 78        ```
+ 79
+ 80        The example above is just for show. It's not a good example for several reasons:
+ 81
+ 82        - Calls blocking function `subprocess.check_output` in asynchronous context
+ 83        - It is preferred to use a versioned string for `dock_image`
+ 84        - `host` compute environment is not guaranteed to exist. Instead, you could
+ 85          call `aiochris.client.authed.AuthenticatedClient.search_compute_resources`
+ 86          or `aiochris.client.authed.AuthenticatedClient.get_all_compute_resources`:
+ 87
+ 88        ```python
+ 89        all_computes = await chris_admin.get_all_compute_resources()
+ 90        await chris_admin.add_plugin(plugin_description=desc, compute_resources=all_computes)
+ 91        ```
+ 92
+ 93        Parameters
+ 94        ----------
+ 95        plugin_description: str | dict
+ 96            JSON description of a plugin.
+ 97            [spec](https://github.com/FNNDSC/CHRIS_docs/blob/5078aaf934bdbe313e85367f88aff7c14730a1d4/specs/ChRIS_Plugins.adoc#descriptor_file)
+ 98        compute_resources
+ 99            Compute resources to register the plugin to. Value can be either a comma-separated `str` of names,
+100            a `aiochris.models.public.ComputeResource`, a sequence of `aiochris.models.public.ComputeResource`,
+101            or a sequence of compute resource names as `str`.
+102        """
+103        compute_names = _serialize_crs(compute_resources)
+104        if not isinstance(plugin_description, str):
+105            plugin_description = json.dumps(plugin_description)
+106        data = aiohttp.FormData()
+107        data.add_field(
+108            "fname",
+109            io.StringIO(plugin_description),
+110            filename="aiochris_add_plugin.json",
+111        )
+112        data.add_field("compute_names", compute_names)
+113        async with self.s.post(self.collection_links.admin, data=data) as res:
+114            await raise_for_status(res)
+115            return deserialize_linked(self, Plugin, await res.json())
+
+ + +

Add a plugin to CUBE.

+ +
Examples
+ +
+
cmd = ['docker', 'run', '--rm', 'fnndsc/pl-mri-preview', 'chris_plugin_info']
+output = subprocess.check_output(cmd, text=True)
+desc = json.loads(output)
+desc['name'] = 'pl-mri-preview'
+desc['public_repo'] = 'https://github.com/FNNDSC/pl-mri-preview'
+desc['dock_image'] = 'fnndsc/pl-mri-preview'
+
+await chris_admin.add_plugin(plugin_description=desc, compute_resources='host')
+
+
+ +

The example above is just for show. It's not a good example for several reasons:

+ + + +
+
all_computes = await chris_admin.get_all_compute_resources()
+await chris_admin.add_plugin(plugin_description=desc, compute_resources=all_computes)
+
+
+ +
Parameters
+ + +
+ + +
+
+ +
+ + async def + create_compute_resource( self, name: Union[str, aiochris.types.ComputeResourceName], compute_url: Union[str, aiochris.types.PfconUrl], compute_user: str, compute_password: str, compute_innetwork: bool = None, description: str = None, compute_auth_url: str = None, compute_auth_token: str = None, max_job_exec_seconds: str = None) -> aiochris.models.public.ComputeResource: + + + +
+ + 
117    async def create_compute_resource(
+118        self,
+119        name: str | ComputeResourceName,
+120        compute_url: str | PfconUrl,
+121        compute_user: str,
+122        compute_password: str,
+123        compute_innetwork: bool = None,
+124        description: str = None,
+125        compute_auth_url: str = None,
+126        compute_auth_token: str = None,
+127        max_job_exec_seconds: str = None,
+128    ) -> ComputeResource:
+129        """
+130        Define a new compute resource.
+131        """
+132        return await (await self._admin).create_compute_resource(
+133            name=name,
+134            compute_url=compute_url,
+135            compute_user=compute_user,
+136            compute_password=compute_password,
+137            compute_innetwork=compute_innetwork,
+138            description=description,
+139            compute_auth_url=compute_auth_url,
+140            compute_auth_token=compute_auth_token,
+141            max_job_exec_seconds=max_job_exec_seconds,
+142        )
+
+ + +

Define a new compute resource.

+
+ + +
+
+
Inherited Members
+
+
aiochris.link.collection_client.CollectionJsonApiClient
+
CollectionJsonApiClient
+
url
+ + +
+ + +
aiochris.link.linked.Linked
+
max_search_requests
+ +
+
+
+
+ +
+ +
+ + async def + acollect(async_iterable: AsyncIterable[~T]) -> list[~T]: + + + +
+ + 
206async def acollect(async_iterable: AsyncIterable[T]) -> list[T]:
+207    """
+208    Simple helper to convert a `Search` to a [`list`](https://docs.python.org/3/library/stdtypes.html#list).
+209
+210    Using this function is not recommended unless you can assume the collection is small.
+211    """
+212    # nb: using tuple here causes
+213    #     TypeError: 'async_generator' object is not iterable
+214    # return tuple(e async for e in async_iterable)
+215    return [e async for e in async_iterable]
+
+ + +

Simple helper to convert a Search to a list.

+ +

Using this function is not recommended unless you can assume the collection is small.

+
+ + +
+
+ +
+ + class + Status(enum.Enum): + + + +
+ + 
 5class Status(enum.Enum):
+ 6    """
+ 7    Possible statuses of a plugin instance.
+ 8    """
+ 9
+10    created = "created"
+11    waiting = "waiting"
+12    scheduled = "scheduled"
+13    started = "started"
+14    registeringFiles = "registeringFiles"
+15    finishedSuccessfully = "finishedSuccessfully"
+16    finishedWithError = "finishedWithError"
+17    cancelled = "cancelled"
+
+ + +

Possible statuses of a plugin instance.

+
+ + +
+
+ created = <Status.created: 'created'> + + +
+ + + + +
+
+
+ waiting = <Status.waiting: 'waiting'> + + +
+ + + + +
+
+
+ scheduled = <Status.scheduled: 'scheduled'> + + +
+ + + + +
+
+
+ started = <Status.started: 'started'> + + +
+ + + + +
+
+
+ registeringFiles = <Status.registeringFiles: 'registeringFiles'> + + +
+ + + + +
+
+
+ finishedSuccessfully = <Status.finishedSuccessfully: 'finishedSuccessfully'> + + +
+ + + + +
+
+
+ finishedWithError = <Status.finishedWithError: 'finishedWithError'> + + +
+ + + + +
+
+
+ cancelled = <Status.cancelled: 'cancelled'> + + +
+ + + + +
+
+
Inherited Members
+
+
enum.Enum
+
name
+
value
+ +
+
+
+
+
+ +
+ + class + ParameterTypeName(enum.Enum): + + + +
+ + 
20class ParameterTypeName(enum.Enum):
+21    """
+22    Plugin parameter types.
+23    """
+24
+25    string = "string"
+26    integer = "integer"
+27    float = "float"
+28    boolean = "boolean"
+
+ + +

Plugin parameter types.

+
+ + +
+
+ string = <ParameterTypeName.string: 'string'> + + +
+ + + + +
+
+
+ integer = <ParameterTypeName.integer: 'integer'> + + +
+ + + + +
+
+
+ float = <ParameterTypeName.float: 'float'> + + +
+ + + + +
+
+
+ boolean = <ParameterTypeName.boolean: 'boolean'> + + +
+ + + + +
+
+
Inherited Members
+
+
enum.Enum
+
name
+
value
+ +
+
+
+
+
+ + \ No newline at end of file diff --git a/v0.5.0a3/aiochris/client.html b/v0.5.0a3/aiochris/client.html new file mode 100644 index 0000000..84bb8ec --- /dev/null +++ b/v0.5.0a3/aiochris/client.html @@ -0,0 +1,244 @@ + + + + + + + aiochris.client API documentation + + + + + + + + + +
+
+

+aiochris.client

+ + + + + +
+
+ + \ No newline at end of file diff --git a/v0.5.0a3/aiochris/client/admin.html b/v0.5.0a3/aiochris/client/admin.html new file mode 100644 index 0000000..f77539b --- /dev/null +++ b/v0.5.0a3/aiochris/client/admin.html @@ -0,0 +1,804 @@ + + + + + + + aiochris.client.admin API documentation + + + + + + + + + +
+
+

+aiochris.client.admin

+ + + + + + + 
  1import io
+  2import json
+  3from typing import Iterable
+  4
+  5import aiohttp
+  6from async_property import async_cached_property
+  7from serde import from_dict
+  8
+  9from aiochris.client.authed import AuthenticatedClient
+ 10from aiochris.link import http
+ 11from aiochris.link.collection_client import CollectionJsonApiClient
+ 12from aiochris.link.linked import deserialize_linked
+ 13from aiochris.models.collection_links import (
+ 14    AdminCollectionLinks,
+ 15    AdminApiCollectionLinks,
+ 16)
+ 17from aiochris.models.logged_in import Plugin
+ 18from aiochris.models.public import ComputeResource
+ 19from aiochris.types import PluginUrl, ComputeResourceName, PfconUrl
+ 20from aiochris.errors import raise_for_status
+ 21
+ 22
+ 23class _AdminApiClient(CollectionJsonApiClient[AdminApiCollectionLinks]):
+ 24    """
+ 25    A client to `/chris-admin/api/v1/`
+ 26    """
+ 27
+ 28    @http.post("compute_resources")
+ 29    async def create_compute_resource(self, **kwargs) -> ComputeResource:
+ 30        ...
+ 31
+ 32
+ 33class ChrisAdminClient(AuthenticatedClient[AdminCollectionLinks, "ChrisAdminClient"]):
+ 34    """
+ 35    A client who has access to `/chris-admin/`. Admins can register new plugins and
+ 36    add new compute resources.
+ 37    """
+ 38
+ 39    @http.post("admin")
+ 40    async def _register_plugin_from_store_raw(
+ 41        self, plugin_store_url: str, compute_names: str
+ 42    ) -> Plugin:
+ 43        ...
+ 44
+ 45    async def register_plugin_from_store(
+ 46        self, plugin_store_url: PluginUrl, compute_names: Iterable[ComputeResourceName]
+ 47    ) -> Plugin:
+ 48        """
+ 49        Register a plugin from a ChRIS Store.
+ 50        """
+ 51        return await self._register_plugin_from_store_raw(
+ 52            plugin_store_url=plugin_store_url, compute_names=",".join(compute_names)
+ 53        )
+ 54
+ 55    async def add_plugin(
+ 56        self,
+ 57        plugin_description: str | dict,
+ 58        compute_resources: str
+ 59        | ComputeResource
+ 60        | Iterable[ComputeResource | ComputeResourceName],
+ 61    ) -> Plugin:
+ 62        """
+ 63        Add a plugin to *CUBE*.
+ 64
+ 65        Examples
+ 66        --------
+ 67
+ 68        ```python
+ 69        cmd = ['docker', 'run', '--rm', 'fnndsc/pl-mri-preview', 'chris_plugin_info']
+ 70        output = subprocess.check_output(cmd, text=True)
+ 71        desc = json.loads(output)
+ 72        desc['name'] = 'pl-mri-preview'
+ 73        desc['public_repo'] = 'https://github.com/FNNDSC/pl-mri-preview'
+ 74        desc['dock_image'] = 'fnndsc/pl-mri-preview'
+ 75
+ 76        await chris_admin.add_plugin(plugin_description=desc, compute_resources='host')
+ 77        ```
+ 78
+ 79        The example above is just for show. It's not a good example for several reasons:
+ 80
+ 81        - Calls blocking function `subprocess.check_output` in asynchronous context
+ 82        - It is preferred to use a versioned string for `dock_image`
+ 83        - `host` compute environment is not guaranteed to exist. Instead, you could
+ 84          call `aiochris.client.authed.AuthenticatedClient.search_compute_resources`
+ 85          or `aiochris.client.authed.AuthenticatedClient.get_all_compute_resources`:
+ 86
+ 87        ```python
+ 88        all_computes = await chris_admin.get_all_compute_resources()
+ 89        await chris_admin.add_plugin(plugin_description=desc, compute_resources=all_computes)
+ 90        ```
+ 91
+ 92        Parameters
+ 93        ----------
+ 94        plugin_description: str | dict
+ 95            JSON description of a plugin.
+ 96            [spec](https://github.com/FNNDSC/CHRIS_docs/blob/5078aaf934bdbe313e85367f88aff7c14730a1d4/specs/ChRIS_Plugins.adoc#descriptor_file)
+ 97        compute_resources
+ 98            Compute resources to register the plugin to. Value can be either a comma-separated `str` of names,
+ 99            a `aiochris.models.public.ComputeResource`, a sequence of `aiochris.models.public.ComputeResource`,
+100            or a sequence of compute resource names as `str`.
+101        """
+102        compute_names = _serialize_crs(compute_resources)
+103        if not isinstance(plugin_description, str):
+104            plugin_description = json.dumps(plugin_description)
+105        data = aiohttp.FormData()
+106        data.add_field(
+107            "fname",
+108            io.StringIO(plugin_description),
+109            filename="aiochris_add_plugin.json",
+110        )
+111        data.add_field("compute_names", compute_names)
+112        async with self.s.post(self.collection_links.admin, data=data) as res:
+113            await raise_for_status(res)
+114            return deserialize_linked(self, Plugin, await res.json())
+115
+116    async def create_compute_resource(
+117        self,
+118        name: str | ComputeResourceName,
+119        compute_url: str | PfconUrl,
+120        compute_user: str,
+121        compute_password: str,
+122        compute_innetwork: bool = None,
+123        description: str = None,
+124        compute_auth_url: str = None,
+125        compute_auth_token: str = None,
+126        max_job_exec_seconds: str = None,
+127    ) -> ComputeResource:
+128        """
+129        Define a new compute resource.
+130        """
+131        return await (await self._admin).create_compute_resource(
+132            name=name,
+133            compute_url=compute_url,
+134            compute_user=compute_user,
+135            compute_password=compute_password,
+136            compute_innetwork=compute_innetwork,
+137            description=description,
+138            compute_auth_url=compute_auth_url,
+139            compute_auth_token=compute_auth_token,
+140            max_job_exec_seconds=max_job_exec_seconds,
+141        )
+142
+143    @async_cached_property
+144    async def _admin(self) -> _AdminApiClient:
+145        """
+146        Get a (sub-)client for `/chris-admin/api/v1/`
+147        """
+148        res = await self.s.get(self.collection_links.admin)
+149        body = await res.json()
+150        links = from_dict(AdminApiCollectionLinks, body["collection_links"])
+151        return _AdminApiClient(
+152            url=self.collection_links.admin,
+153            s=self.s,
+154            collection_links=links,
+155            max_search_requests=self.max_search_requests,
+156        )
+157
+158
+159def _serialize_crs(
+160    c: str | ComputeResource | Iterable[ComputeResource | ComputeResourceName],
+161) -> str:
+162    if isinstance(c, str):
+163        return c
+164    if isinstance(c, ComputeResource):
+165        return c.name
+166    if not isinstance(c, Iterable):
+167        raise TypeError("compute_resources must be str or Iterable")
+168    return ",".join(map(_serialize_cr, c))
+169
+170
+171def _serialize_cr(c: str | ComputeResource):
+172    if isinstance(c, ComputeResource):
+173        return c.name
+174    return str(c)
+
+ + +
+
+ +
+ + class + ChrisAdminClient(aiochris.client.authed.AuthenticatedClient[aiochris.models.collection_links.AdminCollectionLinks, 'ChrisAdminClient']): + + + +
+ + 
 34class ChrisAdminClient(AuthenticatedClient[AdminCollectionLinks, "ChrisAdminClient"]):
+ 35    """
+ 36    A client who has access to `/chris-admin/`. Admins can register new plugins and
+ 37    add new compute resources.
+ 38    """
+ 39
+ 40    @http.post("admin")
+ 41    async def _register_plugin_from_store_raw(
+ 42        self, plugin_store_url: str, compute_names: str
+ 43    ) -> Plugin:
+ 44        ...
+ 45
+ 46    async def register_plugin_from_store(
+ 47        self, plugin_store_url: PluginUrl, compute_names: Iterable[ComputeResourceName]
+ 48    ) -> Plugin:
+ 49        """
+ 50        Register a plugin from a ChRIS Store.
+ 51        """
+ 52        return await self._register_plugin_from_store_raw(
+ 53            plugin_store_url=plugin_store_url, compute_names=",".join(compute_names)
+ 54        )
+ 55
+ 56    async def add_plugin(
+ 57        self,
+ 58        plugin_description: str | dict,
+ 59        compute_resources: str
+ 60        | ComputeResource
+ 61        | Iterable[ComputeResource | ComputeResourceName],
+ 62    ) -> Plugin:
+ 63        """
+ 64        Add a plugin to *CUBE*.
+ 65
+ 66        Examples
+ 67        --------
+ 68
+ 69        ```python
+ 70        cmd = ['docker', 'run', '--rm', 'fnndsc/pl-mri-preview', 'chris_plugin_info']
+ 71        output = subprocess.check_output(cmd, text=True)
+ 72        desc = json.loads(output)
+ 73        desc['name'] = 'pl-mri-preview'
+ 74        desc['public_repo'] = 'https://github.com/FNNDSC/pl-mri-preview'
+ 75        desc['dock_image'] = 'fnndsc/pl-mri-preview'
+ 76
+ 77        await chris_admin.add_plugin(plugin_description=desc, compute_resources='host')
+ 78        ```
+ 79
+ 80        The example above is just for show. It's not a good example for several reasons:
+ 81
+ 82        - Calls blocking function `subprocess.check_output` in asynchronous context
+ 83        - It is preferred to use a versioned string for `dock_image`
+ 84        - `host` compute environment is not guaranteed to exist. Instead, you could
+ 85          call `aiochris.client.authed.AuthenticatedClient.search_compute_resources`
+ 86          or `aiochris.client.authed.AuthenticatedClient.get_all_compute_resources`:
+ 87
+ 88        ```python
+ 89        all_computes = await chris_admin.get_all_compute_resources()
+ 90        await chris_admin.add_plugin(plugin_description=desc, compute_resources=all_computes)
+ 91        ```
+ 92
+ 93        Parameters
+ 94        ----------
+ 95        plugin_description: str | dict
+ 96            JSON description of a plugin.
+ 97            [spec](https://github.com/FNNDSC/CHRIS_docs/blob/5078aaf934bdbe313e85367f88aff7c14730a1d4/specs/ChRIS_Plugins.adoc#descriptor_file)
+ 98        compute_resources
+ 99            Compute resources to register the plugin to. Value can be either a comma-separated `str` of names,
+100            a `aiochris.models.public.ComputeResource`, a sequence of `aiochris.models.public.ComputeResource`,
+101            or a sequence of compute resource names as `str`.
+102        """
+103        compute_names = _serialize_crs(compute_resources)
+104        if not isinstance(plugin_description, str):
+105            plugin_description = json.dumps(plugin_description)
+106        data = aiohttp.FormData()
+107        data.add_field(
+108            "fname",
+109            io.StringIO(plugin_description),
+110            filename="aiochris_add_plugin.json",
+111        )
+112        data.add_field("compute_names", compute_names)
+113        async with self.s.post(self.collection_links.admin, data=data) as res:
+114            await raise_for_status(res)
+115            return deserialize_linked(self, Plugin, await res.json())
+116
+117    async def create_compute_resource(
+118        self,
+119        name: str | ComputeResourceName,
+120        compute_url: str | PfconUrl,
+121        compute_user: str,
+122        compute_password: str,
+123        compute_innetwork: bool = None,
+124        description: str = None,
+125        compute_auth_url: str = None,
+126        compute_auth_token: str = None,
+127        max_job_exec_seconds: str = None,
+128    ) -> ComputeResource:
+129        """
+130        Define a new compute resource.
+131        """
+132        return await (await self._admin).create_compute_resource(
+133            name=name,
+134            compute_url=compute_url,
+135            compute_user=compute_user,
+136            compute_password=compute_password,
+137            compute_innetwork=compute_innetwork,
+138            description=description,
+139            compute_auth_url=compute_auth_url,
+140            compute_auth_token=compute_auth_token,
+141            max_job_exec_seconds=max_job_exec_seconds,
+142        )
+143
+144    @async_cached_property
+145    async def _admin(self) -> _AdminApiClient:
+146        """
+147        Get a (sub-)client for `/chris-admin/api/v1/`
+148        """
+149        res = await self.s.get(self.collection_links.admin)
+150        body = await res.json()
+151        links = from_dict(AdminApiCollectionLinks, body["collection_links"])
+152        return _AdminApiClient(
+153            url=self.collection_links.admin,
+154            s=self.s,
+155            collection_links=links,
+156            max_search_requests=self.max_search_requests,
+157        )
+
+ + +

A client who has access to /chris-admin/. Admins can register new plugins and +add new compute resources.

+
+ + +
+ +
+ + async def + register_plugin_from_store( self, plugin_store_url: aiochris.types.PluginUrl, compute_names: Iterable[aiochris.types.ComputeResourceName]) -> aiochris.models.logged_in.Plugin: + + + +
+ + 
46    async def register_plugin_from_store(
+47        self, plugin_store_url: PluginUrl, compute_names: Iterable[ComputeResourceName]
+48    ) -> Plugin:
+49        """
+50        Register a plugin from a ChRIS Store.
+51        """
+52        return await self._register_plugin_from_store_raw(
+53            plugin_store_url=plugin_store_url, compute_names=",".join(compute_names)
+54        )
+
+ + +

Register a plugin from a ChRIS Store.

+
+ + +
+
+ +
+ + async def + add_plugin( self, plugin_description: str | dict, compute_resources: Union[str, aiochris.models.public.ComputeResource, Iterable[Union[aiochris.models.public.ComputeResource, aiochris.types.ComputeResourceName]]]) -> aiochris.models.logged_in.Plugin: + + + +
+ + 
 56    async def add_plugin(
+ 57        self,
+ 58        plugin_description: str | dict,
+ 59        compute_resources: str
+ 60        | ComputeResource
+ 61        | Iterable[ComputeResource | ComputeResourceName],
+ 62    ) -> Plugin:
+ 63        """
+ 64        Add a plugin to *CUBE*.
+ 65
+ 66        Examples
+ 67        --------
+ 68
+ 69        ```python
+ 70        cmd = ['docker', 'run', '--rm', 'fnndsc/pl-mri-preview', 'chris_plugin_info']
+ 71        output = subprocess.check_output(cmd, text=True)
+ 72        desc = json.loads(output)
+ 73        desc['name'] = 'pl-mri-preview'
+ 74        desc['public_repo'] = 'https://github.com/FNNDSC/pl-mri-preview'
+ 75        desc['dock_image'] = 'fnndsc/pl-mri-preview'
+ 76
+ 77        await chris_admin.add_plugin(plugin_description=desc, compute_resources='host')
+ 78        ```
+ 79
+ 80        The example above is just for show. It's not a good example for several reasons:
+ 81
+ 82        - Calls blocking function `subprocess.check_output` in asynchronous context
+ 83        - It is preferred to use a versioned string for `dock_image`
+ 84        - `host` compute environment is not guaranteed to exist. Instead, you could
+ 85          call `aiochris.client.authed.AuthenticatedClient.search_compute_resources`
+ 86          or `aiochris.client.authed.AuthenticatedClient.get_all_compute_resources`:
+ 87
+ 88        ```python
+ 89        all_computes = await chris_admin.get_all_compute_resources()
+ 90        await chris_admin.add_plugin(plugin_description=desc, compute_resources=all_computes)
+ 91        ```
+ 92
+ 93        Parameters
+ 94        ----------
+ 95        plugin_description: str | dict
+ 96            JSON description of a plugin.
+ 97            [spec](https://github.com/FNNDSC/CHRIS_docs/blob/5078aaf934bdbe313e85367f88aff7c14730a1d4/specs/ChRIS_Plugins.adoc#descriptor_file)
+ 98        compute_resources
+ 99            Compute resources to register the plugin to. Value can be either a comma-separated `str` of names,
+100            a `aiochris.models.public.ComputeResource`, a sequence of `aiochris.models.public.ComputeResource`,
+101            or a sequence of compute resource names as `str`.
+102        """
+103        compute_names = _serialize_crs(compute_resources)
+104        if not isinstance(plugin_description, str):
+105            plugin_description = json.dumps(plugin_description)
+106        data = aiohttp.FormData()
+107        data.add_field(
+108            "fname",
+109            io.StringIO(plugin_description),
+110            filename="aiochris_add_plugin.json",
+111        )
+112        data.add_field("compute_names", compute_names)
+113        async with self.s.post(self.collection_links.admin, data=data) as res:
+114            await raise_for_status(res)
+115            return deserialize_linked(self, Plugin, await res.json())
+
+ + +

Add a plugin to CUBE.

+ +
Examples
+ +
+
cmd = ['docker', 'run', '--rm', 'fnndsc/pl-mri-preview', 'chris_plugin_info']
+output = subprocess.check_output(cmd, text=True)
+desc = json.loads(output)
+desc['name'] = 'pl-mri-preview'
+desc['public_repo'] = 'https://github.com/FNNDSC/pl-mri-preview'
+desc['dock_image'] = 'fnndsc/pl-mri-preview'
+
+await chris_admin.add_plugin(plugin_description=desc, compute_resources='host')
+
+
+ +

The example above is just for show. It's not a good example for several reasons:

+ + + +
+
all_computes = await chris_admin.get_all_compute_resources()
+await chris_admin.add_plugin(plugin_description=desc, compute_resources=all_computes)
+
+
+ +
Parameters
+ + +
+ + +
+
+ +
+ + async def + create_compute_resource( self, name: Union[str, aiochris.types.ComputeResourceName], compute_url: Union[str, aiochris.types.PfconUrl], compute_user: str, compute_password: str, compute_innetwork: bool = None, description: str = None, compute_auth_url: str = None, compute_auth_token: str = None, max_job_exec_seconds: str = None) -> aiochris.models.public.ComputeResource: + + + +
+ + 
117    async def create_compute_resource(
+118        self,
+119        name: str | ComputeResourceName,
+120        compute_url: str | PfconUrl,
+121        compute_user: str,
+122        compute_password: str,
+123        compute_innetwork: bool = None,
+124        description: str = None,
+125        compute_auth_url: str = None,
+126        compute_auth_token: str = None,
+127        max_job_exec_seconds: str = None,
+128    ) -> ComputeResource:
+129        """
+130        Define a new compute resource.
+131        """
+132        return await (await self._admin).create_compute_resource(
+133            name=name,
+134            compute_url=compute_url,
+135            compute_user=compute_user,
+136            compute_password=compute_password,
+137            compute_innetwork=compute_innetwork,
+138            description=description,
+139            compute_auth_url=compute_auth_url,
+140            compute_auth_token=compute_auth_token,
+141            max_job_exec_seconds=max_job_exec_seconds,
+142        )
+
+ + +

Define a new compute resource.

+
+ + +
+
+
Inherited Members
+
+
aiochris.link.collection_client.CollectionJsonApiClient
+
CollectionJsonApiClient
+
url
+ + +
+ + +
aiochris.link.linked.Linked
+
max_search_requests
+ +
+
+
+
+
+ + \ No newline at end of file diff --git a/v0.5.0a3/aiochris/client/anon.html b/v0.5.0a3/aiochris/client/anon.html new file mode 100644 index 0000000..4ad7b47 --- /dev/null +++ b/v0.5.0a3/aiochris/client/anon.html @@ -0,0 +1,445 @@ + + + + + + + aiochris.client.anon API documentation + + + + + + + + + +
+
+

+aiochris.client.anon

+ + + + + + + 
 1from typing import Optional
+ 2
+ 3import aiohttp
+ 4
+ 5from aiochris.client.base import BaseChrisClient
+ 6from aiochris.link import http
+ 7from aiochris.models.collection_links import AnonymousCollectionLinks
+ 8from aiochris.models.public import PublicPlugin
+ 9from aiochris.util.search import Search
+10
+11
+12class AnonChrisClient(BaseChrisClient[AnonymousCollectionLinks, "AnonChrisClient"]):
+13    """
+14    An anonymous ChRIS client. It has access to read-only GET resources,
+15    such as being able to search for plugins.
+16    """
+17
+18    @classmethod
+19    async def from_url(
+20        cls,
+21        url: str,
+22        max_search_requests: int = 100,
+23        connector: Optional[aiohttp.BaseConnector] = None,
+24        connector_owner: bool = True,
+25    ) -> "AnonChrisClient":
+26        """
+27        Create an anonymous client.
+28
+29        See `aiochris.client.base.BaseChrisClient.new` for parameter documentation.
+30        """
+31        return await cls.new(
+32            url=url,
+33            max_search_requests=max_search_requests,
+34            connector=connector,
+35            connector_owner=connector_owner,
+36        )
+37
+38    @http.search("plugins")
+39    def search_plugins(self, **query) -> Search[PublicPlugin]:
+40        """
+41        Search for plugins.
+42
+43        Since this client is not logged in, you cannot create plugin instances using this client.
+44        """
+45        ...
+
+ + +
+
+ +
+ + class + AnonChrisClient(aiochris.client.base.BaseChrisClient[aiochris.models.collection_links.AnonymousCollectionLinks, 'AnonChrisClient']): + + + +
+ + 
13class AnonChrisClient(BaseChrisClient[AnonymousCollectionLinks, "AnonChrisClient"]):
+14    """
+15    An anonymous ChRIS client. It has access to read-only GET resources,
+16    such as being able to search for plugins.
+17    """
+18
+19    @classmethod
+20    async def from_url(
+21        cls,
+22        url: str,
+23        max_search_requests: int = 100,
+24        connector: Optional[aiohttp.BaseConnector] = None,
+25        connector_owner: bool = True,
+26    ) -> "AnonChrisClient":
+27        """
+28        Create an anonymous client.
+29
+30        See `aiochris.client.base.BaseChrisClient.new` for parameter documentation.
+31        """
+32        return await cls.new(
+33            url=url,
+34            max_search_requests=max_search_requests,
+35            connector=connector,
+36            connector_owner=connector_owner,
+37        )
+38
+39    @http.search("plugins")
+40    def search_plugins(self, **query) -> Search[PublicPlugin]:
+41        """
+42        Search for plugins.
+43
+44        Since this client is not logged in, you cannot create plugin instances using this client.
+45        """
+46        ...
+
+ + +

An anonymous ChRIS client. It has access to read-only GET resources, +such as being able to search for plugins.

+
+ + +
+ +
+
@classmethod
+ + async def + from_url( cls, url: str, max_search_requests: int = 100, connector: Optional[aiohttp.connector.BaseConnector] = None, connector_owner: bool = True) -> aiochris.client.anon.AnonChrisClient: + + + +
+ + 
19    @classmethod
+20    async def from_url(
+21        cls,
+22        url: str,
+23        max_search_requests: int = 100,
+24        connector: Optional[aiohttp.BaseConnector] = None,
+25        connector_owner: bool = True,
+26    ) -> "AnonChrisClient":
+27        """
+28        Create an anonymous client.
+29
+30        See `aiochris.client.base.BaseChrisClient.new` for parameter documentation.
+31        """
+32        return await cls.new(
+33            url=url,
+34            max_search_requests=max_search_requests,
+35            connector=connector,
+36            connector_owner=connector_owner,
+37        )
+
+ + +

Create an anonymous client.

+ +

See aiochris.client.base.BaseChrisClient.new for parameter documentation.

+
+ + +
+
+ +
+
@http.search('plugins')
+ + def + search_plugins( self, **query) -> aiochris.util.search.Search[aiochris.models.public.PublicPlugin]: + + + +
+ + 
39    @http.search("plugins")
+40    def search_plugins(self, **query) -> Search[PublicPlugin]:
+41        """
+42        Search for plugins.
+43
+44        Since this client is not logged in, you cannot create plugin instances using this client.
+45        """
+46        ...
+
+ + +

Search for plugins.

+ +

Since this client is not logged in, you cannot create plugin instances using this client.

+
+ + +
+
+
Inherited Members
+
+
aiochris.link.collection_client.CollectionJsonApiClient
+
CollectionJsonApiClient
+
url
+ + +
+ +
aiochris.link.linked.Linked
+
max_search_requests
+ +
+
+
+
+
+ + \ No newline at end of file diff --git a/v0.5.0a3/aiochris/client/authed.html b/v0.5.0a3/aiochris/client/authed.html new file mode 100644 index 0000000..0209081 --- /dev/null +++ b/v0.5.0a3/aiochris/client/authed.html @@ -0,0 +1,1537 @@ + + + + + + + aiochris.client.authed API documentation + + + + + + + + + +
+
+

+aiochris.client.authed

+ + + + + + + 
  1import abc
+  2import os
+  3from pathlib import Path
+  4from typing import Optional, Generic, Callable, Sequence
+  5
+  6import aiohttp
+  7from async_property import async_cached_property
+  8
+  9from aiochris.client.base import BaseChrisClient
+ 10from aiochris.client.base import L, CSelf
+ 11from aiochris.link import http
+ 12from aiochris.link.linked import deserialize_res
+ 13from aiochris.models.logged_in import Plugin, File, User, PluginInstance, Feed, PACSFile
+ 14from aiochris.models.public import ComputeResource
+ 15from aiochris.types import ChrisURL, Username, Password
+ 16from aiochris.errors import IncorrectLoginError, raise_for_status
+ 17from aiochris.util.search import Search, acollect
+ 18from aiochris.client.from_chrs import ChrsLogins
+ 19
+ 20
+ 21class AuthenticatedClient(BaseChrisClient[L, CSelf], Generic[L, CSelf], abc.ABC):
+ 22    """
+ 23    An authenticated ChRIS client.
+ 24    """
+ 25
+ 26    @classmethod
+ 27    async def from_login(
+ 28        cls,
+ 29        url: str | ChrisURL,
+ 30        username: str | Username,
+ 31        password: str | Password,
+ 32        max_search_requests: int = 100,
+ 33        connector: Optional[aiohttp.TCPConnector] = None,
+ 34        connector_owner: bool = True,
+ 35    ) -> CSelf:
+ 36        """
+ 37        Get authentication token using username and password, then construct the client.
+ 38
+ 39        See `aiochris.client.base.BaseChrisClient.new` for parameter documentation.
+ 40        """
+ 41        async with aiohttp.ClientSession(
+ 42            connector=connector, connector_owner=False
+ 43        ) as session:
+ 44            try:
+ 45                c = await cls.__from_login_with(
+ 46                    url=url,
+ 47                    username=username,
+ 48                    password=password,
+ 49                    max_search_requests=max_search_requests,
+ 50                    session=session,
+ 51                    connector_owner=connector_owner,
+ 52                )
+ 53            except BaseException as e:
+ 54                if connector is None:
+ 55                    await session.connector.close()
+ 56                raise e
+ 57        return c
+ 58
+ 59    @classmethod
+ 60    async def __from_login_with(
+ 61        cls,
+ 62        url: str | ChrisURL,
+ 63        username: Username,
+ 64        password: Password,
+ 65        max_search_requests: int,
+ 66        session: aiohttp.ClientSession,
+ 67        connector_owner: bool,
+ 68    ) -> CSelf:
+ 69        """
+ 70        Get authentication token using the given session, and then construct the client.
+ 71        """
+ 72        payload = {"username": username, "password": password}
+ 73        login = await session.post(url + "auth-token/", json=payload)
+ 74        if login.status == 400:
+ 75            raise IncorrectLoginError(await login.text())
+ 76        await raise_for_status(login)
+ 77        data = await login.json()
+ 78        return await cls.from_token(
+ 79            url=url,
+ 80            token=data["token"],
+ 81            max_search_requests=max_search_requests,
+ 82            connector=session.connector,
+ 83            connector_owner=connector_owner,
+ 84        )
+ 85
+ 86    @classmethod
+ 87    async def from_token(
+ 88        cls,
+ 89        url: str | ChrisURL,
+ 90        token: str,
+ 91        max_search_requests: int = 100,
+ 92        connector: Optional[aiohttp.TCPConnector] = None,
+ 93        connector_owner: Optional[bool] = True,
+ 94    ) -> CSelf:
+ 95        """
+ 96        Construct an authenticated client using the given token.
+ 97
+ 98        See `aiochris.client.base.BaseChrisClient.new` for parameter documentation.
+ 99        """
+100        return await cls.new(
+101            url=url,
+102            max_search_requests=max_search_requests,
+103            connector=connector,
+104            connector_owner=connector_owner,
+105            session_modifier=cls.__curry_token(token),
+106        )
+107
+108    @classmethod
+109    async def from_chrs(
+110        cls,
+111        url: Optional[str | ChrisURL] = None,
+112        username: Optional[str | Username] = None,
+113        max_search_requests: int = 100,
+114        connector: Optional[aiohttp.TCPConnector] = None,
+115        connector_owner: Optional[bool] = True,
+116        config_file: Path = Path("~/.config/chrs/login.toml"),
+117    ) -> CSelf:
+118        """
+119        Log in using [`chrs`](https://crates.io/crates/chrs).
+120        *ChRIS* logins can be saved with the `chrs login` command.
+121
+122        In order to call this function, `aiochris` must be installed with the extras `from-chrs`.
+123        Using pip:
+124
+125        ```shell
+126        pip install aiochris[chrs]
+127        ```
+128
+129        Or using Poetry:
+130
+131        ```shell
+132        poetry add -E chrs aiochris
+133        ```
+134
+135        `from_chrs` makes it easy to use `aiochris` in Jupyter Notebook or IPython,
+136        especially since it saves you from having to write your password in a notebook
+137        that you want to share with others. Both Jupyter and IPython support top-level `await`.
+138
+139        ```python
+140        from aiochris import ChrisClient, acollect
+141
+142        chris = await ChrisClient.from_chrs()
+143        await acollect(chris.search_plugins())
+144        ```
+145
+146        When `from_chrs` is called with no parameters, it uses the "preferred account"
+147        i.e. the most recently added account, the same _ChRIS_ account and server as
+148        `chrs` would when called without options. The "preferred account" can be changed
+149        by running `chrs switch`.
+150        """
+151        logins = ChrsLogins.load(config_file)
+152        if (t := logins.get_token_for(url, username)) is None:
+153            raise IncorrectLoginError("No chrs login found.")
+154        url, token = t
+155        return await cls.from_token(
+156            url=url,
+157            token=token,
+158            max_search_requests=max_search_requests,
+159            connector=connector,
+160            connector_owner=connector_owner,
+161        )
+162
+163    @staticmethod
+164    def __curry_token(token: str) -> Callable[[aiohttp.ClientSession], None]:
+165        def add_token_to(session: aiohttp.ClientSession) -> None:
+166            session.headers.update({"Authorization": "Token " + token})
+167
+168        return add_token_to
+169
+170    # ============================================================
+171    # CUBE API methods
+172    # ============================================================
+173
+174    @http.search(".")
+175    def search_feeds(self, **query) -> Search[Feed]:
+176        """
+177        Search for feeds.
+178        """
+179        ...
+180
+181    @http.search("plugins")
+182    def search_plugins(self, **query) -> Search[Plugin]:
+183        """
+184        Search for plugins.
+185        """
+186        ...
+187
+188    @http.search("plugin_instances")
+189    def plugin_instances(self, **query) -> Search[PluginInstance]:
+190        """
+191        Search for plugin instances.
+192        """
+193        ...
+194
+195    async def upload_file(
+196        self, local_file: str | os.PathLike, upload_path: str
+197    ) -> File:
+198        """
+199        Upload a local file to *ChRIS*.
+200
+201        .. warning:: Uses non-async code.
+202                     The file is read using non-async code.
+203                     Performance will suffer with large files and hard drives.
+204                     See [aiolibs/aiohttp#7174](https://github.com/aio-libs/aiohttp/issues/7174)
+205
+206        Examples
+207        --------
+208
+209        Upload a single file:
+210
+211        ```python
+212        aiochris = await ChrisClient.from_login(
+213            username='chris',
+214            password='chris1234',
+215            url='https://cube.chrisproject.org/api/v1/'
+216        )
+217        file = await aiochris.upload_file("./my_data.dat", 'dir/my_data.dat')
+218        assert file.fname == 'aiochris/uploads/dir/my_data.dat'
+219        ```
+220
+221        Upload (in parallel) all `*.txt` files in a directory
+222        `'incoming'` to `aiochris/uploads/big_folder`:
+223
+224        ```python
+225        upload_jobs = (
+226            aiochris.upload_file(p, f'big_folder/{p}')
+227            for p in Path('incoming')
+228        )
+229        await asyncio.gather(upload_jobs)
+230        ```
+231
+232        Parameters
+233        ----------
+234        local_file
+235            Path of an existing local file to upload.
+236        upload_path
+237            A subpath of `{username}/uploads/` where to upload the file to in *CUBE*
+238        """
+239        upload_path = await self._add_upload_prefix(upload_path)
+240        local_file = Path(local_file)
+241        with local_file.open("rb") as f:
+242            data = aiohttp.FormData()
+243            data.add_field("upload_path", upload_path)
+244            data.add_field("fname", f, filename=local_file.name)
+245            sent = self.s.post(self.collection_links.uploadedfiles, data=data)
+246            return await deserialize_res(
+247                sent, self, {"fname": local_file, "upload_path": upload_path}, File
+248            )
+249
+250        # read_stream = _file_sender(local_file, chunk_size)
+251        # file_length = os.stat(local_file).st_size
+252        # return await self.upload_stream(read_stream, upload_path, str(local_file), file_length)
+253
+254    # doesn't work: 411 Length Required
+255    # async def upload_stream(self, read_stream: AsyncIterable[bytes], upload_path: str, fname: str, length: int
+256    #                         ) -> File:
+257    #     """
+258    #     Stream a file upload to *ChRIS*. For a higher-level wrapper which accepts
+259    #     a path argument instead, see `upload`.
+260    #
+261    #     Parameters
+262    #     ----------
+263    #     read_stream
+264    #         bytes stream
+265    #     upload_path
+266    #         uploadedfiles path starting with `'{username}/uploads/`
+267    #     fname
+268    #         file name to use in the multipart POST request
+269    #     length
+270    #         content length
+271    #     """
+272    #     data = aiohttp.FormData()
+273    #     data.add_field('upload_path', upload_path)
+274    #     data.add_field('fname', read_stream, filename=fname)
+275    #     async with self.s.post(self.collection_links.uploadedfiles, data=data) as res:
+276    #         return serde.json.from_json(File, await res.text())
+277    #
+278    #     with aiohttp.MultipartWriter() as mpwriter:
+279    #         mpwriter.append_form({'upload_path': upload_path})
+280    #         mpwriter.append(read_stream, headers={
+281    #             'Content-Disposition': 'form-data; name="fname"; filename="value_goes_here"'
+282    #         })
+283
+284    async def _add_upload_prefix(self, upload_path: str) -> str:
+285        upload_prefix = f"{await self.username()}/uploads/"
+286        if str(upload_path).startswith(upload_prefix):
+287            return upload_path
+288        return f"{upload_prefix}{upload_path}"
+289
+290    @http.get("user")
+291    async def user(self) -> User:
+292        """Gets the user's information."""
+293        ...
+294
+295    @async_cached_property
+296    async def _user(self) -> User:
+297        return await self.user()
+298
+299    async def username(self) -> Username:
+300        """
+301        Gets the username. In contrast to `self.user`, this method will use a cached API call.
+302        """
+303        user = await self._user  # this is weird
+304        return user.username
+305
+306    @http.search("compute_resources")
+307    def search_compute_resources(self, **query) -> Search[ComputeResource]:
+308        """
+309        Search for existing compute resources.
+310
+311        See also
+312        --------
+313        `get_all_compute_resources` :
+314        """
+315        ...
+316
+317    async def get_all_compute_resources(self) -> Sequence[ComputeResource]:
+318        """
+319        Get all compute resources.
+320
+321        This method exists for convenience.
+322        The number of compute resources of a CUBE is typically small so it's ok.
+323
+324        See also
+325        --------
+326        `search_compute_resources` :
+327        """
+328        return await acollect(self.search_compute_resources())
+329
+330    @http.search("pacsfiles")
+331    def search_pacsfiles(self, **query) -> Search[PACSFile]:
+332        """
+333        Search for PACS files.
+334        """
+335        ...
+336
+337
+338# async def _file_sender(file_name: str | os.PathLike, chunk_size: int):
+339#     """
+340#     Stream the reading of a file using an asynchronous generator.
+341#
+342#     https://docs.aiohttp.org/en/stable/client_quickstart.html#streaming-uploads
+343#     """
+344#     async with aiofiles.open(file_name, 'rb') as f:
+345#         chunk = await f.read(chunk_size)
+346#         while chunk:
+347#             yield chunk
+348#             chunk = await f.read(chunk_size)
+
+ + +
+
+ +
+ + class + AuthenticatedClient(aiochris.client.base.BaseChrisClient[~L, ~CSelf], typing.Generic[~L, ~CSelf], abc.ABC): + + + +
+ + 
 22class AuthenticatedClient(BaseChrisClient[L, CSelf], Generic[L, CSelf], abc.ABC):
+ 23    """
+ 24    An authenticated ChRIS client.
+ 25    """
+ 26
+ 27    @classmethod
+ 28    async def from_login(
+ 29        cls,
+ 30        url: str | ChrisURL,
+ 31        username: str | Username,
+ 32        password: str | Password,
+ 33        max_search_requests: int = 100,
+ 34        connector: Optional[aiohttp.TCPConnector] = None,
+ 35        connector_owner: bool = True,
+ 36    ) -> CSelf:
+ 37        """
+ 38        Get authentication token using username and password, then construct the client.
+ 39
+ 40        See `aiochris.client.base.BaseChrisClient.new` for parameter documentation.
+ 41        """
+ 42        async with aiohttp.ClientSession(
+ 43            connector=connector, connector_owner=False
+ 44        ) as session:
+ 45            try:
+ 46                c = await cls.__from_login_with(
+ 47                    url=url,
+ 48                    username=username,
+ 49                    password=password,
+ 50                    max_search_requests=max_search_requests,
+ 51                    session=session,
+ 52                    connector_owner=connector_owner,
+ 53                )
+ 54            except BaseException as e:
+ 55                if connector is None:
+ 56                    await session.connector.close()
+ 57                raise e
+ 58        return c
+ 59
+ 60    @classmethod
+ 61    async def __from_login_with(
+ 62        cls,
+ 63        url: str | ChrisURL,
+ 64        username: Username,
+ 65        password: Password,
+ 66        max_search_requests: int,
+ 67        session: aiohttp.ClientSession,
+ 68        connector_owner: bool,
+ 69    ) -> CSelf:
+ 70        """
+ 71        Get authentication token using the given session, and then construct the client.
+ 72        """
+ 73        payload = {"username": username, "password": password}
+ 74        login = await session.post(url + "auth-token/", json=payload)
+ 75        if login.status == 400:
+ 76            raise IncorrectLoginError(await login.text())
+ 77        await raise_for_status(login)
+ 78        data = await login.json()
+ 79        return await cls.from_token(
+ 80            url=url,
+ 81            token=data["token"],
+ 82            max_search_requests=max_search_requests,
+ 83            connector=session.connector,
+ 84            connector_owner=connector_owner,
+ 85        )
+ 86
+ 87    @classmethod
+ 88    async def from_token(
+ 89        cls,
+ 90        url: str | ChrisURL,
+ 91        token: str,
+ 92        max_search_requests: int = 100,
+ 93        connector: Optional[aiohttp.TCPConnector] = None,
+ 94        connector_owner: Optional[bool] = True,
+ 95    ) -> CSelf:
+ 96        """
+ 97        Construct an authenticated client using the given token.
+ 98
+ 99        See `aiochris.client.base.BaseChrisClient.new` for parameter documentation.
+100        """
+101        return await cls.new(
+102            url=url,
+103            max_search_requests=max_search_requests,
+104            connector=connector,
+105            connector_owner=connector_owner,
+106            session_modifier=cls.__curry_token(token),
+107        )
+108
+109    @classmethod
+110    async def from_chrs(
+111        cls,
+112        url: Optional[str | ChrisURL] = None,
+113        username: Optional[str | Username] = None,
+114        max_search_requests: int = 100,
+115        connector: Optional[aiohttp.TCPConnector] = None,
+116        connector_owner: Optional[bool] = True,
+117        config_file: Path = Path("~/.config/chrs/login.toml"),
+118    ) -> CSelf:
+119        """
+120        Log in using [`chrs`](https://crates.io/crates/chrs).
+121        *ChRIS* logins can be saved with the `chrs login` command.
+122
+123        In order to call this function, `aiochris` must be installed with the extras `from-chrs`.
+124        Using pip:
+125
+126        ```shell
+127        pip install aiochris[chrs]
+128        ```
+129
+130        Or using Poetry:
+131
+132        ```shell
+133        poetry add -E chrs aiochris
+134        ```
+135
+136        `from_chrs` makes it easy to use `aiochris` in Jupyter Notebook or IPython,
+137        especially since it saves you from having to write your password in a notebook
+138        that you want to share with others. Both Jupyter and IPython support top-level `await`.
+139
+140        ```python
+141        from aiochris import ChrisClient, acollect
+142
+143        chris = await ChrisClient.from_chrs()
+144        await acollect(chris.search_plugins())
+145        ```
+146
+147        When `from_chrs` is called with no parameters, it uses the "preferred account"
+148        i.e. the most recently added account, the same _ChRIS_ account and server as
+149        `chrs` would when called without options. The "preferred account" can be changed
+150        by running `chrs switch`.
+151        """
+152        logins = ChrsLogins.load(config_file)
+153        if (t := logins.get_token_for(url, username)) is None:
+154            raise IncorrectLoginError("No chrs login found.")
+155        url, token = t
+156        return await cls.from_token(
+157            url=url,
+158            token=token,
+159            max_search_requests=max_search_requests,
+160            connector=connector,
+161            connector_owner=connector_owner,
+162        )
+163
+164    @staticmethod
+165    def __curry_token(token: str) -> Callable[[aiohttp.ClientSession], None]:
+166        def add_token_to(session: aiohttp.ClientSession) -> None:
+167            session.headers.update({"Authorization": "Token " + token})
+168
+169        return add_token_to
+170
+171    # ============================================================
+172    # CUBE API methods
+173    # ============================================================
+174
+175    @http.search(".")
+176    def search_feeds(self, **query) -> Search[Feed]:
+177        """
+178        Search for feeds.
+179        """
+180        ...
+181
+182    @http.search("plugins")
+183    def search_plugins(self, **query) -> Search[Plugin]:
+184        """
+185        Search for plugins.
+186        """
+187        ...
+188
+189    @http.search("plugin_instances")
+190    def plugin_instances(self, **query) -> Search[PluginInstance]:
+191        """
+192        Search for plugin instances.
+193        """
+194        ...
+195
+196    async def upload_file(
+197        self, local_file: str | os.PathLike, upload_path: str
+198    ) -> File:
+199        """
+200        Upload a local file to *ChRIS*.
+201
+202        .. warning:: Uses non-async code.
+203                     The file is read using non-async code.
+204                     Performance will suffer with large files and hard drives.
+205                     See [aiolibs/aiohttp#7174](https://github.com/aio-libs/aiohttp/issues/7174)
+206
+207        Examples
+208        --------
+209
+210        Upload a single file:
+211
+212        ```python
+213        aiochris = await ChrisClient.from_login(
+214            username='chris',
+215            password='chris1234',
+216            url='https://cube.chrisproject.org/api/v1/'
+217        )
+218        file = await aiochris.upload_file("./my_data.dat", 'dir/my_data.dat')
+219        assert file.fname == 'aiochris/uploads/dir/my_data.dat'
+220        ```
+221
+222        Upload (in parallel) all `*.txt` files in a directory
+223        `'incoming'` to `aiochris/uploads/big_folder`:
+224
+225        ```python
+226        upload_jobs = (
+227            aiochris.upload_file(p, f'big_folder/{p}')
+228            for p in Path('incoming')
+229        )
+230        await asyncio.gather(upload_jobs)
+231        ```
+232
+233        Parameters
+234        ----------
+235        local_file
+236            Path of an existing local file to upload.
+237        upload_path
+238            A subpath of `{username}/uploads/` where to upload the file to in *CUBE*
+239        """
+240        upload_path = await self._add_upload_prefix(upload_path)
+241        local_file = Path(local_file)
+242        with local_file.open("rb") as f:
+243            data = aiohttp.FormData()
+244            data.add_field("upload_path", upload_path)
+245            data.add_field("fname", f, filename=local_file.name)
+246            sent = self.s.post(self.collection_links.uploadedfiles, data=data)
+247            return await deserialize_res(
+248                sent, self, {"fname": local_file, "upload_path": upload_path}, File
+249            )
+250
+251        # read_stream = _file_sender(local_file, chunk_size)
+252        # file_length = os.stat(local_file).st_size
+253        # return await self.upload_stream(read_stream, upload_path, str(local_file), file_length)
+254
+255    # doesn't work: 411 Length Required
+256    # async def upload_stream(self, read_stream: AsyncIterable[bytes], upload_path: str, fname: str, length: int
+257    #                         ) -> File:
+258    #     """
+259    #     Stream a file upload to *ChRIS*. For a higher-level wrapper which accepts
+260    #     a path argument instead, see `upload`.
+261    #
+262    #     Parameters
+263    #     ----------
+264    #     read_stream
+265    #         bytes stream
+266    #     upload_path
+267    #         uploadedfiles path starting with `'{username}/uploads/`
+268    #     fname
+269    #         file name to use in the multipart POST request
+270    #     length
+271    #         content length
+272    #     """
+273    #     data = aiohttp.FormData()
+274    #     data.add_field('upload_path', upload_path)
+275    #     data.add_field('fname', read_stream, filename=fname)
+276    #     async with self.s.post(self.collection_links.uploadedfiles, data=data) as res:
+277    #         return serde.json.from_json(File, await res.text())
+278    #
+279    #     with aiohttp.MultipartWriter() as mpwriter:
+280    #         mpwriter.append_form({'upload_path': upload_path})
+281    #         mpwriter.append(read_stream, headers={
+282    #             'Content-Disposition': 'form-data; name="fname"; filename="value_goes_here"'
+283    #         })
+284
+285    async def _add_upload_prefix(self, upload_path: str) -> str:
+286        upload_prefix = f"{await self.username()}/uploads/"
+287        if str(upload_path).startswith(upload_prefix):
+288            return upload_path
+289        return f"{upload_prefix}{upload_path}"
+290
+291    @http.get("user")
+292    async def user(self) -> User:
+293        """Gets the user's information."""
+294        ...
+295
+296    @async_cached_property
+297    async def _user(self) -> User:
+298        return await self.user()
+299
+300    async def username(self) -> Username:
+301        """
+302        Gets the username. In contrast to `self.user`, this method will use a cached API call.
+303        """
+304        user = await self._user  # this is weird
+305        return user.username
+306
+307    @http.search("compute_resources")
+308    def search_compute_resources(self, **query) -> Search[ComputeResource]:
+309        """
+310        Search for existing compute resources.
+311
+312        See also
+313        --------
+314        `get_all_compute_resources` :
+315        """
+316        ...
+317
+318    async def get_all_compute_resources(self) -> Sequence[ComputeResource]:
+319        """
+320        Get all compute resources.
+321
+322        This method exists for convenience.
+323        The number of compute resources of a CUBE is typically small so it's ok.
+324
+325        See also
+326        --------
+327        `search_compute_resources` :
+328        """
+329        return await acollect(self.search_compute_resources())
+330
+331    @http.search("pacsfiles")
+332    def search_pacsfiles(self, **query) -> Search[PACSFile]:
+333        """
+334        Search for PACS files.
+335        """
+336        ...
+
+ + +

An authenticated ChRIS client.

+
+ + +
+ +
+
@classmethod
+ + async def + from_login( cls, url: Union[str, aiochris.types.ChrisURL], username: Union[str, aiochris.types.Username], password: Union[str, aiochris.types.Password], max_search_requests: int = 100, connector: Optional[aiohttp.connector.TCPConnector] = None, connector_owner: bool = True) -> ~CSelf: + + + +
+ + 
27    @classmethod
+28    async def from_login(
+29        cls,
+30        url: str | ChrisURL,
+31        username: str | Username,
+32        password: str | Password,
+33        max_search_requests: int = 100,
+34        connector: Optional[aiohttp.TCPConnector] = None,
+35        connector_owner: bool = True,
+36    ) -> CSelf:
+37        """
+38        Get authentication token using username and password, then construct the client.
+39
+40        See `aiochris.client.base.BaseChrisClient.new` for parameter documentation.
+41        """
+42        async with aiohttp.ClientSession(
+43            connector=connector, connector_owner=False
+44        ) as session:
+45            try:
+46                c = await cls.__from_login_with(
+47                    url=url,
+48                    username=username,
+49                    password=password,
+50                    max_search_requests=max_search_requests,
+51                    session=session,
+52                    connector_owner=connector_owner,
+53                )
+54            except BaseException as e:
+55                if connector is None:
+56                    await session.connector.close()
+57                raise e
+58        return c
+
+ + +

Get authentication token using username and password, then construct the client.

+ +

See aiochris.client.base.BaseChrisClient.new for parameter documentation.

+
+ + +
+
+ +
+
@classmethod
+ + async def + from_token( cls, url: Union[str, aiochris.types.ChrisURL], token: str, max_search_requests: int = 100, connector: Optional[aiohttp.connector.TCPConnector] = None, connector_owner: Optional[bool] = True) -> ~CSelf: + + + +
+ + 
 87    @classmethod
+ 88    async def from_token(
+ 89        cls,
+ 90        url: str | ChrisURL,
+ 91        token: str,
+ 92        max_search_requests: int = 100,
+ 93        connector: Optional[aiohttp.TCPConnector] = None,
+ 94        connector_owner: Optional[bool] = True,
+ 95    ) -> CSelf:
+ 96        """
+ 97        Construct an authenticated client using the given token.
+ 98
+ 99        See `aiochris.client.base.BaseChrisClient.new` for parameter documentation.
+100        """
+101        return await cls.new(
+102            url=url,
+103            max_search_requests=max_search_requests,
+104            connector=connector,
+105            connector_owner=connector_owner,
+106            session_modifier=cls.__curry_token(token),
+107        )
+
+ + +

Construct an authenticated client using the given token.

+ +

See aiochris.client.base.BaseChrisClient.new for parameter documentation.

+
+ + +
+
+ +
+
@classmethod
+ + async def + from_chrs( cls, url: Union[str, aiochris.types.ChrisURL, NoneType] = None, username: Union[str, aiochris.types.Username, NoneType] = None, max_search_requests: int = 100, connector: Optional[aiohttp.connector.TCPConnector] = None, connector_owner: Optional[bool] = True, config_file: pathlib.Path = PosixPath('~/.config/chrs/login.toml')) -> ~CSelf: + + + +
+ + 
109    @classmethod
+110    async def from_chrs(
+111        cls,
+112        url: Optional[str | ChrisURL] = None,
+113        username: Optional[str | Username] = None,
+114        max_search_requests: int = 100,
+115        connector: Optional[aiohttp.TCPConnector] = None,
+116        connector_owner: Optional[bool] = True,
+117        config_file: Path = Path("~/.config/chrs/login.toml"),
+118    ) -> CSelf:
+119        """
+120        Log in using [`chrs`](https://crates.io/crates/chrs).
+121        *ChRIS* logins can be saved with the `chrs login` command.
+122
+123        In order to call this function, `aiochris` must be installed with the extras `from-chrs`.
+124        Using pip:
+125
+126        ```shell
+127        pip install aiochris[chrs]
+128        ```
+129
+130        Or using Poetry:
+131
+132        ```shell
+133        poetry add -E chrs aiochris
+134        ```
+135
+136        `from_chrs` makes it easy to use `aiochris` in Jupyter Notebook or IPython,
+137        especially since it saves you from having to write your password in a notebook
+138        that you want to share with others. Both Jupyter and IPython support top-level `await`.
+139
+140        ```python
+141        from aiochris import ChrisClient, acollect
+142
+143        chris = await ChrisClient.from_chrs()
+144        await acollect(chris.search_plugins())
+145        ```
+146
+147        When `from_chrs` is called with no parameters, it uses the "preferred account"
+148        i.e. the most recently added account, the same _ChRIS_ account and server as
+149        `chrs` would when called without options. The "preferred account" can be changed
+150        by running `chrs switch`.
+151        """
+152        logins = ChrsLogins.load(config_file)
+153        if (t := logins.get_token_for(url, username)) is None:
+154            raise IncorrectLoginError("No chrs login found.")
+155        url, token = t
+156        return await cls.from_token(
+157            url=url,
+158            token=token,
+159            max_search_requests=max_search_requests,
+160            connector=connector,
+161            connector_owner=connector_owner,
+162        )
+
+ + +

Log in using chrs. +ChRIS logins can be saved with the chrs login command.

+ +

In order to call this function, aiochris must be installed with the extras from-chrs. +Using pip:

+ +
+
pip install aiochris[chrs]
+
+
+ +

Or using Poetry:

+ +
+
poetry add -E chrs aiochris
+
+
+ +

from_chrs makes it easy to use aiochris in Jupyter Notebook or IPython, +especially since it saves you from having to write your password in a notebook +that you want to share with others. Both Jupyter and IPython support top-level await.

+ +
+
from aiochris import ChrisClient, acollect
+
+chris = await ChrisClient.from_chrs()
+await acollect(chris.search_plugins())
+
+
+ +

When from_chrs is called with no parameters, it uses the "preferred account" +i.e. the most recently added account, the same _ChRIS_ account and server as +chrs would when called without options. The "preferred account" can be changed +by running chrs switch.

+
+ + +
+
+ +
+
@http.search('.')
+ + def + search_feeds( self, **query) -> aiochris.util.search.Search[aiochris.models.logged_in.Feed]: + + + +
+ + 
175    @http.search(".")
+176    def search_feeds(self, **query) -> Search[Feed]:
+177        """
+178        Search for feeds.
+179        """
+180        ...
+
+ + +

Search for feeds.

+
+ + +
+
+ +
+
@http.search('plugins')
+ + def + search_plugins( self, **query) -> aiochris.util.search.Search[aiochris.models.logged_in.Plugin]: + + + +
+ + 
182    @http.search("plugins")
+183    def search_plugins(self, **query) -> Search[Plugin]:
+184        """
+185        Search for plugins.
+186        """
+187        ...
+
+ + +

Search for plugins.

+
+ + +
+
+ +
+
@http.search('plugin_instances')
+ + def + plugin_instances( self, **query) -> aiochris.util.search.Search[aiochris.models.logged_in.PluginInstance]: + + + +
+ + 
189    @http.search("plugin_instances")
+190    def plugin_instances(self, **query) -> Search[PluginInstance]:
+191        """
+192        Search for plugin instances.
+193        """
+194        ...
+
+ + +

Search for plugin instances.

+
+ + +
+
+ +
+ + async def + upload_file( self, local_file: str | os.PathLike, upload_path: str) -> aiochris.models.logged_in.File: + + + +
+ + 
196    async def upload_file(
+197        self, local_file: str | os.PathLike, upload_path: str
+198    ) -> File:
+199        """
+200        Upload a local file to *ChRIS*.
+201
+202        .. warning:: Uses non-async code.
+203                     The file is read using non-async code.
+204                     Performance will suffer with large files and hard drives.
+205                     See [aiolibs/aiohttp#7174](https://github.com/aio-libs/aiohttp/issues/7174)
+206
+207        Examples
+208        --------
+209
+210        Upload a single file:
+211
+212        ```python
+213        aiochris = await ChrisClient.from_login(
+214            username='chris',
+215            password='chris1234',
+216            url='https://cube.chrisproject.org/api/v1/'
+217        )
+218        file = await aiochris.upload_file("./my_data.dat", 'dir/my_data.dat')
+219        assert file.fname == 'aiochris/uploads/dir/my_data.dat'
+220        ```
+221
+222        Upload (in parallel) all `*.txt` files in a directory
+223        `'incoming'` to `aiochris/uploads/big_folder`:
+224
+225        ```python
+226        upload_jobs = (
+227            aiochris.upload_file(p, f'big_folder/{p}')
+228            for p in Path('incoming')
+229        )
+230        await asyncio.gather(upload_jobs)
+231        ```
+232
+233        Parameters
+234        ----------
+235        local_file
+236            Path of an existing local file to upload.
+237        upload_path
+238            A subpath of `{username}/uploads/` where to upload the file to in *CUBE*
+239        """
+240        upload_path = await self._add_upload_prefix(upload_path)
+241        local_file = Path(local_file)
+242        with local_file.open("rb") as f:
+243            data = aiohttp.FormData()
+244            data.add_field("upload_path", upload_path)
+245            data.add_field("fname", f, filename=local_file.name)
+246            sent = self.s.post(self.collection_links.uploadedfiles, data=data)
+247            return await deserialize_res(
+248                sent, self, {"fname": local_file, "upload_path": upload_path}, File
+249            )
+250
+251        # read_stream = _file_sender(local_file, chunk_size)
+252        # file_length = os.stat(local_file).st_size
+253        # return await self.upload_stream(read_stream, upload_path, str(local_file), file_length)
+
+ + +

Upload a local file to ChRIS.

+ +
+ +
Uses non-async code.
+ +

The file is read using non-async code. +Performance will suffer with large files and hard drives. +See aiolibs/aiohttp#7174

+ +
+ +
Examples
+ +

Upload a single file:

+ +
+
aiochris = await ChrisClient.from_login(
+    username='chris',
+    password='chris1234',
+    url='https://cube.chrisproject.org/api/v1/'
+)
+file = await aiochris.upload_file("./my_data.dat", 'dir/my_data.dat')
+assert file.fname == 'aiochris/uploads/dir/my_data.dat'
+
+
+ +

Upload (in parallel) all *.txt files in a directory +'incoming' to aiochris/uploads/big_folder:

+ +
+
upload_jobs = (
+    aiochris.upload_file(p, f'big_folder/{p}')
+    for p in Path('incoming')
+)
+await asyncio.gather(upload_jobs)
+
+
+ +
Parameters
+ +
    +
  • local_file: Path of an existing local file to upload.
    • +
  • upload_path: A subpath of {username}/uploads/ where to upload the file to in CUBE
    • +
+
+ + +
+
+ +
+
@http.get('user')
+ + async def + user(self) -> aiochris.models.logged_in.User: + + + +
+ + 
291    @http.get("user")
+292    async def user(self) -> User:
+293        """Gets the user's information."""
+294        ...
+
+ + +

Gets the user's information.

+
+ + +
+
+ +
+ + async def + username(self) -> aiochris.types.Username: + + + +
+ + 
300    async def username(self) -> Username:
+301        """
+302        Gets the username. In contrast to `self.user`, this method will use a cached API call.
+303        """
+304        user = await self._user  # this is weird
+305        return user.username
+
+ + +

Gets the username. In contrast to self.user, this method will use a cached API call.

+
+ + +
+
+ +
+
@http.search('compute_resources')
+ + def + search_compute_resources( self, **query) -> aiochris.util.search.Search[aiochris.models.public.ComputeResource]: + + + +
+ + 
307    @http.search("compute_resources")
+308    def search_compute_resources(self, **query) -> Search[ComputeResource]:
+309        """
+310        Search for existing compute resources.
+311
+312        See also
+313        --------
+314        `get_all_compute_resources` :
+315        """
+316        ...
+
+ + +

Search for existing compute resources.

+ +
See also
+ +

get_all_compute_resources :

+
+ + +
+
+ +
+ + async def + get_all_compute_resources(self) -> Sequence[aiochris.models.public.ComputeResource]: + + + +
+ + 
318    async def get_all_compute_resources(self) -> Sequence[ComputeResource]:
+319        """
+320        Get all compute resources.
+321
+322        This method exists for convenience.
+323        The number of compute resources of a CUBE is typically small so it's ok.
+324
+325        See also
+326        --------
+327        `search_compute_resources` :
+328        """
+329        return await acollect(self.search_compute_resources())
+
+ + +

Get all compute resources.

+ +

This method exists for convenience. +The number of compute resources of a CUBE is typically small so it's ok.

+ +
See also
+ +

search_compute_resources :

+
+ + +
+
+ +
+
@http.search('pacsfiles')
+ + def + search_pacsfiles( self, **query) -> aiochris.util.search.Search[aiochris.models.logged_in.PACSFile]: + + + +
+ + 
331    @http.search("pacsfiles")
+332    def search_pacsfiles(self, **query) -> Search[PACSFile]:
+333        """
+334        Search for PACS files.
+335        """
+336        ...
+
+ + +

Search for PACS files.

+
+ + +
+
+
Inherited Members
+
+
aiochris.link.collection_client.CollectionJsonApiClient
+
CollectionJsonApiClient
+
url
+ + +
+ +
aiochris.link.linked.Linked
+
max_search_requests
+ +
+
+
+
+
+ + \ No newline at end of file diff --git a/v0.5.0a3/aiochris/client/base.html b/v0.5.0a3/aiochris/client/base.html new file mode 100644 index 0000000..7de7321 --- /dev/null +++ b/v0.5.0a3/aiochris/client/base.html @@ -0,0 +1,648 @@ + + + + + + + aiochris.client.base API documentation + + + + + + + + + +
+
+

+aiochris.client.base

+ + + + + + + 
  1import abc
+  2from typing import AsyncContextManager, Generic, Optional, Callable, TypeVar
+  3
+  4import aiohttp
+  5from serde import from_dict
+  6
+  7from aiochris import Search
+  8from aiochris.link.collection_client import L, CollectionJsonApiClient
+  9from aiochris.models.public import PublicPlugin
+ 10from aiochris.errors import raise_for_status
+ 11
+ 12CSelf = TypeVar(
+ 13    "CSelf", bound="BaseChrisClient"
+ 14)  # can't wait for `Self` in Python 3.11!
+ 15
+ 16
+ 17class BaseChrisClient(
+ 18    Generic[L, CSelf],
+ 19    CollectionJsonApiClient[L],
+ 20    AsyncContextManager[CSelf],
+ 21    abc.ABC,
+ 22):
+ 23    """
+ 24    Provides the implementation for most of the read-only GET resources of ChRIS
+ 25    and functions related to the client object's own usage.
+ 26    """
+ 27
+ 28    @classmethod
+ 29    async def new(
+ 30        cls,
+ 31        url: str,
+ 32        max_search_requests: int = 100,
+ 33        connector: Optional[aiohttp.BaseConnector] = None,
+ 34        connector_owner: bool = True,
+ 35        session_modifier: Optional[Callable[[aiohttp.ClientSession], None]] = None,
+ 36    ) -> CSelf:
+ 37        """
+ 38        A constructor which creates the session for the `BaseChrisClient`
+ 39        and makes an initial request to populate `collection_links`.
+ 40
+ 41        Parameters
+ 42        ----------
+ 43        url
+ 44            ChRIS backend url, e.g. "https://cube.chrisproject.org/api/v1/"
+ 45        max_search_requests
+ 46            Maximum number of HTTP requests to make while retrieving items from a
+ 47            paginated endpoint before raising `aiochris.util.search.TooMuchPaginationError`.
+ 48            Use `max_search_requests=-1` to allow for "infinite" pagination
+ 49            (well, you're still limited by Python's stack).
+ 50        connector
+ 51            [`aiohttp.BaseConnector`](https://docs.aiohttp.org/en/v3.8.3/client_advanced.html#connectors) to use.
+ 52            If creating multiple client objects in the same program,
+ 53            reusing connectors between them is more efficient.
+ 54        connector_owner
+ 55            If `True`, this client will close its `aiohttp.BaseConnector`
+ 56        session_modifier
+ 57            Called to mutate the created `aiohttp.ClientSession` for the object.
+ 58            If the client requires authentication, define `session_modifier`
+ 59            to add authentication headers to the session.
+ 60        """
+ 61        if not url.endswith("/api/v1/"):
+ 62            raise ValueError("url must end with /api/v1/")
+ 63        accept_json = {
+ 64            "Accept": "application/json",
+ 65            # 'Content-Type': 'application/vnd.collection+json',
+ 66        }
+ 67        # TODO maybe we want to wrap the session:
+ 68        # - status == 4XX --> print response text
+ 69        # - content-type: application/vnd.collection+json
+ 70        session = aiohttp.ClientSession(
+ 71            headers=accept_json,
+ 72            raise_for_status=False,
+ 73            connector=connector,
+ 74            connector_owner=connector_owner,
+ 75        )
+ 76        if session_modifier is not None:
+ 77            session_modifier(session)
+ 78        try:
+ 79            async with session.get(url) as res:
+ 80                await raise_for_status(res)
+ 81                body = await res.json()
+ 82        except Exception:
+ 83            await session.close()
+ 84            raise
+ 85        links = from_dict(cls._collection_type(), body["collection_links"])
+ 86        return cls(
+ 87            url=url,
+ 88            s=session,
+ 89            collection_links=links,
+ 90            max_search_requests=max_search_requests,
+ 91        )
+ 92
+ 93    async def __aenter__(self) -> CSelf:
+ 94        return self
+ 95
+ 96    async def __aexit__(self, exc_type, exc_val, exc_tb):
+ 97        await self.close()
+ 98
+ 99    async def close(self):
+100        """
+101        Close the HTTP session used by this client.
+102        """
+103        await self.s.close()
+104
+105    @abc.abstractmethod
+106    def search_plugins(self, **query) -> Search[PublicPlugin]:
+107        """
+108        Search for plugins.
+109        """
+110        ...
+
+ + +
+
+ +
+ + class + BaseChrisClient(typing.Generic[~L, ~CSelf], aiochris.link.collection_client.CollectionJsonApiClient[~L], typing.AsyncContextManager[~CSelf], abc.ABC): + + + +
+ + 
 18class BaseChrisClient(
+ 19    Generic[L, CSelf],
+ 20    CollectionJsonApiClient[L],
+ 21    AsyncContextManager[CSelf],
+ 22    abc.ABC,
+ 23):
+ 24    """
+ 25    Provides the implementation for most of the read-only GET resources of ChRIS
+ 26    and functions related to the client object's own usage.
+ 27    """
+ 28
+ 29    @classmethod
+ 30    async def new(
+ 31        cls,
+ 32        url: str,
+ 33        max_search_requests: int = 100,
+ 34        connector: Optional[aiohttp.BaseConnector] = None,
+ 35        connector_owner: bool = True,
+ 36        session_modifier: Optional[Callable[[aiohttp.ClientSession], None]] = None,
+ 37    ) -> CSelf:
+ 38        """
+ 39        A constructor which creates the session for the `BaseChrisClient`
+ 40        and makes an initial request to populate `collection_links`.
+ 41
+ 42        Parameters
+ 43        ----------
+ 44        url
+ 45            ChRIS backend url, e.g. "https://cube.chrisproject.org/api/v1/"
+ 46        max_search_requests
+ 47            Maximum number of HTTP requests to make while retrieving items from a
+ 48            paginated endpoint before raising `aiochris.util.search.TooMuchPaginationError`.
+ 49            Use `max_search_requests=-1` to allow for "infinite" pagination
+ 50            (well, you're still limited by Python's stack).
+ 51        connector
+ 52            [`aiohttp.BaseConnector`](https://docs.aiohttp.org/en/v3.8.3/client_advanced.html#connectors) to use.
+ 53            If creating multiple client objects in the same program,
+ 54            reusing connectors between them is more efficient.
+ 55        connector_owner
+ 56            If `True`, this client will close its `aiohttp.BaseConnector`
+ 57        session_modifier
+ 58            Called to mutate the created `aiohttp.ClientSession` for the object.
+ 59            If the client requires authentication, define `session_modifier`
+ 60            to add authentication headers to the session.
+ 61        """
+ 62        if not url.endswith("/api/v1/"):
+ 63            raise ValueError("url must end with /api/v1/")
+ 64        accept_json = {
+ 65            "Accept": "application/json",
+ 66            # 'Content-Type': 'application/vnd.collection+json',
+ 67        }
+ 68        # TODO maybe we want to wrap the session:
+ 69        # - status == 4XX --> print response text
+ 70        # - content-type: application/vnd.collection+json
+ 71        session = aiohttp.ClientSession(
+ 72            headers=accept_json,
+ 73            raise_for_status=False,
+ 74            connector=connector,
+ 75            connector_owner=connector_owner,
+ 76        )
+ 77        if session_modifier is not None:
+ 78            session_modifier(session)
+ 79        try:
+ 80            async with session.get(url) as res:
+ 81                await raise_for_status(res)
+ 82                body = await res.json()
+ 83        except Exception:
+ 84            await session.close()
+ 85            raise
+ 86        links = from_dict(cls._collection_type(), body["collection_links"])
+ 87        return cls(
+ 88            url=url,
+ 89            s=session,
+ 90            collection_links=links,
+ 91            max_search_requests=max_search_requests,
+ 92        )
+ 93
+ 94    async def __aenter__(self) -> CSelf:
+ 95        return self
+ 96
+ 97    async def __aexit__(self, exc_type, exc_val, exc_tb):
+ 98        await self.close()
+ 99
+100    async def close(self):
+101        """
+102        Close the HTTP session used by this client.
+103        """
+104        await self.s.close()
+105
+106    @abc.abstractmethod
+107    def search_plugins(self, **query) -> Search[PublicPlugin]:
+108        """
+109        Search for plugins.
+110        """
+111        ...
+
+ + +

Provides the implementation for most of the read-only GET resources of ChRIS +and functions related to the client object's own usage.

+
+ + +
+ +
+
@classmethod
+ + async def + new( cls, url: str, max_search_requests: int = 100, connector: Optional[aiohttp.connector.BaseConnector] = None, connector_owner: bool = True, session_modifier: Optional[Callable[[aiohttp.client.ClientSession], NoneType]] = None) -> ~CSelf: + + + +
+ + 
29    @classmethod
+30    async def new(
+31        cls,
+32        url: str,
+33        max_search_requests: int = 100,
+34        connector: Optional[aiohttp.BaseConnector] = None,
+35        connector_owner: bool = True,
+36        session_modifier: Optional[Callable[[aiohttp.ClientSession], None]] = None,
+37    ) -> CSelf:
+38        """
+39        A constructor which creates the session for the `BaseChrisClient`
+40        and makes an initial request to populate `collection_links`.
+41
+42        Parameters
+43        ----------
+44        url
+45            ChRIS backend url, e.g. "https://cube.chrisproject.org/api/v1/"
+46        max_search_requests
+47            Maximum number of HTTP requests to make while retrieving items from a
+48            paginated endpoint before raising `aiochris.util.search.TooMuchPaginationError`.
+49            Use `max_search_requests=-1` to allow for "infinite" pagination
+50            (well, you're still limited by Python's stack).
+51        connector
+52            [`aiohttp.BaseConnector`](https://docs.aiohttp.org/en/v3.8.3/client_advanced.html#connectors) to use.
+53            If creating multiple client objects in the same program,
+54            reusing connectors between them is more efficient.
+55        connector_owner
+56            If `True`, this client will close its `aiohttp.BaseConnector`
+57        session_modifier
+58            Called to mutate the created `aiohttp.ClientSession` for the object.
+59            If the client requires authentication, define `session_modifier`
+60            to add authentication headers to the session.
+61        """
+62        if not url.endswith("/api/v1/"):
+63            raise ValueError("url must end with /api/v1/")
+64        accept_json = {
+65            "Accept": "application/json",
+66            # 'Content-Type': 'application/vnd.collection+json',
+67        }
+68        # TODO maybe we want to wrap the session:
+69        # - status == 4XX --> print response text
+70        # - content-type: application/vnd.collection+json
+71        session = aiohttp.ClientSession(
+72            headers=accept_json,
+73            raise_for_status=False,
+74            connector=connector,
+75            connector_owner=connector_owner,
+76        )
+77        if session_modifier is not None:
+78            session_modifier(session)
+79        try:
+80            async with session.get(url) as res:
+81                await raise_for_status(res)
+82                body = await res.json()
+83        except Exception:
+84            await session.close()
+85            raise
+86        links = from_dict(cls._collection_type(), body["collection_links"])
+87        return cls(
+88            url=url,
+89            s=session,
+90            collection_links=links,
+91            max_search_requests=max_search_requests,
+92        )
+
+ + +

A constructor which creates the session for the BaseChrisClient +and makes an initial request to populate collection_links.

+ +
Parameters
+ +
    +
  • url: ChRIS backend url, e.g. "https://cube.chrisproject.org/api/v1/"
    • +
  • max_search_requests: Maximum number of HTTP requests to make while retrieving items from a +paginated endpoint before raising aiochris.util.search.TooMuchPaginationError. +Use max_search_requests=-1 to allow for "infinite" pagination +(well, you're still limited by Python's stack).
    • +
  • connector: aiohttp.BaseConnector to use. +If creating multiple client objects in the same program, +reusing connectors between them is more efficient.
    • +
  • connector_owner: If True, this client will close its aiohttp.BaseConnector
    • +
  • session_modifier: Called to mutate the created aiohttp.ClientSession for the object. +If the client requires authentication, define session_modifier +to add authentication headers to the session.
    • +
+
+ + +
+
+ +
+ + async def + close(self): + + + +
+ + 
100    async def close(self):
+101        """
+102        Close the HTTP session used by this client.
+103        """
+104        await self.s.close()
+
+ + +

Close the HTTP session used by this client.

+
+ + +
+
+ +
+
@abc.abstractmethod
+ + def + search_plugins( self, **query) -> aiochris.util.search.Search[aiochris.models.public.PublicPlugin]: + + + +
+ + 
106    @abc.abstractmethod
+107    def search_plugins(self, **query) -> Search[PublicPlugin]:
+108        """
+109        Search for plugins.
+110        """
+111        ...
+
+ + +

Search for plugins.

+
+ + +
+
+
Inherited Members
+
+
aiochris.link.collection_client.CollectionJsonApiClient
+
url
+ + +
+
aiochris.link.linked.Linked
+
max_search_requests
+ +
+
+
+
+
+ + \ No newline at end of file diff --git a/v0.5.0a3/aiochris/client/from_chrs.html b/v0.5.0a3/aiochris/client/from_chrs.html new file mode 100644 index 0000000..f27ca9a --- /dev/null +++ b/v0.5.0a3/aiochris/client/from_chrs.html @@ -0,0 +1,824 @@ + + + + + + + aiochris.client.from_chrs API documentation + + + + + + + + + +
+
+

+aiochris.client.from_chrs

+ +

Interoperability with chrs version 0.2.4.

+ +

The functions of this module uses dynamic importing of extras from the chrs group.

+
+ + + + + + 
  1"""
+  2Interoperability with [`chrs`](https://crates.io/crates/chrs) version 0.2.4.
+  3
+  4The functions of this module uses dynamic importing of extras from the `chrs` group.
+  5"""
+  6import dataclasses
+  7from pathlib import Path
+  8
+  9import serde
+ 10from typing import Optional, Literal
+ 11from aiochris.types import Username, ChrisURL
+ 12import functools
+ 13
+ 14_SERVICE = "org.chrisproject.chrs"
+ 15"""
+ 16Keyring service name used by `chrs`.
+ 17
+ 18https://github.com/FNNDSC/chrs/blob/v0.2.4/chrs/src/login/saved.rs#L14
+ 19"""
+ 20
+ 21
+ 22@functools.cache
+ 23def _get_keyring():
+ 24    import keyring
+ 25
+ 26    return keyring.get_keyring()
+ 27
+ 28
+ 29@serde.deserialize
+ 30@dataclasses.dataclass(frozen=True)
+ 31class StoredToken:
+ 32    """
+ 33    https://github.com/FNNDSC/chrs/blob/v0.2.4/chrs/src/login/tokenstore.rs#L18-L24
+ 34    """
+ 35
+ 36    # note: we can't do @serde.deserialize(tagging=serde.AdjacentTagging('store', 'value'))
+ 37    # See https://github.com/yukinarit/pyserde/issues/411
+ 38    store: Literal["Text", "Keyring"]
+ 39    value: Optional[str] = None
+ 40
+ 41    def __post_init__(self):
+ 42        if self.store not in ("Text", "Keyring"):
+ 43            raise ValueError()
+ 44        if self.store == "Text" and self.store is None:
+ 45            raise ValueError()
+ 46
+ 47
+ 48@dataclasses.dataclass(frozen=True)
+ 49class ChrsLogin:
+ 50    """
+ 51    A login saved by `chrs`.
+ 52
+ 53    https://github.com/FNNDSC/chrs/blob/v0.2.4/chrs/src/login/tokenstore.rs#L18-L34
+ 54    """
+ 55
+ 56    address: ChrisURL
+ 57    username: Username
+ 58    store: StoredToken
+ 59
+ 60    def token(self) -> str:
+ 61        if self.store.value is not None:
+ 62            return self.store.value
+ 63        return self._get_token_from_keyring()
+ 64
+ 65    def is_for(self, address: Optional[ChrisURL], username: Optional[Username]) -> bool:
+ 66        """
+ 67        Returns `True` if this login is for the specified _ChRIS_ user account.
+ 68        """
+ 69        if address is None and username is None:
+ 70            return True
+ 71        if address is None and username == self.username:
+ 72            return True
+ 73        if username is None and address == self.address:
+ 74            return True
+ 75        if address == self.address and username == self.username:
+ 76            return True
+ 77        return False
+ 78
+ 79    def to_keyring_username(self) -> str:
+ 80        """
+ 81        Produce the username for this login in the keyring.
+ 82
+ 83        https://github.com/FNNDSC/chrs/blob/v0.2.4/chrs/src/login/tokenstore.rs#L3
+ 84        """
+ 85        return f"{self.username}@{self.address}"
+ 86
+ 87    def _get_token_from_keyring(self) -> str:
+ 88        """
+ 89        https://github.com/FNNDSC/chrs/blob/v0.2.4/chrs/src/login/tokenstore.rs#L110-L112
+ 90        """
+ 91        if self.store.store != "Keyring":
+ 92            raise ChrsKeyringError(
+ 93                "chrs login config is not valid: "
+ 94                f"for address={self.address} and username={self.username}"
+ 95                f"expected store=Keyring, got store={self.store.store}"
+ 96            )
+ 97        keyring_username = self.to_keyring_username()
+ 98        token = _get_keyring().get_password(_SERVICE, keyring_username)
+ 99        if token is None:
+100            raise ChrsKeyringError(f"No keyring password for {keyring_username}")
+101        return token
+102
+103
+104@dataclasses.dataclass(frozen=True)
+105class ChrsLogins:
+106    """
+107    Logins saved by `chrs`.
+108
+109    https://github.com/FNNDSC/chrs/blob/v0.2.4/chrs/src/login/saved.rs#L18-L22
+110    """
+111
+112    cubes: list[ChrsLogin]
+113    """Saved logins in reverse order of preference."""
+114
+115    @classmethod
+116    def load(cls, path: Path) -> "ChrsLogins":
+117        import serde.toml
+118
+119        return serde.toml.from_toml(cls, path.expanduser().read_text())
+120
+121    def get_token_for(
+122        self,
+123        address: Optional[str | ChrisURL] = None,
+124        username: Optional[str | Username] = None,
+125    ) -> Optional[tuple[ChrisURL, str]]:
+126        """
+127        Get token for a login.
+128        """
+129        for login in reversed(self.cubes):
+130            if login.is_for(address, username):
+131                if (token := login.token()) is not None:
+132                    return login.address, token
+133        return None
+134
+135
+136class ChrsKeyringError(Exception):
+137    """Error interacting with Keyring."""
+138
+139    pass
+
+ + +
+
+ +
+
@serde.deserialize
+
@dataclasses.dataclass(frozen=True)
+ + class + StoredToken: + + + +
+ + 
30@serde.deserialize
+31@dataclasses.dataclass(frozen=True)
+32class StoredToken:
+33    """
+34    https://github.com/FNNDSC/chrs/blob/v0.2.4/chrs/src/login/tokenstore.rs#L18-L24
+35    """
+36
+37    # note: we can't do @serde.deserialize(tagging=serde.AdjacentTagging('store', 'value'))
+38    # See https://github.com/yukinarit/pyserde/issues/411
+39    store: Literal["Text", "Keyring"]
+40    value: Optional[str] = None
+41
+42    def __post_init__(self):
+43        if self.store not in ("Text", "Keyring"):
+44            raise ValueError()
+45        if self.store == "Text" and self.store is None:
+46            raise ValueError()
+
+ + +

https://github.com/FNNDSC/chrs/blob/v0.2.4/chrs/src/login/tokenstore.rs#L18-L24

+
+ + +
+
+ + StoredToken(store: Literal['Text', 'Keyring'], value: Optional[str] = None) + + +
+ + + + +
+
+
+ +
+
@dataclasses.dataclass(frozen=True)
+ + class + ChrsLogin: + + + +
+ + 
 49@dataclasses.dataclass(frozen=True)
+ 50class ChrsLogin:
+ 51    """
+ 52    A login saved by `chrs`.
+ 53
+ 54    https://github.com/FNNDSC/chrs/blob/v0.2.4/chrs/src/login/tokenstore.rs#L18-L34
+ 55    """
+ 56
+ 57    address: ChrisURL
+ 58    username: Username
+ 59    store: StoredToken
+ 60
+ 61    def token(self) -> str:
+ 62        if self.store.value is not None:
+ 63            return self.store.value
+ 64        return self._get_token_from_keyring()
+ 65
+ 66    def is_for(self, address: Optional[ChrisURL], username: Optional[Username]) -> bool:
+ 67        """
+ 68        Returns `True` if this login is for the specified _ChRIS_ user account.
+ 69        """
+ 70        if address is None and username is None:
+ 71            return True
+ 72        if address is None and username == self.username:
+ 73            return True
+ 74        if username is None and address == self.address:
+ 75            return True
+ 76        if address == self.address and username == self.username:
+ 77            return True
+ 78        return False
+ 79
+ 80    def to_keyring_username(self) -> str:
+ 81        """
+ 82        Produce the username for this login in the keyring.
+ 83
+ 84        https://github.com/FNNDSC/chrs/blob/v0.2.4/chrs/src/login/tokenstore.rs#L3
+ 85        """
+ 86        return f"{self.username}@{self.address}"
+ 87
+ 88    def _get_token_from_keyring(self) -> str:
+ 89        """
+ 90        https://github.com/FNNDSC/chrs/blob/v0.2.4/chrs/src/login/tokenstore.rs#L110-L112
+ 91        """
+ 92        if self.store.store != "Keyring":
+ 93            raise ChrsKeyringError(
+ 94                "chrs login config is not valid: "
+ 95                f"for address={self.address} and username={self.username}"
+ 96                f"expected store=Keyring, got store={self.store.store}"
+ 97            )
+ 98        keyring_username = self.to_keyring_username()
+ 99        token = _get_keyring().get_password(_SERVICE, keyring_username)
+100        if token is None:
+101            raise ChrsKeyringError(f"No keyring password for {keyring_username}")
+102        return token
+
+ + +

A login saved by chrs.

+ +

https://github.com/FNNDSC/chrs/blob/v0.2.4/chrs/src/login/tokenstore.rs#L18-L34

+
+ + +
+
+ + ChrsLogin( address: aiochris.types.ChrisURL, username: aiochris.types.Username, store: aiochris.client.from_chrs.StoredToken) + + +
+ + + + +
+
+ +
+ + def + token(self) -> str: + + + +
+ + 
61    def token(self) -> str:
+62        if self.store.value is not None:
+63            return self.store.value
+64        return self._get_token_from_keyring()
+
+ + + + +
+
+ +
+ + def + is_for( self, address: Optional[aiochris.types.ChrisURL], username: Optional[aiochris.types.Username]) -> bool: + + + +
+ + 
66    def is_for(self, address: Optional[ChrisURL], username: Optional[Username]) -> bool:
+67        """
+68        Returns `True` if this login is for the specified _ChRIS_ user account.
+69        """
+70        if address is None and username is None:
+71            return True
+72        if address is None and username == self.username:
+73            return True
+74        if username is None and address == self.address:
+75            return True
+76        if address == self.address and username == self.username:
+77            return True
+78        return False
+
+ + +

Returns True if this login is for the specified _ChRIS_ user account.

+
+ + +
+
+ +
+ + def + to_keyring_username(self) -> str: + + + +
+ + 
80    def to_keyring_username(self) -> str:
+81        """
+82        Produce the username for this login in the keyring.
+83
+84        https://github.com/FNNDSC/chrs/blob/v0.2.4/chrs/src/login/tokenstore.rs#L3
+85        """
+86        return f"{self.username}@{self.address}"
+
+ + +

Produce the username for this login in the keyring.

+ +

https://github.com/FNNDSC/chrs/blob/v0.2.4/chrs/src/login/tokenstore.rs#L3

+
+ + +
+
+
+ +
+
@dataclasses.dataclass(frozen=True)
+ + class + ChrsLogins: + + + +
+ + 
105@dataclasses.dataclass(frozen=True)
+106class ChrsLogins:
+107    """
+108    Logins saved by `chrs`.
+109
+110    https://github.com/FNNDSC/chrs/blob/v0.2.4/chrs/src/login/saved.rs#L18-L22
+111    """
+112
+113    cubes: list[ChrsLogin]
+114    """Saved logins in reverse order of preference."""
+115
+116    @classmethod
+117    def load(cls, path: Path) -> "ChrsLogins":
+118        import serde.toml
+119
+120        return serde.toml.from_toml(cls, path.expanduser().read_text())
+121
+122    def get_token_for(
+123        self,
+124        address: Optional[str | ChrisURL] = None,
+125        username: Optional[str | Username] = None,
+126    ) -> Optional[tuple[ChrisURL, str]]:
+127        """
+128        Get token for a login.
+129        """
+130        for login in reversed(self.cubes):
+131            if login.is_for(address, username):
+132                if (token := login.token()) is not None:
+133                    return login.address, token
+134        return None
+
+ + +

Logins saved by chrs.

+ +

https://github.com/FNNDSC/chrs/blob/v0.2.4/chrs/src/login/saved.rs#L18-L22

+
+ + +
+
+ + ChrsLogins(cubes: list[aiochris.client.from_chrs.ChrsLogin]) + + +
+ + + + +
+
+
+ cubes: list[aiochris.client.from_chrs.ChrsLogin] + + +
+ + +

Saved logins in reverse order of preference.

+
+ + +
+
+ +
+
@classmethod
+ + def + load(cls, path: pathlib.Path) -> aiochris.client.from_chrs.ChrsLogins: + + + +
+ + 
116    @classmethod
+117    def load(cls, path: Path) -> "ChrsLogins":
+118        import serde.toml
+119
+120        return serde.toml.from_toml(cls, path.expanduser().read_text())
+
+ + + + +
+
+ +
+ + def + get_token_for( self, address: Union[str, aiochris.types.ChrisURL, NoneType] = None, username: Union[str, aiochris.types.Username, NoneType] = None) -> Optional[tuple[aiochris.types.ChrisURL, str]]: + + + +
+ + 
122    def get_token_for(
+123        self,
+124        address: Optional[str | ChrisURL] = None,
+125        username: Optional[str | Username] = None,
+126    ) -> Optional[tuple[ChrisURL, str]]:
+127        """
+128        Get token for a login.
+129        """
+130        for login in reversed(self.cubes):
+131            if login.is_for(address, username):
+132                if (token := login.token()) is not None:
+133                    return login.address, token
+134        return None
+
+ + +

Get token for a login.

+
+ + +
+
+
+ +
+ + class + ChrsKeyringError(builtins.Exception): + + + +
+ + 
137class ChrsKeyringError(Exception):
+138    """Error interacting with Keyring."""
+139
+140    pass
+
+ + +

Error interacting with Keyring.

+
+ + +
+
Inherited Members
+
+
builtins.Exception
+
Exception
+ +
+
builtins.BaseException
+
with_traceback
+ +
+
+
+
+
+ + \ No newline at end of file diff --git a/v0.5.0a3/aiochris/client/normal.html b/v0.5.0a3/aiochris/client/normal.html new file mode 100644 index 0000000..df1b4ca --- /dev/null +++ b/v0.5.0a3/aiochris/client/normal.html @@ -0,0 +1,434 @@ + + + + + + + aiochris.client.normal API documentation + + + + + + + + + +
+
+

+aiochris.client.normal

+ + + + + + + 
 1from contextlib import asynccontextmanager
+ 2from typing import Optional
+ 3
+ 4import aiohttp
+ 5from serde.json import from_json
+ 6
+ 7from aiochris.client.authed import AuthenticatedClient
+ 8from aiochris.errors import raise_for_status
+ 9from aiochris.models.collection_links import CollectionLinks
+10from aiochris.models.data import UserData
+11from aiochris.types import ChrisURL, Username, Password
+12
+13
+14class ChrisClient(AuthenticatedClient[CollectionLinks, "ChrisClient"]):
+15    """
+16    A normal user *ChRIS* client, who may upload files and create plugin instances.
+17    """
+18
+19    @classmethod
+20    async def create_user(
+21        cls,
+22        url: ChrisURL | str,
+23        username: Username | str,
+24        password: Password | str,
+25        email: str,
+26        session: Optional[aiohttp.ClientSession] = None,
+27    ) -> UserData:
+28        payload = {
+29            "template": {
+30                "data": [
+31                    {"name": "email", "value": email},
+32                    {"name": "username", "value": username},
+33                    {"name": "password", "value": password},
+34                ]
+35            }
+36        }
+37        headers = {
+38            "Content-Type": "application/vnd.collection+json",
+39            "Accept": "application/json",
+40        }
+41        async with _optional_session(session) as session:
+42            res = await session.post(url + "users/", json=payload, headers=headers)
+43            await raise_for_status(res)
+44            return from_json(UserData, await res.text())
+45
+46
+47@asynccontextmanager
+48async def _optional_session(session: Optional[aiohttp.ClientSession]):
+49    if session is not None:
+50        yield session
+51        return
+52    async with aiohttp.ClientSession() as session:
+53        yield session
+
+ + +
+
+ +
+ + class + ChrisClient(aiochris.client.authed.AuthenticatedClient[aiochris.models.collection_links.CollectionLinks, 'ChrisClient']): + + + +
+ + 
15class ChrisClient(AuthenticatedClient[CollectionLinks, "ChrisClient"]):
+16    """
+17    A normal user *ChRIS* client, who may upload files and create plugin instances.
+18    """
+19
+20    @classmethod
+21    async def create_user(
+22        cls,
+23        url: ChrisURL | str,
+24        username: Username | str,
+25        password: Password | str,
+26        email: str,
+27        session: Optional[aiohttp.ClientSession] = None,
+28    ) -> UserData:
+29        payload = {
+30            "template": {
+31                "data": [
+32                    {"name": "email", "value": email},
+33                    {"name": "username", "value": username},
+34                    {"name": "password", "value": password},
+35                ]
+36            }
+37        }
+38        headers = {
+39            "Content-Type": "application/vnd.collection+json",
+40            "Accept": "application/json",
+41        }
+42        async with _optional_session(session) as session:
+43            res = await session.post(url + "users/", json=payload, headers=headers)
+44            await raise_for_status(res)
+45            return from_json(UserData, await res.text())
+
+ + +

A normal user ChRIS client, who may upload files and create plugin instances.

+
+ + +
+ +
+
@classmethod
+ + async def + create_user( cls, url: Union[aiochris.types.ChrisURL, str], username: Union[aiochris.types.Username, str], password: Union[aiochris.types.Password, str], email: str, session: Optional[aiohttp.client.ClientSession] = None) -> aiochris.models.data.UserData: + + + +
+ + 
20    @classmethod
+21    async def create_user(
+22        cls,
+23        url: ChrisURL | str,
+24        username: Username | str,
+25        password: Password | str,
+26        email: str,
+27        session: Optional[aiohttp.ClientSession] = None,
+28    ) -> UserData:
+29        payload = {
+30            "template": {
+31                "data": [
+32                    {"name": "email", "value": email},
+33                    {"name": "username", "value": username},
+34                    {"name": "password", "value": password},
+35                ]
+36            }
+37        }
+38        headers = {
+39            "Content-Type": "application/vnd.collection+json",
+40            "Accept": "application/json",
+41        }
+42        async with _optional_session(session) as session:
+43            res = await session.post(url + "users/", json=payload, headers=headers)
+44            await raise_for_status(res)
+45            return from_json(UserData, await res.text())
+
+ + + + +
+
+
Inherited Members
+
+
aiochris.link.collection_client.CollectionJsonApiClient
+
CollectionJsonApiClient
+
url
+ + +
+ + +
aiochris.link.linked.Linked
+
max_search_requests
+ +
+
+
+
+
+ + \ No newline at end of file diff --git a/v0.5.0a3/aiochris/errors.html b/v0.5.0a3/aiochris/errors.html new file mode 100644 index 0000000..cf96a08 --- /dev/null +++ b/v0.5.0a3/aiochris/errors.html @@ -0,0 +1,560 @@ + + + + + + + aiochris.errors API documentation + + + + + + + + + +
+
+

+aiochris.errors

+ + + + + + + 
 1import aiohttp
+ 2
+ 3
+ 4async def raise_for_status(res: aiohttp.ClientResponse) -> None:
+ 5    """
+ 6    Raises custom exceptions.
+ 7    """
+ 8    if res.status < 400:
+ 9        res.raise_for_status()
+10        return
+11    exception = BadRequestError if res.status < 500 else InternalServerError
+12    try:
+13        raise exception(res.status, res.url, await res.json())
+14    except aiohttp.ClientError:
+15        raise exception(res.status, res.url)
+16
+17
+18class BaseClientError(Exception):
+19    pass
+20
+21
+22class ResponseError(BaseClientError):
+23    pass
+24
+25
+26class BadRequestError(ResponseError):
+27    pass
+28
+29
+30class InternalServerError(ResponseError):
+31    pass
+32
+33
+34class IncorrectLoginError(BaseClientError):
+35    pass
+36
+37
+38class NonsenseResponseError(ResponseError):
+39    """CUBE returned data which does not make sense."""
+40
+41    pass
+
+ + +
+
+ +
+ + async def + raise_for_status(res: aiohttp.client_reqrep.ClientResponse) -> None: + + + +
+ + 
 5async def raise_for_status(res: aiohttp.ClientResponse) -> None:
+ 6    """
+ 7    Raises custom exceptions.
+ 8    """
+ 9    if res.status < 400:
+10        res.raise_for_status()
+11        return
+12    exception = BadRequestError if res.status < 500 else InternalServerError
+13    try:
+14        raise exception(res.status, res.url, await res.json())
+15    except aiohttp.ClientError:
+16        raise exception(res.status, res.url)
+
+ + +

Raises custom exceptions.

+
+ + +
+
+ +
+ + class + BaseClientError(builtins.Exception): + + + +
+ + 
19class BaseClientError(Exception):
+20    pass
+
+ + +

Common base class for all non-exit exceptions.

+
+ + +
+
Inherited Members
+
+
builtins.Exception
+
Exception
+ +
+
builtins.BaseException
+
with_traceback
+ +
+
+
+
+
+ +
+ + class + ResponseError(BaseClientError): + + + +
+ + 
23class ResponseError(BaseClientError):
+24    pass
+
+ + +

Common base class for all non-exit exceptions.

+
+ + +
+
Inherited Members
+
+
builtins.Exception
+
Exception
+ +
+
builtins.BaseException
+
with_traceback
+ +
+
+
+
+
+ +
+ + class + BadRequestError(ResponseError): + + + +
+ + 
27class BadRequestError(ResponseError):
+28    pass
+
+ + +

Common base class for all non-exit exceptions.

+
+ + +
+
Inherited Members
+
+
builtins.Exception
+
Exception
+ +
+
builtins.BaseException
+
with_traceback
+ +
+
+
+
+
+ +
+ + class + InternalServerError(ResponseError): + + + +
+ + 
31class InternalServerError(ResponseError):
+32    pass
+
+ + +

Common base class for all non-exit exceptions.

+
+ + +
+
Inherited Members
+
+
builtins.Exception
+
Exception
+ +
+
builtins.BaseException
+
with_traceback
+ +
+
+
+
+
+ +
+ + class + IncorrectLoginError(BaseClientError): + + + +
+ + 
35class IncorrectLoginError(BaseClientError):
+36    pass
+
+ + +

Common base class for all non-exit exceptions.

+
+ + +
+
Inherited Members
+
+
builtins.Exception
+
Exception
+ +
+
builtins.BaseException
+
with_traceback
+ +
+
+
+
+
+ +
+ + class + NonsenseResponseError(ResponseError): + + + +
+ + 
39class NonsenseResponseError(ResponseError):
+40    """CUBE returned data which does not make sense."""
+41
+42    pass
+
+ + +

CUBE returned data which does not make sense.

+
+ + +
+
Inherited Members
+
+
builtins.Exception
+
Exception
+ +
+
builtins.BaseException
+
with_traceback
+ +
+
+
+
+
+ + \ No newline at end of file diff --git a/v0.5.0a3/aiochris/models.html b/v0.5.0a3/aiochris/models.html new file mode 100644 index 0000000..d8006b4 --- /dev/null +++ b/v0.5.0a3/aiochris/models.html @@ -0,0 +1,249 @@ + + + + + + + aiochris.models API documentation + + + + + + + + + +
+
+

+aiochris.models

+ + + + + + + 
1from aiochris.models.logged_in import *
+2from aiochris.models.public import *
+3from aiochris.models.data import *
+
+ + +
+
+ + \ No newline at end of file diff --git a/v0.5.0a3/aiochris/models/collection_links.html b/v0.5.0a3/aiochris/models/collection_links.html new file mode 100644 index 0000000..dcf3433 --- /dev/null +++ b/v0.5.0a3/aiochris/models/collection_links.html @@ -0,0 +1,674 @@ + + + + + + + aiochris.models.collection_links API documentation + + + + + + + + + +
+
+

+aiochris.models.collection_links

+ + + + + + + 
 1import dataclasses
+ 2import functools
+ 3from dataclasses import dataclass
+ 4from typing import Iterator, Optional
+ 5
+ 6from serde import deserialize
+ 7
+ 8from aiochris.types import ApiUrl, UserUrl, AdminUrl
+ 9
+10
+11@deserialize
+12@dataclass(frozen=True)
+13class AbstractCollectionLinks:
+14    @classmethod
+15    def has_field(cls, field_name: str) -> bool:
+16        return field_name in cls._field_names()
+17
+18    @classmethod
+19    def _field_names(cls) -> Iterator[str]:
+20        return (f.name for f in dataclasses.fields(cls))
+21
+22    def get(self, collection_name: str) -> str:
+23        url = self._dict.get(collection_name, None)
+24        if url is None:
+25            raise TypeError(
+26                f'{self.__class__} does not have link for "{collection_name}"'
+27            )
+28        return url
+29
+30    @functools.cached_property
+31    def _dict(self) -> dict[str, str]:
+32        return dataclasses.asdict(self)
+33
+34
+35@deserialize
+36@dataclass(frozen=True)
+37class AnonymousCollectionLinks(AbstractCollectionLinks):
+38    chrisinstance: ApiUrl
+39    compute_resources: ApiUrl
+40    plugin_metas: ApiUrl
+41    plugins: ApiUrl
+42    plugin_instances: ApiUrl
+43    pipelines: ApiUrl
+44    pipeline_instances: ApiUrl
+45    workflows: ApiUrl
+46    tags: ApiUrl
+47    pacsfiles: ApiUrl
+48    servicefiles: ApiUrl
+49    filebrowser: ApiUrl
+50
+51
+52@deserialize
+53@dataclass(frozen=True)
+54class CollectionLinks(AnonymousCollectionLinks):
+55    user: UserUrl
+56    userfiles: Optional[ApiUrl]
+57    uploadedfiles: Optional[ApiUrl]
+58
+59    def __post_init__(self):
+60        if not ((self.userfiles is None) ^ (self.uploadedfiles is None)):
+61            raise ValueError("Either userfiles or uploadedfiles link must be present")
+62
+63    @property
+64    def useruploadedfiles(self) -> ApiUrl:
+65        if self.userfiles is None:
+66            return self.uploadedfiles
+67        return self.userfiles
+68
+69
+70@deserialize
+71@dataclass(frozen=True)
+72class AdminCollectionLinks(CollectionLinks):
+73    admin: AdminUrl
+74
+75
+76@deserialize
+77@dataclass(frozen=True)
+78class AdminApiCollectionLinks(AbstractCollectionLinks):
+79    compute_resources: ApiUrl
+
+ + +
+ + + + + +
+ + \ No newline at end of file diff --git a/v0.5.0a3/aiochris/models/data.html b/v0.5.0a3/aiochris/models/data.html new file mode 100644 index 0000000..81d85c0 --- /dev/null +++ b/v0.5.0a3/aiochris/models/data.html @@ -0,0 +1,719 @@ + + + + + + + aiochris.models.data API documentation + + + + + + + + + +
+
+

+aiochris.models.data

+ +

Dataclasses describing objects returned from CUBE.

+ +

These classes are extended in the modules aiochris.models.logged_in +and aiochris.models.public with methods to get objects from links.

+
+ + + + + + 
  1"""
+  2Dataclasses describing objects returned from CUBE.
+  3
+  4These classes are extended in the modules `aiochris.models.logged_in`
+  5and `aiochris.models.public` with methods to get objects from links.
+  6"""
+  7
+  8from dataclasses import dataclass
+  9import datetime
+ 10from typing import Optional
+ 11
+ 12from serde import deserialize
+ 13
+ 14from aiochris.link.linked import LinkedModel
+ 15from aiochris.enums import PluginType, Status
+ 16from aiochris.types import *
+ 17
+ 18
+ 19@deserialize
+ 20@dataclass(frozen=True)
+ 21class UserData:
+ 22    """A *CUBE* user."""
+ 23
+ 24    url: UserUrl
+ 25    id: UserId
+ 26    username: Username
+ 27    email: str
+ 28
+ 29
+ 30# TODO It'd be better to use inheritance instead of optionals
+ 31@deserialize
+ 32@dataclass(frozen=True)
+ 33class PluginInstanceData(LinkedModel):
+ 34    """
+ 35    A *plugin instance* in _ChRIS_ is a computing job, i.e. an attempt to run
+ 36    a computation (a non-interactive command-line app) to produce data.
+ 37    """
+ 38
+ 39    url: PluginInstanceUrl
+ 40    id: PluginInstanceId
+ 41    title: str
+ 42    compute_resource_name: ComputeResourceName
+ 43    plugin_id: PluginId
+ 44    plugin_name: PluginName
+ 45    plugin_version: PluginVersion
+ 46    plugin_type: PluginType
+ 47
+ 48    pipeline_inst: Optional[int]
+ 49    feed_id: FeedId
+ 50    start_date: datetime.datetime
+ 51    end_date: datetime.datetime
+ 52    output_path: CubeFilePath
+ 53
+ 54    status: Status
+ 55
+ 56    summary: str
+ 57    raw: str
+ 58    owner_username: Username
+ 59    cpu_limit: int
+ 60    memory_limit: int
+ 61    number_of_workers: int
+ 62    gpu_limit: int
+ 63    error_code: CUBEErrorCode
+ 64
+ 65    previous: Optional[PluginInstanceUrl]
+ 66    feed: FeedUrl
+ 67    plugin: PluginUrl
+ 68    descendants: DescendantsUrl
+ 69    files: FilesUrl
+ 70    parameters: PluginInstanceParamtersUrl
+ 71    compute_resource: ComputeResourceUrl
+ 72    splits: SplitsUrl
+ 73
+ 74    previous_id: Optional[int] = None
+ 75    """
+ 76    FS plugins will not produce a `previous_id` value
+ 77    (even though they will return `"previous": null`)
+ 78    """
+ 79
+ 80    size: Optional[int] = None
+ 81    """
+ 82    IDK what it is the size of.
+ 83
+ 84    This field shows up when the plugin instance is maybe done,
+ 85    but not when the plugin instance is created.
+ 86    """
+ 87    template: Optional[dict] = None
+ 88    """
+ 89    Present only when getting a plugin instance.
+ 90    """
+ 91
+ 92
+ 93@deserialize
+ 94@dataclass(frozen=True)
+ 95class FeedData(LinkedModel):
+ 96    url: FeedUrl
+ 97    id: FeedId
+ 98    creation_date: datetime.datetime
+ 99    modification_date: datetime.datetime
+100    name: str
+101    creator_username: Username
+102    created_jobs: int
+103    waiting_jobs: int
+104    scheduled_jobs: int
+105    started_jobs: int
+106    registering_jobs: int
+107    finished_jobs: int
+108    errored_jobs: int
+109    cancelled_jobs: int
+110    owner: list[UserUrl]
+111    note: NoteUrl
+112    tags: TagsUrl
+113    taggings: TaggingsUrl
+114    comments: CommentsUrl
+115    files: FilesUrl
+116    plugin_instances: PluginInstancesUrl
+117
+118
+119@deserialize
+120@dataclass(frozen=True)
+121class FeedNoteData(LinkedModel):
+122    url: FeedUrl
+123    id: NoteId
+124    title: str
+125    content: str
+126    feed: FeedUrl
+
+ + +
+
+ +
+
@deserialize
+
@dataclass(frozen=True)
+ + class + UserData: + + + +
+ + 
20@deserialize
+21@dataclass(frozen=True)
+22class UserData:
+23    """A *CUBE* user."""
+24
+25    url: UserUrl
+26    id: UserId
+27    username: Username
+28    email: str
+
+ + +

A CUBE user.

+
+ + +
+
+ + UserData( url: aiochris.types.UserUrl, id: aiochris.types.UserId, username: aiochris.types.Username, email: str) + + +
+ + + + +
+
+
+ +
+
@deserialize
+
@dataclass(frozen=True)
+ + class + PluginInstanceData(aiochris.link.linked.LinkedModel): + + + +
+ + 
32@deserialize
+33@dataclass(frozen=True)
+34class PluginInstanceData(LinkedModel):
+35    """
+36    A *plugin instance* in _ChRIS_ is a computing job, i.e. an attempt to run
+37    a computation (a non-interactive command-line app) to produce data.
+38    """
+39
+40    url: PluginInstanceUrl
+41    id: PluginInstanceId
+42    title: str
+43    compute_resource_name: ComputeResourceName
+44    plugin_id: PluginId
+45    plugin_name: PluginName
+46    plugin_version: PluginVersion
+47    plugin_type: PluginType
+48
+49    pipeline_inst: Optional[int]
+50    feed_id: FeedId
+51    start_date: datetime.datetime
+52    end_date: datetime.datetime
+53    output_path: CubeFilePath
+54
+55    status: Status
+56
+57    summary: str
+58    raw: str
+59    owner_username: Username
+60    cpu_limit: int
+61    memory_limit: int
+62    number_of_workers: int
+63    gpu_limit: int
+64    error_code: CUBEErrorCode
+65
+66    previous: Optional[PluginInstanceUrl]
+67    feed: FeedUrl
+68    plugin: PluginUrl
+69    descendants: DescendantsUrl
+70    files: FilesUrl
+71    parameters: PluginInstanceParamtersUrl
+72    compute_resource: ComputeResourceUrl
+73    splits: SplitsUrl
+74
+75    previous_id: Optional[int] = None
+76    """
+77    FS plugins will not produce a `previous_id` value
+78    (even though they will return `"previous": null`)
+79    """
+80
+81    size: Optional[int] = None
+82    """
+83    IDK what it is the size of.
+84
+85    This field shows up when the plugin instance is maybe done,
+86    but not when the plugin instance is created.
+87    """
+88    template: Optional[dict] = None
+89    """
+90    Present only when getting a plugin instance.
+91    """
+
+ + +

A plugin instance in _ChRIS_ is a computing job, i.e. an attempt to run +a computation (a non-interactive command-line app) to produce data.

+
+ + +
+
+ + PluginInstanceData( s: aiohttp.client.ClientSession, max_search_requests: int, url: aiochris.types.PluginInstanceUrl, id: aiochris.types.PluginInstanceId, title: str, compute_resource_name: aiochris.types.ComputeResourceName, plugin_id: aiochris.types.PluginId, plugin_name: aiochris.types.PluginName, plugin_version: aiochris.types.PluginVersion, plugin_type: aiochris.enums.PluginType, pipeline_inst: Optional[int], feed_id: aiochris.types.FeedId, start_date: datetime.datetime, end_date: datetime.datetime, output_path: aiochris.types.CubeFilePath, status: aiochris.enums.Status, summary: str, raw: str, owner_username: aiochris.types.Username, cpu_limit: int, memory_limit: int, number_of_workers: int, gpu_limit: int, error_code: aiochris.types.CUBEErrorCode, previous: Optional[aiochris.types.PluginInstanceUrl], feed: aiochris.types.FeedUrl, plugin: aiochris.types.PluginUrl, descendants: aiochris.types.DescendantsUrl, files: aiochris.types.FilesUrl, parameters: aiochris.types.PluginInstanceParametersUrl, compute_resource: aiochris.types.ComputeResourceUrl, splits: aiochris.types.SplitsUrl, previous_id: Optional[int] = None, size: Optional[int] = None, template: Optional[dict] = None) + + +
+ + + + +
+
+
+ previous_id: Optional[int] = None + + +
+ + +

FS plugins will not produce a previous_id value +(even though they will return "previous": null)

+
+ + +
+
+
+ size: Optional[int] = None + + +
+ + +

IDK what it is the size of.

+ +

This field shows up when the plugin instance is maybe done, +but not when the plugin instance is created.

+
+ + +
+
+
+ template: Optional[dict] = None + + +
+ + +

Present only when getting a plugin instance.

+
+ + +
+
+
Inherited Members
+
+
aiochris.link.linked.Linked
+
max_search_requests
+ +
+
+
+
+
+ +
+
@deserialize
+
@dataclass(frozen=True)
+ + class + FeedData(aiochris.link.linked.LinkedModel): + + + +
+ + 
 94@deserialize
+ 95@dataclass(frozen=True)
+ 96class FeedData(LinkedModel):
+ 97    url: FeedUrl
+ 98    id: FeedId
+ 99    creation_date: datetime.datetime
+100    modification_date: datetime.datetime
+101    name: str
+102    creator_username: Username
+103    created_jobs: int
+104    waiting_jobs: int
+105    scheduled_jobs: int
+106    started_jobs: int
+107    registering_jobs: int
+108    finished_jobs: int
+109    errored_jobs: int
+110    cancelled_jobs: int
+111    owner: list[UserUrl]
+112    note: NoteUrl
+113    tags: TagsUrl
+114    taggings: TaggingsUrl
+115    comments: CommentsUrl
+116    files: FilesUrl
+117    plugin_instances: PluginInstancesUrl
+
+ + + + +
+
+ + FeedData( s: aiohttp.client.ClientSession, max_search_requests: int, url: aiochris.types.FeedUrl, id: aiochris.types.FeedId, creation_date: datetime.datetime, modification_date: datetime.datetime, name: str, creator_username: aiochris.types.Username, created_jobs: int, waiting_jobs: int, scheduled_jobs: int, started_jobs: int, registering_jobs: int, finished_jobs: int, errored_jobs: int, cancelled_jobs: int, owner: list[aiochris.types.UserUrl], note: aiochris.types.NoteUrl, tags: aiochris.types.TagsUrl, taggings: aiochris.types.TaggingsUrl, comments: aiochris.types.CommentsUrl, files: aiochris.types.FilesUrl, plugin_instances: aiochris.types.PluginInstancesUrl) + + +
+ + + + +
+
+
Inherited Members
+
+
aiochris.link.linked.Linked
+
max_search_requests
+ +
+
+
+
+
+ +
+
@deserialize
+
@dataclass(frozen=True)
+ + class + FeedNoteData(aiochris.link.linked.LinkedModel): + + + +
+ + 
120@deserialize
+121@dataclass(frozen=True)
+122class FeedNoteData(LinkedModel):
+123    url: FeedUrl
+124    id: NoteId
+125    title: str
+126    content: str
+127    feed: FeedUrl
+
+ + + + +
+
+ + FeedNoteData( s: aiohttp.client.ClientSession, max_search_requests: int, url: aiochris.types.FeedUrl, id: aiochris.types.NoteId, title: str, content: str, feed: aiochris.types.FeedUrl) + + +
+ + + + +
+
+
Inherited Members
+
+
aiochris.link.linked.Linked
+
max_search_requests
+ +
+
+
+
+
+ + \ No newline at end of file diff --git a/v0.5.0a3/aiochris/models/logged_in.html b/v0.5.0a3/aiochris/models/logged_in.html new file mode 100644 index 0000000..4f9494e --- /dev/null +++ b/v0.5.0a3/aiochris/models/logged_in.html @@ -0,0 +1,1525 @@ + + + + + + + aiochris.models.logged_in API documentation + + + + + + + + + +
+
+

+aiochris.models.logged_in

+ +

Subclasses of classes from aiochris.models.data which are returned +from an aiochris.client.authed.AuthenticatedClient. +These classes may have read-write functionality on the ChRIS API.

+
+ + + + + + 
  1"""
+  2Subclasses of classes from `aiochris.models.data` which are returned
+  3from an `aiochris.client.authed.AuthenticatedClient`.
+  4These classes may have read-write functionality on the *ChRIS* API.
+  5"""
+  6import asyncio
+  7import time
+  8from dataclasses import dataclass
+  9from typing import Optional, Sequence
+ 10
+ 11from serde import deserialize
+ 12
+ 13from aiochris.link import http
+ 14from aiochris.link.linked import LinkedModel
+ 15from aiochris.models.data import PluginInstanceData, FeedData, UserData, FeedNoteData
+ 16from aiochris.enums import PluginType, Status
+ 17from aiochris.models.public import PublicPlugin
+ 18from aiochris.types import *
+ 19
+ 20
+ 21@deserialize
+ 22@dataclass(frozen=True)
+ 23class User(UserData, LinkedModel):
+ 24    pass  # TODO change_email, change_password
+ 25
+ 26
+ 27@deserialize
+ 28@dataclass(frozen=True)
+ 29class File(LinkedModel):
+ 30    """
+ 31    A file in CUBE.
+ 32    """
+ 33
+ 34    url: str
+ 35    fname: FileFname
+ 36    fsize: int
+ 37    file_resource: FileResourceUrl
+ 38
+ 39    @property
+ 40    def parent(self) -> str:
+ 41        """
+ 42        Get the parent (directory) of a file.
+ 43
+ 44        Examples
+ 45        --------
+ 46
+ 47        ```python
+ 48        assert file.fname == 'chris/feed_4/pl-dircopy_7/data/hello-world.txt'
+ 49        assert file.parent == 'chris/feed_4/pl-dircopy_7/data'
+ 50        ```
+ 51        """
+ 52        split = self.fname.split("/")
+ 53        if len(split) <= 1:
+ 54            return self.fname
+ 55        return "/".join(split[:-1])
+ 56
+ 57    # TODO download methods
+ 58
+ 59
+ 60@deserialize
+ 61@dataclass(frozen=True)
+ 62class PACSFile(File):
+ 63    """
+ 64    A file from a PACS server which was pushed into ChRIS.
+ 65    A PACSFile is usually a DICOM file.
+ 66
+ 67    See https://github.com/FNNDSC/ChRIS_ultron_backEnd/blob/a1bf499144df79622eb3f8a459cdb80d8e34cb04/chris_backend/pacsfiles/models.py#L16-L33
+ 68    """
+ 69
+ 70    PatientID: str
+ 71    PatientName: str
+ 72    PatientBirthDate: str
+ 73    PatientAge: int
+ 74    PatientSex: str
+ 75    StudyDate: str  # TODO deserialize
+ 76    AccessionNumber: str
+ 77    Modality: str
+ 78    ProtocolName: str
+ 79    StudyInstanceUID: str
+ 80    StudyDescription: str
+ 81    SeriesInstanceUID: str
+ 82    SeriesDescription: str
+ 83    pacs_identifier: str
+ 84
+ 85
+ 86@deserialize
+ 87@dataclass(frozen=True)
+ 88class PluginInstance(PluginInstanceData):
+ 89    @http.get("feed")
+ 90    async def get_feed(self) -> "Feed":
+ 91        """Get the feed this plugin instance belongs to."""
+ 92        ...
+ 93
+ 94    @http.put("url")
+ 95    async def get(self) -> "PluginInstance":
+ 96        """
+ 97        Get this plugin's state (again).
+ 98        """
+ 99        ...
+100
+101    @http.put("url")
+102    async def set(
+103        self, title: Optional[str] = None, status: Optional[str] = None
+104    ) -> "PluginInstance":
+105        """
+106        Set the title or status of this plugin instance.
+107        """
+108        ...
+109
+110    @http.delete("url")
+111    async def delete(self) -> None:
+112        """Delete this plugin instance."""
+113        ...
+114
+115    async def wait(
+116        self,
+117        status: Status
+118        | Sequence[Status] = (
+119            Status.finishedSuccessfully,
+120            Status.finishedWithError,
+121            Status.cancelled,
+122        ),
+123        timeout: float = 300,
+124        interval: float = 5,
+125    ) -> tuple[float, "PluginInstance"]:
+126        """
+127        Wait until this plugin instance finishes (or some other desired status).
+128
+129        Parameters
+130        ----------
+131        status
+132            Statuses to wait for
+133        timeout
+134            Number of seconds to wait for before giving up
+135        interval
+136            Number of seconds to wait between checking on status
+137
+138        Returns
+139        -------
+140        Returns the number of seconds elapsed and the last state of the plugin instance.
+141        This function will return for one of two reasons: either the plugin instance finished,
+142        or this function timed out. Make sure you check the plugin instance's final status!
+143        """
+144        if status is Status:
+145            status = (status,)
+146        if self.status in status:
+147            return 0.0, self
+148        timeout_ns = timeout * 1e9
+149        start = time.monotonic_ns()
+150        while (cur := await self.get()).status not in status:
+151            elapsed = time.monotonic_ns() - start
+152            if elapsed > timeout_ns:
+153                return elapsed / 1e9, cur
+154            await asyncio.sleep(interval)
+155        return (time.monotonic_ns() - start) / 1e9, cur
+156
+157
+158@deserialize
+159@dataclass(frozen=True)
+160class FeedNote(FeedNoteData):
+161    @http.get("feed")
+162    async def get_feed(self) -> "Feed":
+163        """Get the feed this note belongs to."""
+164        ...
+165
+166    @http.put("url")
+167    async def set(
+168        self, title: Optional[str] = None, content: Optional[str] = None
+169    ) -> "FeedNote":
+170        """Change this note."""
+171        ...
+172
+173
+174@deserialize
+175@dataclass(frozen=True)
+176class Feed(FeedData):
+177    """
+178    A feed of a logged in user.
+179    """
+180
+181    @http.put("url")
+182    async def set(
+183        self, name: Optional[str] = None, owner: Optional[str | Username] = None
+184    ) -> "Feed":
+185        """
+186        Change the name or the owner of this feed.
+187
+188        Parameters
+189        ----------
+190        name
+191            new name for this feed
+192        owner
+193            new owner for this feed
+194        """
+195        ...
+196
+197    @http.get("note")
+198    async def get_note(self) -> FeedNote:
+199        ...
+200
+201
+202@deserialize
+203@dataclass(frozen=True)
+204class Plugin(PublicPlugin):
+205    """
+206    A ChRIS plugin. Create a plugin instance of this plugin to run it.
+207    """
+208
+209    instances: ApiUrl
+210
+211    @http.post("instances")
+212    async def _create_instance_raw(self, **kwargs) -> PluginInstance:
+213        ...
+214
+215    async def create_instance(
+216        self, previous: Optional[PluginInstance] = None, **kwargs
+217    ) -> PluginInstance:
+218        """
+219        Create a plugin instance, i.e. "run" this plugin.
+220
+221        Parameters common to all plugins are described below.
+222        Not all valid parameters are listed, since each plugin's parameters are different.
+223        Some plugins have required parameters too.
+224        To list all possible parameters, make a GET request to the specific plugin's instances link.
+225
+226        Parameters
+227        ----------
+228        previous: chris.models.data.PluginInstanceData
+229            Previous plugin instance
+230        previous_id: int
+231            Previous plugin instance ID number (conflicts with `previous`)
+232        compute_resource_name: Optional[str]
+233            Name of compute resource to use
+234        memory_limit: Optional[str]
+235            Memory limit. Format is *x*Mi or *x*Gi where x is an integer.
+236        cpu_limit: Optional[str]
+237            CPU limit. Format is *x*m for *x* is an integer in millicores.
+238        gpu_limit: Optional[int]
+239            GPU limit.
+240        """
+241        if previous is not None:
+242            if "previous_id" in kwargs:
+243                raise ValueError("Cannot give both previous and previous_id.")
+244            if not isinstance(previous, PluginInstance):
+245                raise TypeError(f"{previous} is not a PluginInstance")
+246            kwargs["previous_id"] = previous.id
+247        if self.plugin_type is PluginType.fs:
+248            if "previous_id" in kwargs:
+249                raise ValueError(
+250                    "Cannot create plugin instance of a fs-type plugin with a previous plugin instance."
+251                )
+252        elif "previous_id" not in kwargs:
+253            raise ValueError(
+254                f'Plugin type is "{self.plugin_type.value}" so previous is a required parameter.'
+255            )
+256        return await self._create_instance_raw(**kwargs)
+
+ + +
+
+ +
+
@deserialize
+
@dataclass(frozen=True)
+ + class + User(aiochris.models.data.UserData, aiochris.link.linked.LinkedModel): + + + +
+ + 
22@deserialize
+23@dataclass(frozen=True)
+24class User(UserData, LinkedModel):
+25    pass  # TODO change_email, change_password
+
+ + + + +
+
+ + User( s: aiohttp.client.ClientSession, max_search_requests: int, url: aiochris.types.UserUrl, id: aiochris.types.UserId, username: aiochris.types.Username, email: str) + + +
+ + + + +
+
+
Inherited Members
+
+
aiochris.link.linked.Linked
+
max_search_requests
+ +
+
+
+
+
+ +
+
@deserialize
+
@dataclass(frozen=True)
+ + class + File(aiochris.link.linked.LinkedModel): + + + +
+ + 
28@deserialize
+29@dataclass(frozen=True)
+30class File(LinkedModel):
+31    """
+32    A file in CUBE.
+33    """
+34
+35    url: str
+36    fname: FileFname
+37    fsize: int
+38    file_resource: FileResourceUrl
+39
+40    @property
+41    def parent(self) -> str:
+42        """
+43        Get the parent (directory) of a file.
+44
+45        Examples
+46        --------
+47
+48        ```python
+49        assert file.fname == 'chris/feed_4/pl-dircopy_7/data/hello-world.txt'
+50        assert file.parent == 'chris/feed_4/pl-dircopy_7/data'
+51        ```
+52        """
+53        split = self.fname.split("/")
+54        if len(split) <= 1:
+55            return self.fname
+56        return "/".join(split[:-1])
+57
+58    # TODO download methods
+
+ + +

A file in CUBE.

+
+ + +
+
+ + File( s: aiohttp.client.ClientSession, max_search_requests: int, url: str, fname: aiochris.types.FileFname, fsize: int, file_resource: aiochris.types.FileResourceUrl) + + +
+ + + + +
+
+
+ parent: str + + +
+ + +

Get the parent (directory) of a file.

+ +
Examples
+ +
+
assert file.fname == 'chris/feed_4/pl-dircopy_7/data/hello-world.txt'
+assert file.parent == 'chris/feed_4/pl-dircopy_7/data'
+
+
+
+ + +
+
+
Inherited Members
+
+
aiochris.link.linked.Linked
+
max_search_requests
+ +
+
+
+
+
+ +
+
@deserialize
+
@dataclass(frozen=True)
+ + class + PACSFile(File): + + + +
+ + 
61@deserialize
+62@dataclass(frozen=True)
+63class PACSFile(File):
+64    """
+65    A file from a PACS server which was pushed into ChRIS.
+66    A PACSFile is usually a DICOM file.
+67
+68    See https://github.com/FNNDSC/ChRIS_ultron_backEnd/blob/a1bf499144df79622eb3f8a459cdb80d8e34cb04/chris_backend/pacsfiles/models.py#L16-L33
+69    """
+70
+71    PatientID: str
+72    PatientName: str
+73    PatientBirthDate: str
+74    PatientAge: int
+75    PatientSex: str
+76    StudyDate: str  # TODO deserialize
+77    AccessionNumber: str
+78    Modality: str
+79    ProtocolName: str
+80    StudyInstanceUID: str
+81    StudyDescription: str
+82    SeriesInstanceUID: str
+83    SeriesDescription: str
+84    pacs_identifier: str
+
+ + +

A file from a PACS server which was pushed into ChRIS. +A PACSFile is usually a DICOM file.

+ +

See https://github.com/FNNDSC/ChRIS_ultron_backEnd/blob/a1bf499144df79622eb3f8a459cdb80d8e34cb04/chris_backend/pacsfiles/models.py#L16-L33

+
+ + +
+
+ + PACSFile( s: aiohttp.client.ClientSession, max_search_requests: int, url: str, fname: aiochris.types.FileFname, fsize: int, file_resource: aiochris.types.FileResourceUrl, PatientID: str, PatientName: str, PatientBirthDate: str, PatientAge: int, PatientSex: str, StudyDate: str, AccessionNumber: str, Modality: str, ProtocolName: str, StudyInstanceUID: str, StudyDescription: str, SeriesInstanceUID: str, SeriesDescription: str, pacs_identifier: str) + + +
+ + + + +
+
+
Inherited Members
+
+
File
+
parent
+ +
+
aiochris.link.linked.Linked
+
max_search_requests
+ +
+
+
+
+
+ +
+
@deserialize
+
@dataclass(frozen=True)
+ + class + PluginInstance(aiochris.models.data.PluginInstanceData): + + + +
+ + 
 87@deserialize
+ 88@dataclass(frozen=True)
+ 89class PluginInstance(PluginInstanceData):
+ 90    @http.get("feed")
+ 91    async def get_feed(self) -> "Feed":
+ 92        """Get the feed this plugin instance belongs to."""
+ 93        ...
+ 94
+ 95    @http.put("url")
+ 96    async def get(self) -> "PluginInstance":
+ 97        """
+ 98        Get this plugin's state (again).
+ 99        """
+100        ...
+101
+102    @http.put("url")
+103    async def set(
+104        self, title: Optional[str] = None, status: Optional[str] = None
+105    ) -> "PluginInstance":
+106        """
+107        Set the title or status of this plugin instance.
+108        """
+109        ...
+110
+111    @http.delete("url")
+112    async def delete(self) -> None:
+113        """Delete this plugin instance."""
+114        ...
+115
+116    async def wait(
+117        self,
+118        status: Status
+119        | Sequence[Status] = (
+120            Status.finishedSuccessfully,
+121            Status.finishedWithError,
+122            Status.cancelled,
+123        ),
+124        timeout: float = 300,
+125        interval: float = 5,
+126    ) -> tuple[float, "PluginInstance"]:
+127        """
+128        Wait until this plugin instance finishes (or some other desired status).
+129
+130        Parameters
+131        ----------
+132        status
+133            Statuses to wait for
+134        timeout
+135            Number of seconds to wait for before giving up
+136        interval
+137            Number of seconds to wait between checking on status
+138
+139        Returns
+140        -------
+141        Returns the number of seconds elapsed and the last state of the plugin instance.
+142        This function will return for one of two reasons: either the plugin instance finished,
+143        or this function timed out. Make sure you check the plugin instance's final status!
+144        """
+145        if status is Status:
+146            status = (status,)
+147        if self.status in status:
+148            return 0.0, self
+149        timeout_ns = timeout * 1e9
+150        start = time.monotonic_ns()
+151        while (cur := await self.get()).status not in status:
+152            elapsed = time.monotonic_ns() - start
+153            if elapsed > timeout_ns:
+154                return elapsed / 1e9, cur
+155            await asyncio.sleep(interval)
+156        return (time.monotonic_ns() - start) / 1e9, cur
+
+ + + + +
+
+ + PluginInstance( s: aiohttp.client.ClientSession, max_search_requests: int, url: aiochris.types.PluginInstanceUrl, id: aiochris.types.PluginInstanceId, title: str, compute_resource_name: aiochris.types.ComputeResourceName, plugin_id: aiochris.types.PluginId, plugin_name: aiochris.types.PluginName, plugin_version: aiochris.types.PluginVersion, plugin_type: aiochris.enums.PluginType, pipeline_inst: Optional[int], feed_id: aiochris.types.FeedId, start_date: datetime.datetime, end_date: datetime.datetime, output_path: aiochris.types.CubeFilePath, status: aiochris.enums.Status, summary: str, raw: str, owner_username: aiochris.types.Username, cpu_limit: int, memory_limit: int, number_of_workers: int, gpu_limit: int, error_code: aiochris.types.CUBEErrorCode, previous: Optional[aiochris.types.PluginInstanceUrl], feed: aiochris.types.FeedUrl, plugin: aiochris.types.PluginUrl, descendants: aiochris.types.DescendantsUrl, files: aiochris.types.FilesUrl, parameters: aiochris.types.PluginInstanceParametersUrl, compute_resource: aiochris.types.ComputeResourceUrl, splits: aiochris.types.SplitsUrl, previous_id: Optional[int] = None, size: Optional[int] = None, template: Optional[dict] = None) + + +
+ + + + +
+
+ +
+
@http.get('feed')
+ + async def + get_feed(self) -> aiochris.models.logged_in.Feed: + + + +
+ + 
90    @http.get("feed")
+91    async def get_feed(self) -> "Feed":
+92        """Get the feed this plugin instance belongs to."""
+93        ...
+
+ + +

Get the feed this plugin instance belongs to.

+
+ + +
+
+ +
+
@http.put('url')
+ + async def + get(self) -> aiochris.models.logged_in.PluginInstance: + + + +
+ + 
 95    @http.put("url")
+ 96    async def get(self) -> "PluginInstance":
+ 97        """
+ 98        Get this plugin's state (again).
+ 99        """
+100        ...
+
+ + +

Get this plugin's state (again).

+
+ + +
+
+ +
+
@http.put('url')
+ + async def + set( self, title: Optional[str] = None, status: Optional[str] = None) -> aiochris.models.logged_in.PluginInstance: + + + +
+ + 
102    @http.put("url")
+103    async def set(
+104        self, title: Optional[str] = None, status: Optional[str] = None
+105    ) -> "PluginInstance":
+106        """
+107        Set the title or status of this plugin instance.
+108        """
+109        ...
+
+ + +

Set the title or status of this plugin instance.

+
+ + +
+
+ +
+
@http.delete('url')
+ + async def + delete(self) -> None: + + + +
+ + 
111    @http.delete("url")
+112    async def delete(self) -> None:
+113        """Delete this plugin instance."""
+114        ...
+
+ + +

Delete this plugin instance.

+
+ + +
+
+ +
+ + async def + wait( self, status: Union[aiochris.enums.Status, Sequence[aiochris.enums.Status]] = (<Status.finishedSuccessfully: 'finishedSuccessfully'>, <Status.finishedWithError: 'finishedWithError'>, <Status.cancelled: 'cancelled'>), timeout: float = 300, interval: float = 5) -> tuple[float, aiochris.models.logged_in.PluginInstance]: + + + +
+ + 
116    async def wait(
+117        self,
+118        status: Status
+119        | Sequence[Status] = (
+120            Status.finishedSuccessfully,
+121            Status.finishedWithError,
+122            Status.cancelled,
+123        ),
+124        timeout: float = 300,
+125        interval: float = 5,
+126    ) -> tuple[float, "PluginInstance"]:
+127        """
+128        Wait until this plugin instance finishes (or some other desired status).
+129
+130        Parameters
+131        ----------
+132        status
+133            Statuses to wait for
+134        timeout
+135            Number of seconds to wait for before giving up
+136        interval
+137            Number of seconds to wait between checking on status
+138
+139        Returns
+140        -------
+141        Returns the number of seconds elapsed and the last state of the plugin instance.
+142        This function will return for one of two reasons: either the plugin instance finished,
+143        or this function timed out. Make sure you check the plugin instance's final status!
+144        """
+145        if status is Status:
+146            status = (status,)
+147        if self.status in status:
+148            return 0.0, self
+149        timeout_ns = timeout * 1e9
+150        start = time.monotonic_ns()
+151        while (cur := await self.get()).status not in status:
+152            elapsed = time.monotonic_ns() - start
+153            if elapsed > timeout_ns:
+154                return elapsed / 1e9, cur
+155            await asyncio.sleep(interval)
+156        return (time.monotonic_ns() - start) / 1e9, cur
+
+ + +

Wait until this plugin instance finishes (or some other desired status).

+ +
Parameters
+ +
    +
  • status: Statuses to wait for
    • +
  • timeout: Number of seconds to wait for before giving up
    • +
  • interval: Number of seconds to wait between checking on status
    • +
+ +
Returns
+ +
    +
  • Returns the number of seconds elapsed and the last state of the plugin instance.
    • +

  • This function will return for one of two reasons (either the plugin instance finished,):

    • +

  • or this function timed out. Make sure you check the plugin instance's final status!

    • +
+
+ + +
+
+
Inherited Members
+
+ +
aiochris.link.linked.Linked
+
max_search_requests
+ +
+
+
+
+
+ +
+
@deserialize
+
@dataclass(frozen=True)
+ + class + FeedNote(aiochris.models.data.FeedNoteData): + + + +
+ + 
159@deserialize
+160@dataclass(frozen=True)
+161class FeedNote(FeedNoteData):
+162    @http.get("feed")
+163    async def get_feed(self) -> "Feed":
+164        """Get the feed this note belongs to."""
+165        ...
+166
+167    @http.put("url")
+168    async def set(
+169        self, title: Optional[str] = None, content: Optional[str] = None
+170    ) -> "FeedNote":
+171        """Change this note."""
+172        ...
+
+ + + + +
+
+ + FeedNote( s: aiohttp.client.ClientSession, max_search_requests: int, url: aiochris.types.FeedUrl, id: aiochris.types.NoteId, title: str, content: str, feed: aiochris.types.FeedUrl) + + +
+ + + + +
+
+ +
+
@http.get('feed')
+ + async def + get_feed(self) -> aiochris.models.logged_in.Feed: + + + +
+ + 
162    @http.get("feed")
+163    async def get_feed(self) -> "Feed":
+164        """Get the feed this note belongs to."""
+165        ...
+
+ + +

Get the feed this note belongs to.

+
+ + +
+
+ +
+
@http.put('url')
+ + async def + set( self, title: Optional[str] = None, content: Optional[str] = None) -> aiochris.models.logged_in.FeedNote: + + + +
+ + 
167    @http.put("url")
+168    async def set(
+169        self, title: Optional[str] = None, content: Optional[str] = None
+170    ) -> "FeedNote":
+171        """Change this note."""
+172        ...
+
+ + +

Change this note.

+
+ + +
+
+
Inherited Members
+
+
aiochris.link.linked.Linked
+
max_search_requests
+ +
+
+
+
+
+ +
+
@deserialize
+
@dataclass(frozen=True)
+ + class + Feed(aiochris.models.data.FeedData): + + + +
+ + 
175@deserialize
+176@dataclass(frozen=True)
+177class Feed(FeedData):
+178    """
+179    A feed of a logged in user.
+180    """
+181
+182    @http.put("url")
+183    async def set(
+184        self, name: Optional[str] = None, owner: Optional[str | Username] = None
+185    ) -> "Feed":
+186        """
+187        Change the name or the owner of this feed.
+188
+189        Parameters
+190        ----------
+191        name
+192            new name for this feed
+193        owner
+194            new owner for this feed
+195        """
+196        ...
+197
+198    @http.get("note")
+199    async def get_note(self) -> FeedNote:
+200        ...
+
+ + +

A feed of a logged in user.

+
+ + +
+
+ + Feed( s: aiohttp.client.ClientSession, max_search_requests: int, url: aiochris.types.FeedUrl, id: aiochris.types.FeedId, creation_date: datetime.datetime, modification_date: datetime.datetime, name: str, creator_username: aiochris.types.Username, created_jobs: int, waiting_jobs: int, scheduled_jobs: int, started_jobs: int, registering_jobs: int, finished_jobs: int, errored_jobs: int, cancelled_jobs: int, owner: list[aiochris.types.UserUrl], note: aiochris.types.NoteUrl, tags: aiochris.types.TagsUrl, taggings: aiochris.types.TaggingsUrl, comments: aiochris.types.CommentsUrl, files: aiochris.types.FilesUrl, plugin_instances: aiochris.types.PluginInstancesUrl) + + +
+ + + + +
+
+ +
+
@http.put('url')
+ + async def + set( self, name: Optional[str] = None, owner: Union[str, aiochris.types.Username, NoneType] = None) -> aiochris.models.logged_in.Feed: + + + +
+ + 
182    @http.put("url")
+183    async def set(
+184        self, name: Optional[str] = None, owner: Optional[str | Username] = None
+185    ) -> "Feed":
+186        """
+187        Change the name or the owner of this feed.
+188
+189        Parameters
+190        ----------
+191        name
+192            new name for this feed
+193        owner
+194            new owner for this feed
+195        """
+196        ...
+
+ + +

Change the name or the owner of this feed.

+ +
Parameters
+ +
    +
  • name: new name for this feed
    • +
  • owner: new owner for this feed
    • +
+
+ + +
+
+ +
+
@http.get('note')
+ + async def + get_note(self) -> aiochris.models.logged_in.FeedNote: + + + +
+ + 
198    @http.get("note")
+199    async def get_note(self) -> FeedNote:
+200        ...
+
+ + + + +
+
+
Inherited Members
+
+
aiochris.link.linked.Linked
+
max_search_requests
+ +
+
+
+
+
+ +
+
@deserialize
+
@dataclass(frozen=True)
+ + class + Plugin(aiochris.models.public.PublicPlugin): + + + +
+ + 
203@deserialize
+204@dataclass(frozen=True)
+205class Plugin(PublicPlugin):
+206    """
+207    A ChRIS plugin. Create a plugin instance of this plugin to run it.
+208    """
+209
+210    instances: ApiUrl
+211
+212    @http.post("instances")
+213    async def _create_instance_raw(self, **kwargs) -> PluginInstance:
+214        ...
+215
+216    async def create_instance(
+217        self, previous: Optional[PluginInstance] = None, **kwargs
+218    ) -> PluginInstance:
+219        """
+220        Create a plugin instance, i.e. "run" this plugin.
+221
+222        Parameters common to all plugins are described below.
+223        Not all valid parameters are listed, since each plugin's parameters are different.
+224        Some plugins have required parameters too.
+225        To list all possible parameters, make a GET request to the specific plugin's instances link.
+226
+227        Parameters
+228        ----------
+229        previous: chris.models.data.PluginInstanceData
+230            Previous plugin instance
+231        previous_id: int
+232            Previous plugin instance ID number (conflicts with `previous`)
+233        compute_resource_name: Optional[str]
+234            Name of compute resource to use
+235        memory_limit: Optional[str]
+236            Memory limit. Format is *x*Mi or *x*Gi where x is an integer.
+237        cpu_limit: Optional[str]
+238            CPU limit. Format is *x*m for *x* is an integer in millicores.
+239        gpu_limit: Optional[int]
+240            GPU limit.
+241        """
+242        if previous is not None:
+243            if "previous_id" in kwargs:
+244                raise ValueError("Cannot give both previous and previous_id.")
+245            if not isinstance(previous, PluginInstance):
+246                raise TypeError(f"{previous} is not a PluginInstance")
+247            kwargs["previous_id"] = previous.id
+248        if self.plugin_type is PluginType.fs:
+249            if "previous_id" in kwargs:
+250                raise ValueError(
+251                    "Cannot create plugin instance of a fs-type plugin with a previous plugin instance."
+252                )
+253        elif "previous_id" not in kwargs:
+254            raise ValueError(
+255                f'Plugin type is "{self.plugin_type.value}" so previous is a required parameter.'
+256            )
+257        return await self._create_instance_raw(**kwargs)
+
+ + +

A ChRIS plugin. Create a plugin instance of this plugin to run it.

+
+ + +
+
+ + Plugin( s: aiohttp.client.ClientSession, max_search_requests: int, url: aiochris.types.PluginUrl, id: aiochris.types.PluginId, name: aiochris.types.PluginName, version: aiochris.types.PluginVersion, dock_image: aiochris.types.ImageTag, public_repo: str, compute_resources: aiochris.types.ComputeResourceUrl, parameters: aiochris.types.PluginParametersUrl, plugin_type: aiochris.enums.PluginType, instances: aiochris.types.ApiUrl) + + +
+ + + + +
+
+ +
+ + async def + create_instance( self, previous: Optional[aiochris.models.logged_in.PluginInstance] = None, **kwargs) -> aiochris.models.logged_in.PluginInstance: + + + +
+ + 
216    async def create_instance(
+217        self, previous: Optional[PluginInstance] = None, **kwargs
+218    ) -> PluginInstance:
+219        """
+220        Create a plugin instance, i.e. "run" this plugin.
+221
+222        Parameters common to all plugins are described below.
+223        Not all valid parameters are listed, since each plugin's parameters are different.
+224        Some plugins have required parameters too.
+225        To list all possible parameters, make a GET request to the specific plugin's instances link.
+226
+227        Parameters
+228        ----------
+229        previous: chris.models.data.PluginInstanceData
+230            Previous plugin instance
+231        previous_id: int
+232            Previous plugin instance ID number (conflicts with `previous`)
+233        compute_resource_name: Optional[str]
+234            Name of compute resource to use
+235        memory_limit: Optional[str]
+236            Memory limit. Format is *x*Mi or *x*Gi where x is an integer.
+237        cpu_limit: Optional[str]
+238            CPU limit. Format is *x*m for *x* is an integer in millicores.
+239        gpu_limit: Optional[int]
+240            GPU limit.
+241        """
+242        if previous is not None:
+243            if "previous_id" in kwargs:
+244                raise ValueError("Cannot give both previous and previous_id.")
+245            if not isinstance(previous, PluginInstance):
+246                raise TypeError(f"{previous} is not a PluginInstance")
+247            kwargs["previous_id"] = previous.id
+248        if self.plugin_type is PluginType.fs:
+249            if "previous_id" in kwargs:
+250                raise ValueError(
+251                    "Cannot create plugin instance of a fs-type plugin with a previous plugin instance."
+252                )
+253        elif "previous_id" not in kwargs:
+254            raise ValueError(
+255                f'Plugin type is "{self.plugin_type.value}" so previous is a required parameter.'
+256            )
+257        return await self._create_instance_raw(**kwargs)
+
+ + +

Create a plugin instance, i.e. "run" this plugin.

+ +

Parameters common to all plugins are described below. +Not all valid parameters are listed, since each plugin's parameters are different. +Some plugins have required parameters too. +To list all possible parameters, make a GET request to the specific plugin's instances link.

+ +
Parameters
+ +
    +
  • previous (chris.models.data.PluginInstanceData): +Previous plugin instance
    • +
  • previous_id (int): +Previous plugin instance ID number (conflicts with previous)
    • +
  • compute_resource_name (Optional[str]): +Name of compute resource to use
    • +
  • memory_limit (Optional[str]): +Memory limit. Format is xMi or xGi where x is an integer.
    • +
  • cpu_limit (Optional[str]): +CPU limit. Format is xm for x is an integer in millicores.
    • +
  • gpu_limit (Optional[int]): +GPU limit.
    • +
+
+ + +
+
+
Inherited Members
+
+ +
aiochris.link.linked.Linked
+
max_search_requests
+ +
+
+
+
+
+ + \ No newline at end of file diff --git a/v0.5.0a3/aiochris/models/public.html b/v0.5.0a3/aiochris/models/public.html new file mode 100644 index 0000000..c9edcd5 --- /dev/null +++ b/v0.5.0a3/aiochris/models/public.html @@ -0,0 +1,630 @@ + + + + + + + aiochris.models.public API documentation + + + + + + + + + +
+
+

+aiochris.models.public

+ +

Read-only models for CUBE resources.

+
+ + + + + + 
 1"""
+ 2Read-only models for CUBE resources.
+ 3"""
+ 4import sys
+ 5from dataclasses import dataclass
+ 6from typing import Optional, Literal, TextIO, Any
+ 7
+ 8import serde
+ 9from serde import deserialize
+10
+11from aiochris.link import http
+12from aiochris.link.linked import LinkedModel
+13from aiochris.enums import PluginType
+14from aiochris.types import *
+15from aiochris.util.search import Search
+16
+17
+18@deserialize
+19@dataclass(frozen=True)
+20class ComputeResource:
+21    url: ApiUrl
+22    id: ComputeResourceId
+23    creation_date: str
+24    modification_date: str
+25    name: ComputeResourceName
+26    compute_url: PfconUrl
+27    compute_auth_url: str
+28    description: str
+29    max_job_exec_seconds: int
+30
+31
+32@deserialize
+33@dataclass(frozen=True)
+34class PluginParameter(LinkedModel):
+35    """
+36    Information about a parameter (a command-line option/flag) of a plugin.
+37    """
+38
+39    url: PluginParameterUrl
+40    id: PluginParameterId
+41    name: ParameterName
+42    type: ParameterType
+43    optional: bool
+44    default: Optional[ParameterType]
+45    flag: str
+46    short_flag: str
+47    action: Literal["store", "store_true", "store_false"]
+48    help: str
+49    ui_exposed: bool
+50    plugin: PluginUrl
+51
+52
+53@deserialize
+54@dataclass(frozen=True)
+55class PublicPlugin(LinkedModel):
+56    """
+57    A ChRIS plugin.
+58    """
+59
+60    url: PluginUrl
+61    id: PluginId
+62    name: PluginName
+63    version: PluginVersion
+64    dock_image: ImageTag
+65    public_repo: str
+66    compute_resources: ComputeResourceUrl
+67    parameters: PluginParametersUrl
+68    plugin_type: PluginType = serde.field(rename="type")
+69
+70    @http.search("compute_resources", subpath="")
+71    def get_compute_resources(self) -> Search[ComputeResource]:
+72        """Get the compute resources this plugin is registered to."""
+73        ...
+74
+75    @http.search("parameters", subpath="")
+76    def get_parameters(self) -> Search[PluginParameter]:
+77        """Get the parameters of this plugin."""
+78        ...
+79
+80    async def print_help(self, out: TextIO = sys.stdout) -> None:
+81        """
+82        Display the help messages for this plugin's parameters.
+83        """
+84        async for param in self.get_parameters():
+85            left = f"{param.name} ({param.flag})"
+86            out.write(f"{left:>20}: {param.help}")
+87            if param.default is not None:
+88                out.write(f" (default: {param.default})")
+89            out.write("\n")
+
+ + +
+
+ +
+
@deserialize
+
@dataclass(frozen=True)
+ + class + ComputeResource: + + + +
+ + 
19@deserialize
+20@dataclass(frozen=True)
+21class ComputeResource:
+22    url: ApiUrl
+23    id: ComputeResourceId
+24    creation_date: str
+25    modification_date: str
+26    name: ComputeResourceName
+27    compute_url: PfconUrl
+28    compute_auth_url: str
+29    description: str
+30    max_job_exec_seconds: int
+
+ + + + +
+
+ + ComputeResource( url: aiochris.types.ApiUrl, id: aiochris.types.ComputeResourceId, creation_date: str, modification_date: str, name: aiochris.types.ComputeResourceName, compute_url: aiochris.types.PfconUrl, compute_auth_url: str, description: str, max_job_exec_seconds: int) + + +
+ + + + +
+
+
+ +
+
@deserialize
+
@dataclass(frozen=True)
+ + class + PluginParameter(aiochris.link.linked.LinkedModel): + + + +
+ + 
33@deserialize
+34@dataclass(frozen=True)
+35class PluginParameter(LinkedModel):
+36    """
+37    Information about a parameter (a command-line option/flag) of a plugin.
+38    """
+39
+40    url: PluginParameterUrl
+41    id: PluginParameterId
+42    name: ParameterName
+43    type: ParameterType
+44    optional: bool
+45    default: Optional[ParameterType]
+46    flag: str
+47    short_flag: str
+48    action: Literal["store", "store_true", "store_false"]
+49    help: str
+50    ui_exposed: bool
+51    plugin: PluginUrl
+
+ + +

Information about a parameter (a command-line option/flag) of a plugin.

+
+ + +
+
+ + PluginParameter( s: aiohttp.client.ClientSession, max_search_requests: int, url: aiochris.types.PluginParameterUrl, id: aiochris.types.ParameterGlobalId, name: aiochris.types.ParameterName, type: Union[str, int, float, bool], optional: bool, default: Union[str, int, float, bool, NoneType], flag: str, short_flag: str, action: Literal['store', 'store_true', 'store_false'], help: str, ui_exposed: bool, plugin: aiochris.types.PluginUrl) + + +
+ + + + +
+
+
Inherited Members
+
+
aiochris.link.linked.Linked
+
max_search_requests
+ +
+
+
+
+
+ +
+
@deserialize
+
@dataclass(frozen=True)
+ + class + PublicPlugin(aiochris.link.linked.LinkedModel): + + + +
+ + 
54@deserialize
+55@dataclass(frozen=True)
+56class PublicPlugin(LinkedModel):
+57    """
+58    A ChRIS plugin.
+59    """
+60
+61    url: PluginUrl
+62    id: PluginId
+63    name: PluginName
+64    version: PluginVersion
+65    dock_image: ImageTag
+66    public_repo: str
+67    compute_resources: ComputeResourceUrl
+68    parameters: PluginParametersUrl
+69    plugin_type: PluginType = serde.field(rename="type")
+70
+71    @http.search("compute_resources", subpath="")
+72    def get_compute_resources(self) -> Search[ComputeResource]:
+73        """Get the compute resources this plugin is registered to."""
+74        ...
+75
+76    @http.search("parameters", subpath="")
+77    def get_parameters(self) -> Search[PluginParameter]:
+78        """Get the parameters of this plugin."""
+79        ...
+80
+81    async def print_help(self, out: TextIO = sys.stdout) -> None:
+82        """
+83        Display the help messages for this plugin's parameters.
+84        """
+85        async for param in self.get_parameters():
+86            left = f"{param.name} ({param.flag})"
+87            out.write(f"{left:>20}: {param.help}")
+88            if param.default is not None:
+89                out.write(f" (default: {param.default})")
+90            out.write("\n")
+
+ + +

A ChRIS plugin.

+
+ + +
+
+ + PublicPlugin( s: aiohttp.client.ClientSession, max_search_requests: int, url: aiochris.types.PluginUrl, id: aiochris.types.PluginId, name: aiochris.types.PluginName, version: aiochris.types.PluginVersion, dock_image: aiochris.types.ImageTag, public_repo: str, compute_resources: aiochris.types.ComputeResourceUrl, parameters: aiochris.types.PluginParametersUrl, plugin_type: aiochris.enums.PluginType) + + +
+ + + + +
+
+ +
+
@http.search('compute_resources', subpath='')
+ + def + get_compute_resources( self) -> aiochris.util.search.Search[aiochris.models.public.ComputeResource]: + + + +
+ + 
71    @http.search("compute_resources", subpath="")
+72    def get_compute_resources(self) -> Search[ComputeResource]:
+73        """Get the compute resources this plugin is registered to."""
+74        ...
+
+ + +

Get the compute resources this plugin is registered to.

+
+ + +
+
+ +
+
@http.search('parameters', subpath='')
+ + def + get_parameters( self) -> aiochris.util.search.Search[aiochris.models.public.PluginParameter]: + + + +
+ + 
76    @http.search("parameters", subpath="")
+77    def get_parameters(self) -> Search[PluginParameter]:
+78        """Get the parameters of this plugin."""
+79        ...
+
+ + +

Get the parameters of this plugin.

+
+ + +
+
+ +
+ + async def + print_help(self, out: <class 'TextIO'> = <_io.StringIO object>) -> None: + + + +
+ + 
81    async def print_help(self, out: TextIO = sys.stdout) -> None:
+82        """
+83        Display the help messages for this plugin's parameters.
+84        """
+85        async for param in self.get_parameters():
+86            left = f"{param.name} ({param.flag})"
+87            out.write(f"{left:>20}: {param.help}")
+88            if param.default is not None:
+89                out.write(f" (default: {param.default})")
+90            out.write("\n")
+
+ + +

Display the help messages for this plugin's parameters.

+
+ + +
+
+
Inherited Members
+
+
aiochris.link.linked.Linked
+
max_search_requests
+ +
+
+
+
+
+ + \ No newline at end of file diff --git a/v0.5.0a3/aiochris/types.html b/v0.5.0a3/aiochris/types.html new file mode 100644 index 0000000..e4b8544 --- /dev/null +++ b/v0.5.0a3/aiochris/types.html @@ -0,0 +1,555 @@ + + + + + + + aiochris.types API documentation + + + + + + + + + +
+
+

+aiochris.types

+ +

NewTypes for ChRIS models.

+
+ + + + + + 
  1"""
+  2NewTypes for ChRIS models.
+  3"""
+  4
+  5from typing import NewType, Union
+  6
+  7Username = NewType("Username", str)
+  8"""ChRIS user account username"""
+  9Password = NewType("Password", str)
+ 10"""ChRIS user account password"""
+ 11ChrisURL = NewType("ChrisURL", str)
+ 12"""ChRIS backend API base URL"""
+ 13
+ 14ApiUrl = NewType("ApiUrl", str)
+ 15"""Any CUBE URL which I am too lazy to be more specific about."""
+ 16ResourceId = NewType("ResourceId", int)
+ 17"""ID number which I am too lazy to be more specific about."""
+ 18PluginName = NewType("PluginName", str)
+ 19"""Name of a ChRIS plugin"""
+ 20ImageTag = NewType("ImageTag", str)
+ 21"""OCI image tag (informally, a Docker Image name)"""
+ 22PluginVersion = NewType("PluginVersion", str)
+ 23"""Version string of a ChRIS plugin"""
+ 24
+ 25PluginUrl = NewType("PluginUrl", str)
+ 26"""
+ 27URL of a ChRIS plugin.
+ 28
+ 29## Examples
+ 30
+ 31- https://chrisstore.co/api/v1/plugins/5/
+ 32- https://cube.chrisproject.org/api/v1/plugins/6/
+ 33"""
+ 34PluginSearchUrl = NewType("PluginSearchUrl", str)
+ 35
+ 36PluginId = NewType("PluginId", int)
+ 37
+ 38UserUrl = NewType("UserUrl", str)
+ 39UserId = NewType("UserId", int)
+ 40
+ 41AdminUrl = NewType("AdminUrl", str)
+ 42"""A admin resource URL ending with `/chris-admin/api/v1/`"""
+ 43ComputeResourceName = NewType("ComputeResourceName", str)
+ 44ComputeResourceId = NewType("ComputeResourceId", str)
+ 45
+ 46PfconUrl = NewType("PfconUrl", str)
+ 47
+ 48FeedId = NewType("FeedId", str)
+ 49
+ 50
+ 51CubeFilePath = NewType("CubeFilePath", str)
+ 52
+ 53
+ 54CUBEErrorCode = NewType("CUBEErrorCode", str)
+ 55
+ 56ContainerImageTag = NewType("ContainerImageTag", str)
+ 57
+ 58PipingId = NewType("PipingId", int)
+ 59PipelineId = NewType("PipelineId", int)
+ 60
+ 61
+ 62ParameterName = NewType("ParameterName", str)
+ 63ParameterType = Union[str, int, float, bool]
+ 64
+ 65PipelineParameterId = NewType("ParameterLocalId", int)
+ 66PluginParameterId = NewType("ParameterGlobalId", int)
+ 67PluginInstanceId = NewType("PluginInstanceId", int)
+ 68
+ 69FileFname = NewType("FileFname", str)
+ 70FileResourceName = NewType("FileResourceName", str)
+ 71FileId = NewType("FileId", int)
+ 72
+ 73FilesUrl = NewType("FilesUrl", str)
+ 74FileResourceUrl = NewType("FileResourceUrl", str)
+ 75PipelineUrl = NewType("PipelineUrl", str)
+ 76PipingsUrl = NewType("PipingsUrl", str)
+ 77PipelinePluginsUrl = NewType("PipelinePluginsUrl", str)
+ 78PipelineDefaultParametersUrl = NewType("PipelineDefaultParametersUrl", str)
+ 79PipingUrl = NewType("PipingUrl", str)
+ 80
+ 81PipelineParameterUrl = NewType("PipingParameterUrl", str)
+ 82PluginInstanceUrl = NewType("PluginInstanceUrl", str)
+ 83PluginInstancesUrl = NewType("PluginInstancesUrl", str)
+ 84DescendantsUrl = NewType("DescendantsUrl", str)
+ 85PipelineInstancesUrl = NewType("PipelineInstancesUrl", str)
+ 86PluginInstanceParamtersUrl = NewType("PluginInstanceParametersUrl", str)
+ 87ComputeResourceUrl = NewType("ComputeResourceUrl", str)
+ 88SplitsUrl = NewType("SplitsUrl", str)
+ 89FeedUrl = NewType("FeedUrl", str)
+ 90NoteId = NewType("NoteId", int)
+ 91"""A feed note's ID number."""
+ 92NoteUrl = NewType("NoteUrl", str)
+ 93"""
+ 94A feed's note URL.
+ 95
+ 96## Examples
+ 97
+ 98- https://cube.chrisproject.org/api/v1/note4/
+ 99"""
+100PluginParametersUrl = NewType("PluginParametersUrl", str)
+101TagsUrl = NewType("TagsUrl", str)
+102TaggingsUrl = NewType("TaggingsUrl", str)
+103CommentsUrl = NewType("CommentsUrl", str)
+104
+105PluginParameterUrl = NewType("PluginParameterUrl", str)
+
+ + +
+
+
+ Username = aiochris.types.Username + + +
+ + +

ChRIS user account username

+
+ + +
+
+
+ Password = aiochris.types.Password + + +
+ + +

ChRIS user account password

+
+ + +
+
+
+ ChrisURL = aiochris.types.ChrisURL + + +
+ + +

ChRIS backend API base URL

+
+ + +
+
+
+ ApiUrl = aiochris.types.ApiUrl + + +
+ + +

Any CUBE URL which I am too lazy to be more specific about.

+
+ + +
+
+
+ ResourceId = aiochris.types.ResourceId + + +
+ + +

ID number which I am too lazy to be more specific about.

+
+ + +
+
+
+ PluginName = aiochris.types.PluginName + + +
+ + +

Name of a ChRIS plugin

+
+ + +
+
+
+ ImageTag = aiochris.types.ImageTag + + +
+ + +

OCI image tag (informally, a Docker Image name)

+
+ + +
+
+
+ PluginVersion = aiochris.types.PluginVersion + + +
+ + +

Version string of a ChRIS plugin

+
+ + +
+
+
+ PluginUrl = aiochris.types.PluginUrl + + +
+ + +

URL of a ChRIS plugin.

+ +

Examples

+ + +
+ + +
+
+
+ AdminUrl = aiochris.types.AdminUrl + + +
+ + +

A admin resource URL ending with /chris-admin/api/v1/

+
+ + +
+
+
+ NoteId = aiochris.types.NoteId + + +
+ + +

A feed note's ID number.

+
+ + +
+
+
+ NoteUrl = aiochris.types.NoteUrl + + +
+ + +

A feed's note URL.

+ +

Examples

+ + +
+ + +
+
+ + \ No newline at end of file diff --git a/v0.5.0a3/aiochris/util.html b/v0.5.0a3/aiochris/util.html new file mode 100644 index 0000000..42f27d0 --- /dev/null +++ b/v0.5.0a3/aiochris/util.html @@ -0,0 +1,262 @@ + + + + + + + aiochris.util API documentation + + + + + + + + + +
+
+

+aiochris.util

+ + + + + + + 
1__all__ = ["search", "errors"]
+
+ + +
+
+
+ errors + + +
+ + + + +
+
+ + \ No newline at end of file diff --git a/v0.5.0a3/aiochris/util/search.html b/v0.5.0a3/aiochris/util/search.html new file mode 100644 index 0000000..6a47a3c --- /dev/null +++ b/v0.5.0a3/aiochris/util/search.html @@ -0,0 +1,1047 @@ + + + + + + + aiochris.util.search API documentation + + + + + + + + + +
+
+

+aiochris.util.search

+ + + + + + + 
  1import copy
+  2import logging
+  3from dataclasses import dataclass
+  4from typing import (
+  5    Optional,
+  6    TypeVar,
+  7    AsyncGenerator,
+  8    Type,
+  9    AsyncIterable,
+ 10    Any,
+ 11    Generic,
+ 12    AsyncIterator,
+ 13)
+ 14
+ 15import yarl
+ 16from serde import deserialize
+ 17from serde.json import from_json
+ 18
+ 19from aiochris.link.linked import deserialize_linked, Linked
+ 20from aiochris.errors import (
+ 21    BaseClientError,
+ 22    raise_for_status,
+ 23    NonsenseResponseError,
+ 24)
+ 25
+ 26logger = logging.getLogger(__name__)
+ 27
+ 28T = TypeVar("T")
+ 29
+ 30
+ 31@deserialize
+ 32class _Paginated:
+ 33    """
+ 34    Response from a paginated endpoint.
+ 35    """
+ 36
+ 37    count: int
+ 38    next: Optional[str]
+ 39    previous: Optional[str]
+ 40    results: list[Any]
+ 41
+ 42
+ 43@dataclass
+ 44class Search(Generic[T], AsyncIterable[T]):
+ 45    """
+ 46    Abstraction over paginated collection responses from *CUBE*.
+ 47    `Search` objects are returned by methods for search endpoints of the *CUBE* API.
+ 48    It is an [asynchronous iterable](https://docs.python.org/3/glossary.html#term-asynchronous-iterable)
+ 49    which produces items from responses that return multiple results.
+ 50    HTTP requests are fired as-neede, they happen in the background during iteration.
+ 51    No request is made before the first time a `Search` object is called.
+ 52
+ 53    .. note:: Pagination is handled internally and automatically.
+ 54             The query parameters `limit` and `offset` can be explicitly given, but they shouldn't.
+ 55
+ 56    Examples
+ 57    --------
+ 58
+ 59    Use an `async for` loop to print the name of every feed:
+ 60
+ 61    ```python
+ 62    all_feeds = chris.search_feeds()  # returns a Search[Feed]
+ 63    async for feed in all_feeds:
+ 64        print(feed.name)
+ 65    ```
+ 66    """
+ 67
+ 68    base_url: str
+ 69    params: dict[str, Any]
+ 70    client: Linked
+ 71    Item: Type[T]
+ 72    max_requests: int = 100
+ 73    subpath: str = "search/"
+ 74
+ 75    def __aiter__(self) -> AsyncIterator[T]:
+ 76        return self._paginate(self.url)
+ 77
+ 78    async def first(self) -> Optional[T]:
+ 79        """
+ 80        Get the first item.
+ 81
+ 82        See also
+ 83        --------
+ 84        `get_only` : similar use, but more strict
+ 85        """
+ 86        return await anext(self._first_aiter(), None)
+ 87
+ 88    async def get_only(self, allow_multiple=False) -> T:
+ 89        """
+ 90        Get the *only* item from a search with one result.
+ 91
+ 92        Examples
+ 93        --------
+ 94
+ 95        This method is very commonly used for getting "one thing" from CUBE.
+ 96
+ 97        ```python
+ 98        await chris.search_plugins(name_exact="pl-dircopy", version="2.1.1").get_only()
+ 99        ```
+100
+101        In the example above, a search for plugins given (`name_exact`, `version`)
+102        is guaranteed to return either 0 or 1 result.
+103
+104        Raises
+105        ------
+106        aiochris.util.search.NoneSearchError
+107            If this search is empty.
+108        aiochris.util.search.ManySearchError
+109            If this search has more than one item and `allow_multiple` is `False`
+110
+111        See also
+112        --------
+113        `first` : does the same thing but without checks.
+114
+115        Parameters
+116        ----------
+117        allow_multiple: bool
+118            if `True`, do not raise `ManySearchError` if `count > 1`
+119        """
+120        one = await self._get_one()
+121        if one.count == 0:
+122            raise NoneSearchError(self.url)
+123        if not allow_multiple and one.count > 1:
+124            raise ManySearchError(self.url)
+125        if len(one.results) < 1:
+126            raise NonsenseResponseError(
+127                f"Response has count={one.count} but the results are empty.", one
+128            )
+129        return deserialize_linked(self.client, self.Item, one.results[0])
+130
+131    async def count(self) -> int:
+132        """
+133        Get the number of items in this collection search.
+134
+135        Examples
+136        --------
+137
+138        `count` is useful for rendering a progress bar. TODO example with files
+139        """
+140        one = await self._get_one()
+141        return one.count
+142
+143    async def _get_one(self) -> _Paginated:
+144        async with self.client.s.get(self._first_url) as res:
+145            await raise_for_status(res)
+146            return from_json(_Paginated, await res.text())
+147
+148    def _paginate(self, url: yarl.URL) -> AsyncIterator[T]:
+149        return _get_paginated(
+150            client=self.client,
+151            url=url,
+152            item_type=self.Item,
+153            max_requests=self.max_requests,
+154        )
+155
+156    @property
+157    def url(self) -> yarl.URL:
+158        return self._search_url_with(self.params)
+159
+160    def _first_aiter(self) -> AsyncIterator[T]:
+161        return self._paginate(self._first_url)
+162
+163    @property
+164    def _first_url(self) -> yarl.URL:
+165        params = copy.copy(self.params)
+166        params["limit"] = 1
+167        params["offset"] = 0
+168        return self._search_url_with(params)
+169
+170    @property
+171    def _search_url(self) -> yarl.URL:
+172        return yarl.URL(self.base_url) / self.subpath
+173
+174    def _search_url_with(self, query: dict[str, Any]):
+175        return yarl.URL(self._search_url).with_query(query)
+176
+177
+178async def _get_paginated(
+179    client: Linked,
+180    url: yarl.URL | str,
+181    item_type: Type[T],
+182    max_requests: int,
+183) -> AsyncGenerator[T, None]:
+184    """
+185    Make HTTP GET requests to a paginated endpoint. Further requests to the
+186    "next" URL are made in the background as needed.
+187    """
+188    logger.debug("GET, max_requests=%d, --> %s", max_requests, url)
+189    if max_requests != -1 and max_requests == 0:
+190        raise TooMuchPaginationError(
+191            f"too many requests made to {url}. "
+192            f"If this is expected, then pass the argument max_search_requests=-1 to "
+193            f"the client constructor classmethod."
+194        )
+195    async with client.s.get(url) as res:  # N.B. not checking for 4XX, 5XX statuses
+196        data: _Paginated = from_json(_Paginated, await res.text())
+197        for element in data.results:
+198            yield deserialize_linked(client, item_type, element)
+199    if data.next is not None:
+200        next_results = _get_paginated(client, data.next, item_type, max_requests - 1)
+201        async for next_element in next_results:
+202            yield next_element
+203
+204
+205async def acollect(async_iterable: AsyncIterable[T]) -> list[T]:
+206    """
+207    Simple helper to convert a `Search` to a [`list`](https://docs.python.org/3/library/stdtypes.html#list).
+208
+209    Using this function is not recommended unless you can assume the collection is small.
+210    """
+211    # nb: using tuple here causes
+212    #     TypeError: 'async_generator' object is not iterable
+213    # return tuple(e async for e in async_iterable)
+214    return [e async for e in async_iterable]
+215
+216
+217class TooMuchPaginationError(BaseClientError):
+218    """Specified maximum number of requests exceeded while retrieving results from a paginated resource."""
+219
+220    pass
+221
+222
+223class GetOnlyError(BaseClientError):
+224    """Search does not have exactly one result."""
+225
+226    pass
+227
+228
+229class NoneSearchError(GetOnlyError):
+230    """A search expected to have at least one element, has none."""
+231
+232    pass
+233
+234
+235class ManySearchError(GetOnlyError):
+236    """A search expected to have only one result, has several."""
+237
+238    pass
+
+ + +
+ +
+ +
+ + async def + acollect(async_iterable: AsyncIterable[~T]) -> list[~T]: + + + +
+ + 
206async def acollect(async_iterable: AsyncIterable[T]) -> list[T]:
+207    """
+208    Simple helper to convert a `Search` to a [`list`](https://docs.python.org/3/library/stdtypes.html#list).
+209
+210    Using this function is not recommended unless you can assume the collection is small.
+211    """
+212    # nb: using tuple here causes
+213    #     TypeError: 'async_generator' object is not iterable
+214    # return tuple(e async for e in async_iterable)
+215    return [e async for e in async_iterable]
+
+ + +

Simple helper to convert a Search to a list.

+ +

Using this function is not recommended unless you can assume the collection is small.

+
+ + +
+
+ +
+ + class + TooMuchPaginationError(aiochris.errors.BaseClientError): + + + +
+ + 
218class TooMuchPaginationError(BaseClientError):
+219    """Specified maximum number of requests exceeded while retrieving results from a paginated resource."""
+220
+221    pass
+
+ + +

Specified maximum number of requests exceeded while retrieving results from a paginated resource.

+
+ + +
+
Inherited Members
+
+
builtins.Exception
+
Exception
+ +
+
builtins.BaseException
+
with_traceback
+ +
+
+
+
+
+ +
+ + class + GetOnlyError(aiochris.errors.BaseClientError): + + + +
+ + 
224class GetOnlyError(BaseClientError):
+225    """Search does not have exactly one result."""
+226
+227    pass
+
+ + +

Search does not have exactly one result.

+
+ + +
+
Inherited Members
+
+
builtins.Exception
+
Exception
+ +
+
builtins.BaseException
+
with_traceback
+ +
+
+
+
+
+ +
+ + class + NoneSearchError(GetOnlyError): + + + +
+ + 
230class NoneSearchError(GetOnlyError):
+231    """A search expected to have at least one element, has none."""
+232
+233    pass
+
+ + +

A search expected to have at least one element, has none.

+
+ + +
+
Inherited Members
+
+
builtins.Exception
+
Exception
+ +
+
builtins.BaseException
+
with_traceback
+ +
+
+
+
+
+ +
+ + class + ManySearchError(GetOnlyError): + + + +
+ + 
236class ManySearchError(GetOnlyError):
+237    """A search expected to have only one result, has several."""
+238
+239    pass
+
+ + +

A search expected to have only one result, has several.

+
+ + +
+
Inherited Members
+
+
builtins.Exception
+
Exception
+ +
+
builtins.BaseException
+
with_traceback
+ +
+
+
+
+
+ + \ No newline at end of file diff --git a/v0.5.0a3/index.html b/v0.5.0a3/index.html new file mode 100644 index 0000000..b5ec362 --- /dev/null +++ b/v0.5.0a3/index.html @@ -0,0 +1,7 @@ + + + + + + + diff --git a/v0.5.0a3/search.js b/v0.5.0a3/search.js new file mode 100644 index 0000000..284e2f2 --- /dev/null +++ b/v0.5.0a3/search.js @@ -0,0 +1,46 @@ +window.pdocSearch = (function(){ +/** elasticlunr - http://weixsong.github.io * Copyright (C) 2017 Oliver Nightingale * Copyright (C) 2017 Wei Song * MIT Licensed */!function(){function e(e){if(null===e||"object"!=typeof e)return e;var t=e.constructor();for(var n in e)e.hasOwnProperty(n)&&(t[n]=e[n]);return t}var t=function(e){var n=new t.Index;return n.pipeline.add(t.trimmer,t.stopWordFilter,t.stemmer),e&&e.call(n,n),n};t.version="0.9.5",lunr=t,t.utils={},t.utils.warn=function(e){return function(t){e.console&&console.warn&&console.warn(t)}}(this),t.utils.toString=function(e){return void 0===e||null===e?"":e.toString()},t.EventEmitter=function(){this.events={}},t.EventEmitter.prototype.addListener=function(){var e=Array.prototype.slice.call(arguments),t=e.pop(),n=e;if("function"!=typeof t)throw new TypeError("last argument must be a function");n.forEach(function(e){this.hasHandler(e)||(this.events[e]=[]),this.events[e].push(t)},this)},t.EventEmitter.prototype.removeListener=function(e,t){if(this.hasHandler(e)){var n=this.events[e].indexOf(t);-1!==n&&(this.events[e].splice(n,1),0==this.events[e].length&&delete this.events[e])}},t.EventEmitter.prototype.emit=function(e){if(this.hasHandler(e)){var t=Array.prototype.slice.call(arguments,1);this.events[e].forEach(function(e){e.apply(void 0,t)},this)}},t.EventEmitter.prototype.hasHandler=function(e){return e in this.events},t.tokenizer=function(e){if(!arguments.length||null===e||void 0===e)return[];if(Array.isArray(e)){var n=e.filter(function(e){return null===e||void 0===e?!1:!0});n=n.map(function(e){return t.utils.toString(e).toLowerCase()});var i=[];return n.forEach(function(e){var n=e.split(t.tokenizer.seperator);i=i.concat(n)},this),i}return e.toString().trim().toLowerCase().split(t.tokenizer.seperator)},t.tokenizer.defaultSeperator=/[\s\-]+/,t.tokenizer.seperator=t.tokenizer.defaultSeperator,t.tokenizer.setSeperator=function(e){null!==e&&void 0!==e&&"object"==typeof e&&(t.tokenizer.seperator=e)},t.tokenizer.resetSeperator=function(){t.tokenizer.seperator=t.tokenizer.defaultSeperator},t.tokenizer.getSeperator=function(){return t.tokenizer.seperator},t.Pipeline=function(){this._queue=[]},t.Pipeline.registeredFunctions={},t.Pipeline.registerFunction=function(e,n){n in t.Pipeline.registeredFunctions&&t.utils.warn("Overwriting existing registered function: "+n),e.label=n,t.Pipeline.registeredFunctions[n]=e},t.Pipeline.getRegisteredFunction=function(e){return e in t.Pipeline.registeredFunctions!=!0?null:t.Pipeline.registeredFunctions[e]},t.Pipeline.warnIfFunctionNotRegistered=function(e){var n=e.label&&e.label in this.registeredFunctions;n||t.utils.warn("Function is not registered with pipeline. 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t=[],n=e.length,i=this._queue.length,o=0;n>o;o++){for(var r=e[o],s=0;i>s&&(r=this._queue[s](r,o,e),void 0!==r&&null!==r);s++);void 0!==r&&null!==r&&t.push(r)}return t},t.Pipeline.prototype.reset=function(){this._queue=[]},t.Pipeline.prototype.get=function(){return this._queue},t.Pipeline.prototype.toJSON=function(){return this._queue.map(function(e){return t.Pipeline.warnIfFunctionNotRegistered(e),e.label})},t.Index=function(){this._fields=[],this._ref="id",this.pipeline=new t.Pipeline,this.documentStore=new t.DocumentStore,this.index={},this.eventEmitter=new t.EventEmitter,this._idfCache={},this.on("add","remove","update",function(){this._idfCache={}}.bind(this))},t.Index.prototype.on=function(){var e=Array.prototype.slice.call(arguments);return this.eventEmitter.addListener.apply(this.eventEmitter,e)},t.Index.prototype.off=function(e,t){return this.eventEmitter.removeListener(e,t)},t.Index.load=function(e){e.version!==t.version&&t.utils.warn("version mismatch: current "+t.version+" importing "+e.version);var n=new this;n._fields=e.fields,n._ref=e.ref,n.documentStore=t.DocumentStore.load(e.documentStore),n.pipeline=t.Pipeline.load(e.pipeline),n.index={};for(var i in e.index)n.index[i]=t.InvertedIndex.load(e.index[i]);return n},t.Index.prototype.addField=function(e){return this._fields.push(e),this.index[e]=new t.InvertedIndex,this},t.Index.prototype.setRef=function(e){return this._ref=e,this},t.Index.prototype.saveDocument=function(e){return this.documentStore=new t.DocumentStore(e),this},t.Index.prototype.addDoc=function(e,n){if(e){var n=void 0===n?!0:n,i=e[this._ref];this.documentStore.addDoc(i,e),this._fields.forEach(function(n){var o=this.pipeline.run(t.tokenizer(e[n]));this.documentStore.addFieldLength(i,n,o.length);var r={};o.forEach(function(e){e in r?r[e]+=1:r[e]=1},this);for(var s in r){var u=r[s];u=Math.sqrt(u),this.index[n].addToken(s,{ref:i,tf:u})}},this),n&&this.eventEmitter.emit("add",e,this)}},t.Index.prototype.removeDocByRef=function(e){if(e&&this.documentStore.isDocStored()!==!1&&this.documentStore.hasDoc(e)){var t=this.documentStore.getDoc(e);this.removeDoc(t,!1)}},t.Index.prototype.removeDoc=function(e,n){if(e){var n=void 0===n?!0:n,i=e[this._ref];this.documentStore.hasDoc(i)&&(this.documentStore.removeDoc(i),this._fields.forEach(function(n){var o=this.pipeline.run(t.tokenizer(e[n]));o.forEach(function(e){this.index[n].removeToken(e,i)},this)},this),n&&this.eventEmitter.emit("remove",e,this))}},t.Index.prototype.updateDoc=function(e,t){var t=void 0===t?!0:t;this.removeDocByRef(e[this._ref],!1),this.addDoc(e,!1),t&&this.eventEmitter.emit("update",e,this)},t.Index.prototype.idf=function(e,t){var n="@"+t+"/"+e;if(Object.prototype.hasOwnProperty.call(this._idfCache,n))return this._idfCache[n];var i=this.index[t].getDocFreq(e),o=1+Math.log(this.documentStore.length/(i+1));return this._idfCache[n]=o,o},t.Index.prototype.getFields=function(){return this._fields.slice()},t.Index.prototype.search=function(e,n){if(!e)return[];e="string"==typeof e?{any:e}:JSON.parse(JSON.stringify(e));var i=null;null!=n&&(i=JSON.stringify(n));for(var o=new t.Configuration(i,this.getFields()).get(),r={},s=Object.keys(e),u=0;u0&&t.push(e);for(var i in n)"docs"!==i&&"df"!==i&&this.expandToken(e+i,t,n[i]);return t},t.InvertedIndex.prototype.toJSON=function(){return{root:this.root}},t.Configuration=function(e,n){var e=e||"";if(void 0==n||null==n)throw new Error("fields should not be null");this.config={};var i;try{i=JSON.parse(e),this.buildUserConfig(i,n)}catch(o){t.utils.warn("user configuration parse failed, will use default configuration"),this.buildDefaultConfig(n)}},t.Configuration.prototype.buildDefaultConfig=function(e){this.reset(),e.forEach(function(e){this.config[e]={boost:1,bool:"OR",expand:!1}},this)},t.Configuration.prototype.buildUserConfig=function(e,n){var i="OR",o=!1;if(this.reset(),"bool"in e&&(i=e.bool||i),"expand"in e&&(o=e.expand||o),"fields"in e)for(var r in e.fields)if(n.indexOf(r)>-1){var s=e.fields[r],u=o;void 0!=s.expand&&(u=s.expand),this.config[r]={boost:s.boost||0===s.boost?s.boost:1,bool:s.bool||i,expand:u}}else t.utils.warn("field name in user configuration not found in index instance fields");else this.addAllFields2UserConfig(i,o,n)},t.Configuration.prototype.addAllFields2UserConfig=function(e,t,n){n.forEach(function(n){this.config[n]={boost:1,bool:e,expand:t}},this)},t.Configuration.prototype.get=function(){return this.config},t.Configuration.prototype.reset=function(){this.config={}},lunr.SortedSet=function(){this.length=0,this.elements=[]},lunr.SortedSet.load=function(e){var t=new this;return t.elements=e,t.length=e.length,t},lunr.SortedSet.prototype.add=function(){var e,t;for(e=0;e1;){if(r===e)return o;e>r&&(t=o),r>e&&(n=o),i=n-t,o=t+Math.floor(i/2),r=this.elements[o]}return r===e?o:-1},lunr.SortedSet.prototype.locationFor=function(e){for(var t=0,n=this.elements.length,i=n-t,o=t+Math.floor(i/2),r=this.elements[o];i>1;)e>r&&(t=o),r>e&&(n=o),i=n-t,o=t+Math.floor(i/2),r=this.elements[o];return r>e?o:e>r?o+1:void 0},lunr.SortedSet.prototype.intersect=function(e){for(var t=new lunr.SortedSet,n=0,i=0,o=this.length,r=e.length,s=this.elements,u=e.elements;;){if(n>o-1||i>r-1)break;s[n]!==u[i]?s[n]u[i]&&i++:(t.add(s[n]),n++,i++)}return t},lunr.SortedSet.prototype.clone=function(){var e=new lunr.SortedSet;return e.elements=this.toArray(),e.length=e.elements.length,e},lunr.SortedSet.prototype.union=function(e){var t,n,i;this.length>=e.length?(t=this,n=e):(t=e,n=this),i=t.clone();for(var o=0,r=n.toArray();oChRIS Python client library built on\naiohttp (async HTTP client) and\npyserde\n(dataclasses deserializer).

\n\n

Installation

\n\n

Requires Python 3.10 or 3.11.

\n\n
\n
pip install aiochris\n# or\npoetry add aiochris\n
\n
\n\n

Brief Example

\n\n
\n
from aiochris import ChrisClient\n\nchris = await ChrisClient.from_login(\n    username='chris',\n    password='chris1234',\n    url='https://cube.chrisproject.org/api/v1/'\n)\ndircopy = await chris.search_plugins(name_exact='pl-brainmgz', version='2.0.3').get_only()\nplinst = await dircopy.create_instance(compute_resource_name='host')\nawait plinst.set(title="copies brain image files into feed")\n
\n
\n\n

Introduction

\n\n

aiochris provides three core classes: AnonChrisClient, ChrisClient, and ChrisAdminClient.\nThese clients differ in permissions.

\n\n

\nMethods are only defined for what the client has permission to see or do.

\n\n
\n
anon_client = await AnonChrisClient.from_url('https://cube.chrisproject.org/api/v1/')\n# ok: can search for plugins without logging in...\nplugin = await anon_client.search_plugins(name_exact='pl-mri10yr06mo01da_normal').first()\n# IMPOSSIBLE! AnonChrisClient.create_instance not defined...\nawait plugin.create_instance()\n\n# IMPOSSIBLE! authentication required for ChrisClient\nauthed_client = await ChrisClient.from_url('https://cube.chrisproject.org/api/v1/')\nauthed_client = await ChrisClient.from_login(\n    url='https://cube.chrisproject.org/api/v1/',\n    username='chris',\n    password='chris1234'\n)\n# authenticated client can also search for plugins\nplugin = await authed_client.search_plugins(name_exact='pl-mri10yr06mo01da_normal').first()\nawait plugin.create_instance()  # works!\n
\n
\n\n

\n\n

Client Constructors

\n\n
    \n
  • AnonChrisClient.from_url: create a CUBE client without logging in.
    • \n
  • ChrisClient.from_login: create a CUBE client using a username and password.
    • \n
  • ChrisClient.from_token: create a CUBE client using a token from /api/v1/auth-token/.
    • \n
  • ChrisClient.from_chrs: create a CUBE client using logins saved by chrs.
    • \n
  • ChrisAdminClient.from_login: create an admin client using a username and password.
    • \n
  • ChrisAdminClient.from_token: create an admin client using a token from /api/v1/auth-token/.
    • \n
\n\n

aiochris in Jupyter Notebook

\n\n

Jupyter and IPython support top-level await. This, in conjunction with ChrisClient.from_chrs,\nmake aiochris a great way to use _ChRIS_ interactively with code.

\n\n

For a walkthrough, see https://github.com/FNNDSC/aiochris/blob/master/examples/aiochris_as_a_shell.ipynb

\n\n

Working with aiohttp

\n\n

aiochris hides the implementation detail that it is built upon aiohttp,\nhowever one thing is important to keep in mind:\nbe sure to call ChrisClient.close at the end of your program.

\n\n
\n
chris = await ChrisClient.from_login(...)\n# -- snip --\nawait chris.close()\n
\n
\n\n

You can also use an\nasynchronous context manager.

\n\n
\n
async with (await ChrisClient.from_login(...)) as chris:\n    await chris.upload_file('./something.dat', 'something.dat')\n    ...\n
\n
\n\n

Efficiency with Multiple Clients

\n\n

If using more than one aiohttp client in an application, it's more efficient\nto use the same\nconnector.\nOne connector instance should be shared among every client object,\nincluding all aiochris clients and other aiohttp clients.

\n\n

\nExample: efficiently using multiple aiohttp clients

\n\n
\n
import aiohttp\nfrom aiochris import ChrisClient\n\nwith aiohttp.TCPConnector() as connector:\n    chris_client1 = await ChrisClient.from_login(\n        url='https://example.com/cube/api/v1/',\n        username='user1',\n        password='user1234',\n        connector=connector,\n        connector_owner=False\n    )\n    chris_client2 = await ChrisClient.from_login(\n        url='https://example.com/cube/api/v1/',\n        username='user2',\n        password='user4321',\n        connector=connector,\n        connector_owner=False\n    )\n    plain_http_client = aiohttp.ClientSession(connector=connector, connector_owner=False)\n
\n
\n\n

\n\n

Advice for Getting Started

\n\n

Searching for things (plugins, plugin instances, files) in CUBE is a common task,\nand CUBE often returns multiple items per response.\nHence, it is important to understand how the Search helper class works.\nIt simplifies how we interact with paginated collection responses from CUBE.

\n\n

When performing batch operations, use\nasyncio.gather\nto run async functions concurrently.

\n\n

aiochris uses many generic types, so it is recommended you use an IDE\nwith good support for type hints, such as\nPyCharm\nor VSCodium with\nPylance configured.

\n\n

Examples

\n\n

Create a client given username and password

\n\n
\n
from aiochris import ChrisClient\n\nchris = await ChrisClient.from_login(\n    url='https://cube.chrisproject.org/api/v1/',\n    username='chris',\n    password='chris1234'\n)\n
\n
\n\n

Search for a plugin

\n\n
\n
# it's recommended to specify plugin version\nplugin = await chris.search_plugins(name_exact="pl-dcm2niix", version="0.1.0").get_only()\n\n# but if you don't care about plugin version...\nplugin = await chris.search_plugins(name_exact="pl-dcm2niix").first()\n
\n
\n\n

Create a feed by uploading a file

\n\n
\n
uploaded_file = await chris.upload_file('./brain.nii', 'my_experiment/brain.nii')\ndircopy = await chris.search_plugins(name_exact='pl-dircopy', version="2.1.1").get_only()\nplinst = await dircopy.create_instance(dir=uploaded_file.parent)\nfeed = await plinst.get_feed()\nawait feed.set(name="An experiment on uploaded file brain.nii")\n
\n
\n\n

Run a ds-type ChRIS plugin

\n\n
\n
# search for plugin to run\nplugin = await chris.search_plugins(name_exact="pl-dcm2niix", version="0.1.0").get_only()\n\n# search for parent node \nprevious = await chris.plugin_instances(id=44).get_only()\n\nawait plugin.create_instance(\n    previous=previous,               # required. alternatively, specify previous_id\n    title="convert DICOM to NIFTI",  # optional\n    compute_resource_name="galena",  # optional\n    memory_limit="2000Mi",           # optional\n    d=9,                             # optional parameter of pl-dcm2niix\n)\n
\n
\n\n

Search for plugin instances

\n\n
\n
finished_freesurfers = chris.plugin_instances(\n    plugin_name_exact='pl-fshack',\n    status='finishedSuccessfully'\n)\nasync for p in finished_freesurfers:\n    print(f'"{p.title}" finished on date: {p.end_date}')\n
\n
\n\n

Delete all plugin instances with a given title, in parallel

\n\n
\n
import asyncio\nfrom aiochris import ChrisClient, acollect\n\nchris = ChrisClient.from_login(...)\nsearch = chris.plugin_instances(title="delete me")\nplugin_instances = await acollect(search)\nawait asyncio.gather(*(p.delete() for p in plugin_instances))\n
\n
\n\n

Enable Debug Logging

\n\n

A log message will be printed to stderr before every HTTP request is sent.

\n\n
\n
import logging\n\nlogging.basicConfig(level=logging.DEBUG)\n
\n
\n"}, "aiochris.AnonChrisClient": {"fullname": "aiochris.AnonChrisClient", "modulename": "aiochris", "qualname": "AnonChrisClient", "kind": "class", "doc": "

An anonymous ChRIS client. It has access to read-only GET resources,\nsuch as being able to search for plugins.

\n", "bases": "aiochris.client.base.BaseChrisClient[aiochris.models.collection_links.AnonymousCollectionLinks, 'AnonChrisClient']"}, "aiochris.AnonChrisClient.from_url": {"fullname": "aiochris.AnonChrisClient.from_url", "modulename": "aiochris", "qualname": "AnonChrisClient.from_url", "kind": "function", "doc": "

Create an anonymous client.

\n\n

See aiochris.client.base.BaseChrisClient.new for parameter documentation.

\n", "signature": "(\tcls,\turl: str,\tmax_search_requests: int = 100,\tconnector: Optional[aiohttp.connector.BaseConnector] = None,\tconnector_owner: bool = True) -> aiochris.client.anon.AnonChrisClient:", "funcdef": "async def"}, "aiochris.AnonChrisClient.search_plugins": {"fullname": "aiochris.AnonChrisClient.search_plugins", "modulename": "aiochris", "qualname": "AnonChrisClient.search_plugins", "kind": "function", "doc": "

Search for plugins.

\n\n

Since this client is not logged in, you cannot create plugin instances using this client.

\n", "signature": "(\tself,\t**query) -> aiochris.util.search.Search[aiochris.models.public.PublicPlugin]:", "funcdef": "def"}, "aiochris.ChrisClient": {"fullname": "aiochris.ChrisClient", "modulename": "aiochris", "qualname": "ChrisClient", "kind": "class", "doc": "

A normal user ChRIS client, who may upload files and create plugin instances.

\n", "bases": "aiochris.client.authed.AuthenticatedClient[aiochris.models.collection_links.CollectionLinks, 'ChrisClient']"}, "aiochris.ChrisClient.create_user": {"fullname": "aiochris.ChrisClient.create_user", "modulename": "aiochris", "qualname": "ChrisClient.create_user", "kind": "function", "doc": "

\n", "signature": "(\tcls,\turl: Union[aiochris.types.ChrisURL, str],\tusername: Union[aiochris.types.Username, str],\tpassword: Union[aiochris.types.Password, str],\temail: str,\tsession: Optional[aiohttp.client.ClientSession] = None) -> aiochris.models.data.UserData:", "funcdef": "async def"}, "aiochris.ChrisAdminClient": {"fullname": "aiochris.ChrisAdminClient", "modulename": "aiochris", "qualname": "ChrisAdminClient", "kind": "class", "doc": "

A client who has access to /chris-admin/. Admins can register new plugins and\nadd new compute resources.

\n", "bases": "aiochris.client.authed.AuthenticatedClient[aiochris.models.collection_links.AdminCollectionLinks, 'ChrisAdminClient']"}, "aiochris.ChrisAdminClient.register_plugin_from_store": {"fullname": "aiochris.ChrisAdminClient.register_plugin_from_store", "modulename": "aiochris", "qualname": "ChrisAdminClient.register_plugin_from_store", "kind": "function", "doc": "

Register a plugin from a ChRIS Store.

\n", "signature": "(\tself,\tplugin_store_url: aiochris.types.PluginUrl,\tcompute_names: Iterable[aiochris.types.ComputeResourceName]) -> aiochris.models.logged_in.Plugin:", "funcdef": "async def"}, "aiochris.ChrisAdminClient.add_plugin": {"fullname": "aiochris.ChrisAdminClient.add_plugin", "modulename": "aiochris", "qualname": "ChrisAdminClient.add_plugin", "kind": "function", "doc": "

Add a plugin to CUBE.

\n\n
Examples
\n\n
\n
cmd = ['docker', 'run', '--rm', 'fnndsc/pl-mri-preview', 'chris_plugin_info']\noutput = subprocess.check_output(cmd, text=True)\ndesc = json.loads(output)\ndesc['name'] = 'pl-mri-preview'\ndesc['public_repo'] = 'https://github.com/FNNDSC/pl-mri-preview'\ndesc['dock_image'] = 'fnndsc/pl-mri-preview'\n\nawait chris_admin.add_plugin(plugin_description=desc, compute_resources='host')\n
\n
\n\n

The example above is just for show. It's not a good example for several reasons:

\n\n
    \n
  • Calls blocking function subprocess.check_output in asynchronous context
    • \n
  • It is preferred to use a versioned string for dock_image
    • \n
  • host compute environment is not guaranteed to exist. Instead, you could\ncall aiochris.client.authed.AuthenticatedClient.search_compute_resources\nor aiochris.client.authed.AuthenticatedClient.get_all_compute_resources:
    • \n
\n\n
\n
all_computes = await chris_admin.get_all_compute_resources()\nawait chris_admin.add_plugin(plugin_description=desc, compute_resources=all_computes)\n
\n
\n\n
Parameters
\n\n
    \n
  • plugin_description (str | dict):\nJSON description of a plugin.\nspec
    • \n
  • compute_resources: Compute resources to register the plugin to. Value can be either a comma-separated str of names,\na aiochris.models.public.ComputeResource, a sequence of aiochris.models.public.ComputeResource,\nor a sequence of compute resource names as str.
    • \n
\n", "signature": "(\tself,\tplugin_description: str | dict,\tcompute_resources: Union[str, aiochris.models.public.ComputeResource, Iterable[Union[aiochris.models.public.ComputeResource, aiochris.types.ComputeResourceName]]]) -> aiochris.models.logged_in.Plugin:", "funcdef": "async def"}, "aiochris.ChrisAdminClient.create_compute_resource": {"fullname": "aiochris.ChrisAdminClient.create_compute_resource", "modulename": "aiochris", "qualname": "ChrisAdminClient.create_compute_resource", "kind": "function", "doc": "

Define a new compute resource.

\n", "signature": "(\tself,\tname: Union[str, aiochris.types.ComputeResourceName],\tcompute_url: Union[str, aiochris.types.PfconUrl],\tcompute_user: str,\tcompute_password: str,\tcompute_innetwork: bool = None,\tdescription: str = None,\tcompute_auth_url: str = None,\tcompute_auth_token: str = None,\tmax_job_exec_seconds: str = None) -> aiochris.models.public.ComputeResource:", "funcdef": "async def"}, "aiochris.Search": {"fullname": "aiochris.Search", "modulename": "aiochris", "qualname": "Search", "kind": "class", "doc": "

Abstraction over paginated collection responses from CUBE.\nSearch objects are returned by methods for search endpoints of the CUBE API.\nIt is an asynchronous iterable\nwhich produces items from responses that return multiple results.\nHTTP requests are fired as-neede, they happen in the background during iteration.\nNo request is made before the first time a Search object is called.

\n\n
\n\n
Pagination is handled internally and automatically.
\n\n

The query parameters limit and offset can be explicitly given, but they shouldn't.

\n\n
\n\n
Examples
\n\n

Use an async for loop to print the name of every feed:

\n\n
\n
all_feeds = chris.search_feeds()  # returns a Search[Feed]\nasync for feed in all_feeds:\n    print(feed.name)\n
\n
\n", "bases": "typing.Generic[~T], typing.AsyncIterable[~T]"}, "aiochris.Search.__init__": {"fullname": "aiochris.Search.__init__", "modulename": "aiochris", "qualname": "Search.__init__", "kind": "function", "doc": "

\n", "signature": "(\tbase_url: str,\tparams: dict[str, typing.Any],\tclient: aiochris.link.linked.Linked,\tItem: Type[~T],\tmax_requests: int = 100,\tsubpath: str = 'search/')"}, "aiochris.Search.first": {"fullname": "aiochris.Search.first", "modulename": "aiochris", "qualname": "Search.first", "kind": "function", "doc": "

Get the first item.

\n\n
See also
\n\n

get_only : similar use, but more strict

\n", "signature": "(self) -> Optional[~T]:", "funcdef": "async def"}, "aiochris.Search.get_only": {"fullname": "aiochris.Search.get_only", "modulename": "aiochris", "qualname": "Search.get_only", "kind": "function", "doc": "

Get the only item from a search with one result.

\n\n
Examples
\n\n

This method is very commonly used for getting \"one thing\" from CUBE.

\n\n
\n
await chris.search_plugins(name_exact="pl-dircopy", version="2.1.1").get_only()\n
\n
\n\n

In the example above, a search for plugins given (name_exact, version)\nis guaranteed to return either 0 or 1 result.

\n\n
Raises
\n\n
    \n
  • aiochris.util.search.NoneSearchError: If this search is empty.
    • \n
  • aiochris.util.search.ManySearchError: If this search has more than one item and allow_multiple is False
    • \n
\n\n
See also
\n\n

first : does the same thing but without checks.

\n\n
Parameters
\n\n
    \n
  • allow_multiple (bool):\nif True, do not raise ManySearchError if count > 1
    • \n
\n", "signature": "(self, allow_multiple=False) -> ~T:", "funcdef": "async def"}, "aiochris.Search.count": {"fullname": "aiochris.Search.count", "modulename": "aiochris", "qualname": "Search.count", "kind": "function", "doc": "

Get the number of items in this collection search.

\n\n
Examples
\n\n

count is useful for rendering a progress bar. TODO example with files

\n", "signature": "(self) -> int:", "funcdef": "async def"}, "aiochris.acollect": {"fullname": "aiochris.acollect", "modulename": "aiochris", "qualname": "acollect", "kind": "function", "doc": "

Simple helper to convert a Search to a list.

\n\n

Using this function is not recommended unless you can assume the collection is small.

\n", "signature": "(async_iterable: AsyncIterable[~T]) -> list[~T]:", "funcdef": "async def"}, "aiochris.Status": {"fullname": "aiochris.Status", "modulename": "aiochris", "qualname": "Status", "kind": "class", "doc": "

Possible statuses of a plugin instance.

\n", "bases": "enum.Enum"}, "aiochris.Status.created": {"fullname": "aiochris.Status.created", "modulename": "aiochris", "qualname": "Status.created", "kind": "variable", "doc": "

\n", "default_value": " = <Status.created: 'created'>"}, "aiochris.Status.waiting": {"fullname": "aiochris.Status.waiting", "modulename": "aiochris", "qualname": "Status.waiting", "kind": "variable", "doc": "

\n", "default_value": " = <Status.waiting: 'waiting'>"}, "aiochris.Status.scheduled": {"fullname": "aiochris.Status.scheduled", "modulename": "aiochris", "qualname": "Status.scheduled", "kind": "variable", "doc": "

\n", "default_value": " = <Status.scheduled: 'scheduled'>"}, "aiochris.Status.started": {"fullname": "aiochris.Status.started", "modulename": "aiochris", "qualname": "Status.started", "kind": "variable", "doc": "

\n", "default_value": " = <Status.started: 'started'>"}, "aiochris.Status.registeringFiles": {"fullname": "aiochris.Status.registeringFiles", "modulename": "aiochris", "qualname": "Status.registeringFiles", "kind": "variable", "doc": "

\n", "default_value": " = <Status.registeringFiles: 'registeringFiles'>"}, "aiochris.Status.finishedSuccessfully": {"fullname": "aiochris.Status.finishedSuccessfully", "modulename": "aiochris", "qualname": "Status.finishedSuccessfully", "kind": "variable", "doc": "

\n", "default_value": " = <Status.finishedSuccessfully: 'finishedSuccessfully'>"}, "aiochris.Status.finishedWithError": {"fullname": "aiochris.Status.finishedWithError", "modulename": "aiochris", "qualname": "Status.finishedWithError", "kind": "variable", "doc": "

\n", "default_value": " = <Status.finishedWithError: 'finishedWithError'>"}, "aiochris.Status.cancelled": {"fullname": "aiochris.Status.cancelled", "modulename": "aiochris", "qualname": "Status.cancelled", "kind": "variable", "doc": "

\n", "default_value": " = <Status.cancelled: 'cancelled'>"}, "aiochris.ParameterTypeName": {"fullname": "aiochris.ParameterTypeName", "modulename": "aiochris", "qualname": "ParameterTypeName", "kind": "class", "doc": "

Plugin parameter types.

\n", "bases": "enum.Enum"}, "aiochris.ParameterTypeName.string": {"fullname": "aiochris.ParameterTypeName.string", "modulename": "aiochris", "qualname": "ParameterTypeName.string", "kind": "variable", "doc": "

\n", "default_value": " = <ParameterTypeName.string: 'string'>"}, "aiochris.ParameterTypeName.integer": {"fullname": "aiochris.ParameterTypeName.integer", "modulename": "aiochris", "qualname": "ParameterTypeName.integer", "kind": "variable", "doc": "

\n", "default_value": " = <ParameterTypeName.integer: 'integer'>"}, "aiochris.ParameterTypeName.float": {"fullname": "aiochris.ParameterTypeName.float", "modulename": "aiochris", "qualname": "ParameterTypeName.float", "kind": "variable", "doc": "

\n", "default_value": " = <ParameterTypeName.float: 'float'>"}, "aiochris.ParameterTypeName.boolean": {"fullname": "aiochris.ParameterTypeName.boolean", "modulename": "aiochris", "qualname": "ParameterTypeName.boolean", "kind": "variable", "doc": "

\n", "default_value": " = <ParameterTypeName.boolean: 'boolean'>"}, "aiochris.client": {"fullname": "aiochris.client", "modulename": "aiochris.client", "kind": "module", "doc": "

\n"}, "aiochris.client.admin": {"fullname": "aiochris.client.admin", "modulename": "aiochris.client.admin", "kind": "module", "doc": "

\n"}, "aiochris.client.admin.ChrisAdminClient": {"fullname": "aiochris.client.admin.ChrisAdminClient", "modulename": "aiochris.client.admin", "qualname": "ChrisAdminClient", "kind": "class", "doc": "

A client who has access to /chris-admin/. Admins can register new plugins and\nadd new compute resources.

\n", "bases": "aiochris.client.authed.AuthenticatedClient[aiochris.models.collection_links.AdminCollectionLinks, 'ChrisAdminClient']"}, "aiochris.client.admin.ChrisAdminClient.register_plugin_from_store": {"fullname": "aiochris.client.admin.ChrisAdminClient.register_plugin_from_store", "modulename": "aiochris.client.admin", "qualname": "ChrisAdminClient.register_plugin_from_store", "kind": "function", "doc": "

Register a plugin from a ChRIS Store.

\n", "signature": "(\tself,\tplugin_store_url: aiochris.types.PluginUrl,\tcompute_names: Iterable[aiochris.types.ComputeResourceName]) -> aiochris.models.logged_in.Plugin:", "funcdef": "async def"}, "aiochris.client.admin.ChrisAdminClient.add_plugin": {"fullname": "aiochris.client.admin.ChrisAdminClient.add_plugin", "modulename": "aiochris.client.admin", "qualname": "ChrisAdminClient.add_plugin", "kind": "function", "doc": "

Add a plugin to CUBE.

\n\n
Examples
\n\n
\n
cmd = ['docker', 'run', '--rm', 'fnndsc/pl-mri-preview', 'chris_plugin_info']\noutput = subprocess.check_output(cmd, text=True)\ndesc = json.loads(output)\ndesc['name'] = 'pl-mri-preview'\ndesc['public_repo'] = 'https://github.com/FNNDSC/pl-mri-preview'\ndesc['dock_image'] = 'fnndsc/pl-mri-preview'\n\nawait chris_admin.add_plugin(plugin_description=desc, compute_resources='host')\n
\n
\n\n

The example above is just for show. It's not a good example for several reasons:

\n\n
    \n
  • Calls blocking function subprocess.check_output in asynchronous context
    • \n
  • It is preferred to use a versioned string for dock_image
    • \n
  • host compute environment is not guaranteed to exist. Instead, you could\ncall aiochris.client.authed.AuthenticatedClient.search_compute_resources\nor aiochris.client.authed.AuthenticatedClient.get_all_compute_resources:
    • \n
\n\n
\n
all_computes = await chris_admin.get_all_compute_resources()\nawait chris_admin.add_plugin(plugin_description=desc, compute_resources=all_computes)\n
\n
\n\n
Parameters
\n\n
    \n
  • plugin_description (str | dict):\nJSON description of a plugin.\nspec
    • \n
  • compute_resources: Compute resources to register the plugin to. Value can be either a comma-separated str of names,\na aiochris.models.public.ComputeResource, a sequence of aiochris.models.public.ComputeResource,\nor a sequence of compute resource names as str.
    • \n
\n", "signature": "(\tself,\tplugin_description: str | dict,\tcompute_resources: Union[str, aiochris.models.public.ComputeResource, Iterable[Union[aiochris.models.public.ComputeResource, aiochris.types.ComputeResourceName]]]) -> aiochris.models.logged_in.Plugin:", "funcdef": "async def"}, "aiochris.client.admin.ChrisAdminClient.create_compute_resource": {"fullname": "aiochris.client.admin.ChrisAdminClient.create_compute_resource", "modulename": "aiochris.client.admin", "qualname": "ChrisAdminClient.create_compute_resource", "kind": "function", "doc": "

Define a new compute resource.

\n", "signature": "(\tself,\tname: Union[str, aiochris.types.ComputeResourceName],\tcompute_url: Union[str, aiochris.types.PfconUrl],\tcompute_user: str,\tcompute_password: str,\tcompute_innetwork: bool = None,\tdescription: str = None,\tcompute_auth_url: str = None,\tcompute_auth_token: str = None,\tmax_job_exec_seconds: str = None) -> aiochris.models.public.ComputeResource:", "funcdef": "async def"}, "aiochris.client.anon": {"fullname": "aiochris.client.anon", "modulename": "aiochris.client.anon", "kind": "module", "doc": "

\n"}, "aiochris.client.anon.AnonChrisClient": {"fullname": "aiochris.client.anon.AnonChrisClient", "modulename": "aiochris.client.anon", "qualname": "AnonChrisClient", "kind": "class", "doc": "

An anonymous ChRIS client. It has access to read-only GET resources,\nsuch as being able to search for plugins.

\n", "bases": "aiochris.client.base.BaseChrisClient[aiochris.models.collection_links.AnonymousCollectionLinks, 'AnonChrisClient']"}, "aiochris.client.anon.AnonChrisClient.from_url": {"fullname": "aiochris.client.anon.AnonChrisClient.from_url", "modulename": "aiochris.client.anon", "qualname": "AnonChrisClient.from_url", "kind": "function", "doc": "

Create an anonymous client.

\n\n

See aiochris.client.base.BaseChrisClient.new for parameter documentation.

\n", "signature": "(\tcls,\turl: str,\tmax_search_requests: int = 100,\tconnector: Optional[aiohttp.connector.BaseConnector] = None,\tconnector_owner: bool = True) -> aiochris.client.anon.AnonChrisClient:", "funcdef": "async def"}, "aiochris.client.anon.AnonChrisClient.search_plugins": {"fullname": "aiochris.client.anon.AnonChrisClient.search_plugins", "modulename": "aiochris.client.anon", "qualname": "AnonChrisClient.search_plugins", "kind": "function", "doc": "

Search for plugins.

\n\n

Since this client is not logged in, you cannot create plugin instances using this client.

\n", "signature": "(\tself,\t**query) -> aiochris.util.search.Search[aiochris.models.public.PublicPlugin]:", "funcdef": "def"}, "aiochris.client.authed": {"fullname": "aiochris.client.authed", "modulename": "aiochris.client.authed", "kind": "module", "doc": "

\n"}, "aiochris.client.authed.AuthenticatedClient": {"fullname": "aiochris.client.authed.AuthenticatedClient", "modulename": "aiochris.client.authed", "qualname": "AuthenticatedClient", "kind": "class", "doc": "

An authenticated ChRIS client.

\n", "bases": "aiochris.client.base.BaseChrisClient[~L, ~CSelf], typing.Generic[~L, ~CSelf], abc.ABC"}, "aiochris.client.authed.AuthenticatedClient.from_login": {"fullname": "aiochris.client.authed.AuthenticatedClient.from_login", "modulename": "aiochris.client.authed", "qualname": "AuthenticatedClient.from_login", "kind": "function", "doc": "

Get authentication token using username and password, then construct the client.

\n\n

See aiochris.client.base.BaseChrisClient.new for parameter documentation.

\n", "signature": "(\tcls,\turl: Union[str, aiochris.types.ChrisURL],\tusername: Union[str, aiochris.types.Username],\tpassword: Union[str, aiochris.types.Password],\tmax_search_requests: int = 100,\tconnector: Optional[aiohttp.connector.TCPConnector] = None,\tconnector_owner: bool = True) -> ~CSelf:", "funcdef": "async def"}, "aiochris.client.authed.AuthenticatedClient.from_token": {"fullname": "aiochris.client.authed.AuthenticatedClient.from_token", "modulename": "aiochris.client.authed", "qualname": "AuthenticatedClient.from_token", "kind": "function", "doc": "

Construct an authenticated client using the given token.

\n\n

See aiochris.client.base.BaseChrisClient.new for parameter documentation.

\n", "signature": "(\tcls,\turl: Union[str, aiochris.types.ChrisURL],\ttoken: str,\tmax_search_requests: int = 100,\tconnector: Optional[aiohttp.connector.TCPConnector] = None,\tconnector_owner: Optional[bool] = True) -> ~CSelf:", "funcdef": "async def"}, "aiochris.client.authed.AuthenticatedClient.from_chrs": {"fullname": "aiochris.client.authed.AuthenticatedClient.from_chrs", "modulename": "aiochris.client.authed", "qualname": "AuthenticatedClient.from_chrs", "kind": "function", "doc": "

Log in using chrs.\nChRIS logins can be saved with the chrs login command.

\n\n

In order to call this function, aiochris must be installed with the extras from-chrs.\nUsing pip:

\n\n
\n
pip install aiochris[chrs]\n
\n
\n\n

Or using Poetry:

\n\n
\n
poetry add -E chrs aiochris\n
\n
\n\n

from_chrs makes it easy to use aiochris in Jupyter Notebook or IPython,\nespecially since it saves you from having to write your password in a notebook\nthat you want to share with others. Both Jupyter and IPython support top-level await.

\n\n
\n
from aiochris import ChrisClient, acollect\n\nchris = await ChrisClient.from_chrs()\nawait acollect(chris.search_plugins())\n
\n
\n\n

When from_chrs is called with no parameters, it uses the \"preferred account\"\ni.e. the most recently added account, the same _ChRIS_ account and server as\nchrs would when called without options. The \"preferred account\" can be changed\nby running chrs switch.

\n", "signature": "(\tcls,\turl: Union[str, aiochris.types.ChrisURL, NoneType] = None,\tusername: Union[str, aiochris.types.Username, NoneType] = None,\tmax_search_requests: int = 100,\tconnector: Optional[aiohttp.connector.TCPConnector] = None,\tconnector_owner: Optional[bool] = True,\tconfig_file: pathlib.Path = PosixPath('~/.config/chrs/login.toml')) -> ~CSelf:", "funcdef": "async def"}, "aiochris.client.authed.AuthenticatedClient.search_feeds": {"fullname": "aiochris.client.authed.AuthenticatedClient.search_feeds", "modulename": "aiochris.client.authed", "qualname": "AuthenticatedClient.search_feeds", "kind": "function", "doc": "

Search for feeds.

\n", "signature": "(\tself,\t**query) -> aiochris.util.search.Search[aiochris.models.logged_in.Feed]:", "funcdef": "def"}, "aiochris.client.authed.AuthenticatedClient.search_plugins": {"fullname": "aiochris.client.authed.AuthenticatedClient.search_plugins", "modulename": "aiochris.client.authed", "qualname": "AuthenticatedClient.search_plugins", "kind": "function", "doc": "

Search for plugins.

\n", "signature": "(\tself,\t**query) -> aiochris.util.search.Search[aiochris.models.logged_in.Plugin]:", "funcdef": "def"}, "aiochris.client.authed.AuthenticatedClient.plugin_instances": {"fullname": "aiochris.client.authed.AuthenticatedClient.plugin_instances", "modulename": "aiochris.client.authed", "qualname": "AuthenticatedClient.plugin_instances", "kind": "function", "doc": "

Search for plugin instances.

\n", "signature": "(\tself,\t**query) -> aiochris.util.search.Search[aiochris.models.logged_in.PluginInstance]:", "funcdef": "def"}, "aiochris.client.authed.AuthenticatedClient.upload_file": {"fullname": "aiochris.client.authed.AuthenticatedClient.upload_file", "modulename": "aiochris.client.authed", "qualname": "AuthenticatedClient.upload_file", "kind": "function", "doc": "

Upload a local file to ChRIS.

\n\n
\n\n
Uses non-async code.
\n\n

The file is read using non-async code.\nPerformance will suffer with large files and hard drives.\nSee aiolibs/aiohttp#7174

\n\n
\n\n
Examples
\n\n

Upload a single file:

\n\n
\n
aiochris = await ChrisClient.from_login(\n    username='chris',\n    password='chris1234',\n    url='https://cube.chrisproject.org/api/v1/'\n)\nfile = await aiochris.upload_file("./my_data.dat", 'dir/my_data.dat')\nassert file.fname == 'aiochris/uploads/dir/my_data.dat'\n
\n
\n\n

Upload (in parallel) all *.txt files in a directory\n'incoming' to aiochris/uploads/big_folder:

\n\n
\n
upload_jobs = (\n    aiochris.upload_file(p, f'big_folder/{p}')\n    for p in Path('incoming')\n)\nawait asyncio.gather(upload_jobs)\n
\n
\n\n
Parameters
\n\n
    \n
  • local_file: Path of an existing local file to upload.
    • \n
  • upload_path: A subpath of {username}/uploads/ where to upload the file to in CUBE
    • \n
\n", "signature": "(\tself,\tlocal_file: str | os.PathLike,\tupload_path: str) -> aiochris.models.logged_in.File:", "funcdef": "async def"}, "aiochris.client.authed.AuthenticatedClient.user": {"fullname": "aiochris.client.authed.AuthenticatedClient.user", "modulename": "aiochris.client.authed", "qualname": "AuthenticatedClient.user", "kind": "function", "doc": "

Gets the user's information.

\n", "signature": "(self) -> aiochris.models.logged_in.User:", "funcdef": "async def"}, "aiochris.client.authed.AuthenticatedClient.username": {"fullname": "aiochris.client.authed.AuthenticatedClient.username", "modulename": "aiochris.client.authed", "qualname": "AuthenticatedClient.username", "kind": "function", "doc": "

Gets the username. In contrast to self.user, this method will use a cached API call.

\n", "signature": "(self) -> aiochris.types.Username:", "funcdef": "async def"}, "aiochris.client.authed.AuthenticatedClient.search_compute_resources": {"fullname": "aiochris.client.authed.AuthenticatedClient.search_compute_resources", "modulename": "aiochris.client.authed", "qualname": "AuthenticatedClient.search_compute_resources", "kind": "function", "doc": "

Search for existing compute resources.

\n\n
See also
\n\n

get_all_compute_resources :

\n", "signature": "(\tself,\t**query) -> aiochris.util.search.Search[aiochris.models.public.ComputeResource]:", "funcdef": "def"}, "aiochris.client.authed.AuthenticatedClient.get_all_compute_resources": {"fullname": "aiochris.client.authed.AuthenticatedClient.get_all_compute_resources", "modulename": "aiochris.client.authed", "qualname": "AuthenticatedClient.get_all_compute_resources", "kind": "function", "doc": "

Get all compute resources.

\n\n

This method exists for convenience.\nThe number of compute resources of a CUBE is typically small so it's ok.

\n\n
See also
\n\n

search_compute_resources :

\n", "signature": "(self) -> Sequence[aiochris.models.public.ComputeResource]:", "funcdef": "async def"}, "aiochris.client.authed.AuthenticatedClient.search_pacsfiles": {"fullname": "aiochris.client.authed.AuthenticatedClient.search_pacsfiles", "modulename": "aiochris.client.authed", "qualname": "AuthenticatedClient.search_pacsfiles", "kind": "function", "doc": "

Search for PACS files.

\n", "signature": "(\tself,\t**query) -> aiochris.util.search.Search[aiochris.models.logged_in.PACSFile]:", "funcdef": "def"}, "aiochris.client.base": {"fullname": "aiochris.client.base", "modulename": "aiochris.client.base", "kind": "module", "doc": "

\n"}, "aiochris.client.base.BaseChrisClient": {"fullname": "aiochris.client.base.BaseChrisClient", "modulename": "aiochris.client.base", "qualname": "BaseChrisClient", "kind": "class", "doc": "

Provides the implementation for most of the read-only GET resources of ChRIS\nand functions related to the client object's own usage.

\n", "bases": "typing.Generic[~L, ~CSelf], aiochris.link.collection_client.CollectionJsonApiClient[~L], typing.AsyncContextManager[~CSelf], abc.ABC"}, "aiochris.client.base.BaseChrisClient.new": {"fullname": "aiochris.client.base.BaseChrisClient.new", "modulename": "aiochris.client.base", "qualname": "BaseChrisClient.new", "kind": "function", "doc": "

A constructor which creates the session for the BaseChrisClient\nand makes an initial request to populate collection_links.

\n\n
Parameters
\n\n
    \n
  • url: ChRIS backend url, e.g. \"https://cube.chrisproject.org/api/v1/\"
    • \n
  • max_search_requests: Maximum number of HTTP requests to make while retrieving items from a\npaginated endpoint before raising aiochris.util.search.TooMuchPaginationError.\nUse max_search_requests=-1 to allow for \"infinite\" pagination\n(well, you're still limited by Python's stack).
    • \n
  • connector: aiohttp.BaseConnector to use.\nIf creating multiple client objects in the same program,\nreusing connectors between them is more efficient.
    • \n
  • connector_owner: If True, this client will close its aiohttp.BaseConnector
    • \n
  • session_modifier: Called to mutate the created aiohttp.ClientSession for the object.\nIf the client requires authentication, define session_modifier\nto add authentication headers to the session.
    • \n
\n", "signature": "(\tcls,\turl: str,\tmax_search_requests: int = 100,\tconnector: Optional[aiohttp.connector.BaseConnector] = None,\tconnector_owner: bool = True,\tsession_modifier: Optional[Callable[[aiohttp.client.ClientSession], NoneType]] = None) -> ~CSelf:", "funcdef": "async def"}, "aiochris.client.base.BaseChrisClient.close": {"fullname": "aiochris.client.base.BaseChrisClient.close", "modulename": "aiochris.client.base", "qualname": "BaseChrisClient.close", "kind": "function", "doc": "

Close the HTTP session used by this client.

\n", "signature": "(self):", "funcdef": "async def"}, "aiochris.client.base.BaseChrisClient.search_plugins": {"fullname": "aiochris.client.base.BaseChrisClient.search_plugins", "modulename": "aiochris.client.base", "qualname": "BaseChrisClient.search_plugins", "kind": "function", "doc": "

Search for plugins.

\n", "signature": "(\tself,\t**query) -> aiochris.util.search.Search[aiochris.models.public.PublicPlugin]:", "funcdef": "def"}, "aiochris.client.from_chrs": {"fullname": "aiochris.client.from_chrs", "modulename": "aiochris.client.from_chrs", "kind": "module", "doc": "

Interoperability with chrs version 0.2.4.

\n\n

The functions of this module uses dynamic importing of extras from the chrs group.

\n"}, "aiochris.client.from_chrs.StoredToken": {"fullname": "aiochris.client.from_chrs.StoredToken", "modulename": "aiochris.client.from_chrs", "qualname": "StoredToken", "kind": "class", "doc": "

https://github.com/FNNDSC/chrs/blob/v0.2.4/chrs/src/login/tokenstore.rs#L18-L24

\n"}, "aiochris.client.from_chrs.StoredToken.__init__": {"fullname": "aiochris.client.from_chrs.StoredToken.__init__", "modulename": "aiochris.client.from_chrs", "qualname": "StoredToken.__init__", "kind": "function", "doc": "

\n", "signature": "(store: Literal['Text', 'Keyring'], value: Optional[str] = None)"}, "aiochris.client.from_chrs.ChrsLogin": {"fullname": "aiochris.client.from_chrs.ChrsLogin", "modulename": "aiochris.client.from_chrs", "qualname": "ChrsLogin", "kind": "class", "doc": "

A login saved by chrs.

\n\n

https://github.com/FNNDSC/chrs/blob/v0.2.4/chrs/src/login/tokenstore.rs#L18-L34

\n"}, "aiochris.client.from_chrs.ChrsLogin.__init__": {"fullname": "aiochris.client.from_chrs.ChrsLogin.__init__", "modulename": "aiochris.client.from_chrs", "qualname": "ChrsLogin.__init__", "kind": "function", "doc": "

\n", "signature": "(\taddress: aiochris.types.ChrisURL,\tusername: aiochris.types.Username,\tstore: aiochris.client.from_chrs.StoredToken)"}, "aiochris.client.from_chrs.ChrsLogin.token": {"fullname": "aiochris.client.from_chrs.ChrsLogin.token", "modulename": "aiochris.client.from_chrs", "qualname": "ChrsLogin.token", "kind": "function", "doc": "

\n", "signature": "(self) -> str:", "funcdef": "def"}, "aiochris.client.from_chrs.ChrsLogin.is_for": {"fullname": "aiochris.client.from_chrs.ChrsLogin.is_for", "modulename": "aiochris.client.from_chrs", "qualname": "ChrsLogin.is_for", "kind": "function", "doc": "

Returns True if this login is for the specified _ChRIS_ user account.

\n", "signature": "(\tself,\taddress: Optional[aiochris.types.ChrisURL],\tusername: Optional[aiochris.types.Username]) -> bool:", "funcdef": "def"}, "aiochris.client.from_chrs.ChrsLogin.to_keyring_username": {"fullname": "aiochris.client.from_chrs.ChrsLogin.to_keyring_username", "modulename": "aiochris.client.from_chrs", "qualname": "ChrsLogin.to_keyring_username", "kind": "function", "doc": "

Produce the username for this login in the keyring.

\n\n

https://github.com/FNNDSC/chrs/blob/v0.2.4/chrs/src/login/tokenstore.rs#L3

\n", "signature": "(self) -> str:", "funcdef": "def"}, "aiochris.client.from_chrs.ChrsLogins": {"fullname": "aiochris.client.from_chrs.ChrsLogins", "modulename": "aiochris.client.from_chrs", "qualname": "ChrsLogins", "kind": "class", "doc": "

Logins saved by chrs.

\n\n

https://github.com/FNNDSC/chrs/blob/v0.2.4/chrs/src/login/saved.rs#L18-L22

\n"}, "aiochris.client.from_chrs.ChrsLogins.__init__": {"fullname": "aiochris.client.from_chrs.ChrsLogins.__init__", "modulename": "aiochris.client.from_chrs", "qualname": "ChrsLogins.__init__", "kind": "function", "doc": "

\n", "signature": "(cubes: list[aiochris.client.from_chrs.ChrsLogin])"}, "aiochris.client.from_chrs.ChrsLogins.cubes": {"fullname": "aiochris.client.from_chrs.ChrsLogins.cubes", "modulename": "aiochris.client.from_chrs", "qualname": "ChrsLogins.cubes", "kind": "variable", "doc": "

Saved logins in reverse order of preference.

\n", "annotation": ": list[aiochris.client.from_chrs.ChrsLogin]"}, "aiochris.client.from_chrs.ChrsLogins.load": {"fullname": "aiochris.client.from_chrs.ChrsLogins.load", "modulename": "aiochris.client.from_chrs", "qualname": "ChrsLogins.load", "kind": "function", "doc": "

\n", "signature": "(cls, path: pathlib.Path) -> aiochris.client.from_chrs.ChrsLogins:", "funcdef": "def"}, "aiochris.client.from_chrs.ChrsLogins.get_token_for": {"fullname": "aiochris.client.from_chrs.ChrsLogins.get_token_for", "modulename": "aiochris.client.from_chrs", "qualname": "ChrsLogins.get_token_for", "kind": "function", "doc": "

Get token for a login.

\n", "signature": "(\tself,\taddress: Union[str, aiochris.types.ChrisURL, NoneType] = None,\tusername: Union[str, aiochris.types.Username, NoneType] = None) -> Optional[tuple[aiochris.types.ChrisURL, str]]:", "funcdef": "def"}, "aiochris.client.from_chrs.ChrsKeyringError": {"fullname": "aiochris.client.from_chrs.ChrsKeyringError", "modulename": "aiochris.client.from_chrs", "qualname": "ChrsKeyringError", "kind": "class", "doc": "

Error interacting with Keyring.

\n", "bases": "builtins.Exception"}, "aiochris.client.normal": {"fullname": "aiochris.client.normal", "modulename": "aiochris.client.normal", "kind": "module", "doc": "

\n"}, "aiochris.client.normal.ChrisClient": {"fullname": "aiochris.client.normal.ChrisClient", "modulename": "aiochris.client.normal", "qualname": "ChrisClient", "kind": "class", "doc": "

A normal user ChRIS client, who may upload files and create plugin instances.

\n", "bases": "aiochris.client.authed.AuthenticatedClient[aiochris.models.collection_links.CollectionLinks, 'ChrisClient']"}, "aiochris.client.normal.ChrisClient.create_user": {"fullname": "aiochris.client.normal.ChrisClient.create_user", "modulename": "aiochris.client.normal", "qualname": "ChrisClient.create_user", "kind": "function", "doc": "

\n", "signature": "(\tcls,\turl: Union[aiochris.types.ChrisURL, str],\tusername: Union[aiochris.types.Username, str],\tpassword: Union[aiochris.types.Password, str],\temail: str,\tsession: Optional[aiohttp.client.ClientSession] = None) -> aiochris.models.data.UserData:", "funcdef": "async def"}, "aiochris.errors": {"fullname": "aiochris.errors", "modulename": "aiochris.errors", "kind": "module", "doc": "

\n"}, "aiochris.errors.raise_for_status": {"fullname": "aiochris.errors.raise_for_status", "modulename": "aiochris.errors", "qualname": "raise_for_status", "kind": "function", "doc": "

Raises custom exceptions.

\n", "signature": "(res: aiohttp.client_reqrep.ClientResponse) -> None:", "funcdef": "async def"}, "aiochris.errors.BaseClientError": {"fullname": "aiochris.errors.BaseClientError", "modulename": "aiochris.errors", "qualname": "BaseClientError", "kind": "class", "doc": "

Common base class for all non-exit exceptions.

\n", "bases": "builtins.Exception"}, "aiochris.errors.ResponseError": {"fullname": "aiochris.errors.ResponseError", "modulename": "aiochris.errors", "qualname": "ResponseError", "kind": "class", "doc": "

Common base class for all non-exit exceptions.

\n", "bases": "BaseClientError"}, "aiochris.errors.BadRequestError": {"fullname": "aiochris.errors.BadRequestError", "modulename": "aiochris.errors", "qualname": "BadRequestError", "kind": "class", "doc": "

Common base class for all non-exit exceptions.

\n", "bases": "ResponseError"}, "aiochris.errors.InternalServerError": {"fullname": "aiochris.errors.InternalServerError", "modulename": "aiochris.errors", "qualname": "InternalServerError", "kind": "class", "doc": "

Common base class for all non-exit exceptions.

\n", "bases": "ResponseError"}, "aiochris.errors.IncorrectLoginError": {"fullname": "aiochris.errors.IncorrectLoginError", "modulename": "aiochris.errors", "qualname": "IncorrectLoginError", "kind": "class", "doc": "

Common base class for all non-exit exceptions.

\n", "bases": "BaseClientError"}, "aiochris.errors.NonsenseResponseError": {"fullname": "aiochris.errors.NonsenseResponseError", "modulename": "aiochris.errors", "qualname": "NonsenseResponseError", "kind": "class", "doc": "

CUBE returned data which does not make sense.

\n", "bases": "ResponseError"}, "aiochris.models": {"fullname": "aiochris.models", "modulename": "aiochris.models", "kind": "module", "doc": "

\n"}, "aiochris.models.collection_links": {"fullname": "aiochris.models.collection_links", "modulename": "aiochris.models.collection_links", "kind": "module", "doc": "

\n"}, "aiochris.models.collection_links.AbstractCollectionLinks": {"fullname": "aiochris.models.collection_links.AbstractCollectionLinks", "modulename": "aiochris.models.collection_links", "qualname": "AbstractCollectionLinks", "kind": "class", "doc": "

\n"}, "aiochris.models.collection_links.AbstractCollectionLinks.__init__": {"fullname": "aiochris.models.collection_links.AbstractCollectionLinks.__init__", "modulename": "aiochris.models.collection_links", "qualname": "AbstractCollectionLinks.__init__", "kind": "function", "doc": "

\n", "signature": "()"}, "aiochris.models.collection_links.AbstractCollectionLinks.has_field": {"fullname": "aiochris.models.collection_links.AbstractCollectionLinks.has_field", "modulename": "aiochris.models.collection_links", "qualname": "AbstractCollectionLinks.has_field", "kind": "function", "doc": "

\n", "signature": "(cls, field_name: str) -> bool:", "funcdef": "def"}, "aiochris.models.collection_links.AbstractCollectionLinks.get": {"fullname": "aiochris.models.collection_links.AbstractCollectionLinks.get", "modulename": "aiochris.models.collection_links", "qualname": "AbstractCollectionLinks.get", "kind": "function", "doc": "

\n", "signature": "(self, collection_name: str) -> str:", "funcdef": "def"}, "aiochris.models.collection_links.AnonymousCollectionLinks": {"fullname": "aiochris.models.collection_links.AnonymousCollectionLinks", "modulename": "aiochris.models.collection_links", "qualname": "AnonymousCollectionLinks", "kind": "class", "doc": "

\n", "bases": "AbstractCollectionLinks"}, "aiochris.models.collection_links.AnonymousCollectionLinks.__init__": {"fullname": "aiochris.models.collection_links.AnonymousCollectionLinks.__init__", "modulename": "aiochris.models.collection_links", "qualname": "AnonymousCollectionLinks.__init__", "kind": "function", "doc": "

\n", "signature": "(\tchrisinstance: aiochris.types.ApiUrl,\tcompute_resources: aiochris.types.ApiUrl,\tplugin_metas: aiochris.types.ApiUrl,\tplugins: aiochris.types.ApiUrl,\tplugin_instances: aiochris.types.ApiUrl,\tpipelines: aiochris.types.ApiUrl,\tpipeline_instances: aiochris.types.ApiUrl,\tworkflows: aiochris.types.ApiUrl,\ttags: aiochris.types.ApiUrl,\tpacsfiles: aiochris.types.ApiUrl,\tservicefiles: aiochris.types.ApiUrl,\tfilebrowser: aiochris.types.ApiUrl)"}, "aiochris.models.collection_links.CollectionLinks": {"fullname": "aiochris.models.collection_links.CollectionLinks", "modulename": "aiochris.models.collection_links", "qualname": "CollectionLinks", "kind": "class", "doc": "

\n", "bases": "AnonymousCollectionLinks"}, "aiochris.models.collection_links.CollectionLinks.__init__": {"fullname": "aiochris.models.collection_links.CollectionLinks.__init__", "modulename": "aiochris.models.collection_links", "qualname": "CollectionLinks.__init__", "kind": "function", "doc": "

\n", "signature": "(\tchrisinstance: aiochris.types.ApiUrl,\tcompute_resources: aiochris.types.ApiUrl,\tplugin_metas: aiochris.types.ApiUrl,\tplugins: aiochris.types.ApiUrl,\tplugin_instances: aiochris.types.ApiUrl,\tpipelines: aiochris.types.ApiUrl,\tpipeline_instances: aiochris.types.ApiUrl,\tworkflows: aiochris.types.ApiUrl,\ttags: aiochris.types.ApiUrl,\tpacsfiles: aiochris.types.ApiUrl,\tservicefiles: aiochris.types.ApiUrl,\tfilebrowser: aiochris.types.ApiUrl,\tuser: aiochris.types.UserUrl,\tuserfiles: Optional[aiochris.types.ApiUrl],\tuploadedfiles: Optional[aiochris.types.ApiUrl])"}, "aiochris.models.collection_links.AdminCollectionLinks": {"fullname": "aiochris.models.collection_links.AdminCollectionLinks", "modulename": "aiochris.models.collection_links", "qualname": "AdminCollectionLinks", "kind": "class", "doc": "

\n", "bases": "CollectionLinks"}, "aiochris.models.collection_links.AdminCollectionLinks.__init__": {"fullname": "aiochris.models.collection_links.AdminCollectionLinks.__init__", "modulename": "aiochris.models.collection_links", "qualname": "AdminCollectionLinks.__init__", "kind": "function", "doc": "

\n", "signature": "(\tchrisinstance: aiochris.types.ApiUrl,\tcompute_resources: aiochris.types.ApiUrl,\tplugin_metas: aiochris.types.ApiUrl,\tplugins: aiochris.types.ApiUrl,\tplugin_instances: aiochris.types.ApiUrl,\tpipelines: aiochris.types.ApiUrl,\tpipeline_instances: aiochris.types.ApiUrl,\tworkflows: aiochris.types.ApiUrl,\ttags: aiochris.types.ApiUrl,\tpacsfiles: aiochris.types.ApiUrl,\tservicefiles: aiochris.types.ApiUrl,\tfilebrowser: aiochris.types.ApiUrl,\tuser: aiochris.types.UserUrl,\tuserfiles: Optional[aiochris.types.ApiUrl],\tuploadedfiles: Optional[aiochris.types.ApiUrl],\tadmin: aiochris.types.AdminUrl)"}, "aiochris.models.collection_links.AdminApiCollectionLinks": {"fullname": "aiochris.models.collection_links.AdminApiCollectionLinks", "modulename": "aiochris.models.collection_links", "qualname": "AdminApiCollectionLinks", "kind": "class", "doc": "

\n", "bases": "AbstractCollectionLinks"}, "aiochris.models.collection_links.AdminApiCollectionLinks.__init__": {"fullname": "aiochris.models.collection_links.AdminApiCollectionLinks.__init__", "modulename": "aiochris.models.collection_links", "qualname": "AdminApiCollectionLinks.__init__", "kind": "function", "doc": "

\n", "signature": "(compute_resources: aiochris.types.ApiUrl)"}, "aiochris.models.data": {"fullname": "aiochris.models.data", "modulename": "aiochris.models.data", "kind": "module", "doc": "

Dataclasses describing objects returned from CUBE.

\n\n

These classes are extended in the modules aiochris.models.logged_in\nand aiochris.models.public with methods to get objects from links.

\n"}, "aiochris.models.data.UserData": {"fullname": "aiochris.models.data.UserData", "modulename": "aiochris.models.data", "qualname": "UserData", "kind": "class", "doc": "

A CUBE user.

\n"}, "aiochris.models.data.UserData.__init__": {"fullname": "aiochris.models.data.UserData.__init__", "modulename": "aiochris.models.data", "qualname": "UserData.__init__", "kind": "function", "doc": "

\n", "signature": "(\turl: aiochris.types.UserUrl,\tid: aiochris.types.UserId,\tusername: aiochris.types.Username,\temail: str)"}, "aiochris.models.data.PluginInstanceData": {"fullname": "aiochris.models.data.PluginInstanceData", "modulename": "aiochris.models.data", "qualname": "PluginInstanceData", "kind": "class", "doc": "

A plugin instance in _ChRIS_ is a computing job, i.e. an attempt to run\na computation (a non-interactive command-line app) to produce data.

\n", "bases": "aiochris.link.linked.LinkedModel"}, "aiochris.models.data.PluginInstanceData.__init__": {"fullname": "aiochris.models.data.PluginInstanceData.__init__", "modulename": "aiochris.models.data", "qualname": "PluginInstanceData.__init__", "kind": "function", "doc": "

\n", "signature": "(\ts: aiohttp.client.ClientSession,\tmax_search_requests: int,\turl: aiochris.types.PluginInstanceUrl,\tid: aiochris.types.PluginInstanceId,\ttitle: str,\tcompute_resource_name: aiochris.types.ComputeResourceName,\tplugin_id: aiochris.types.PluginId,\tplugin_name: aiochris.types.PluginName,\tplugin_version: aiochris.types.PluginVersion,\tplugin_type: aiochris.enums.PluginType,\tpipeline_inst: Optional[int],\tfeed_id: aiochris.types.FeedId,\tstart_date: datetime.datetime,\tend_date: datetime.datetime,\toutput_path: aiochris.types.CubeFilePath,\tstatus: aiochris.enums.Status,\tsummary: str,\traw: str,\towner_username: aiochris.types.Username,\tcpu_limit: int,\tmemory_limit: int,\tnumber_of_workers: int,\tgpu_limit: int,\terror_code: aiochris.types.CUBEErrorCode,\tprevious: Optional[aiochris.types.PluginInstanceUrl],\tfeed: aiochris.types.FeedUrl,\tplugin: aiochris.types.PluginUrl,\tdescendants: aiochris.types.DescendantsUrl,\tfiles: aiochris.types.FilesUrl,\tparameters: aiochris.types.PluginInstanceParametersUrl,\tcompute_resource: aiochris.types.ComputeResourceUrl,\tsplits: aiochris.types.SplitsUrl,\tprevious_id: Optional[int] = None,\tsize: Optional[int] = None,\ttemplate: Optional[dict] = None)"}, "aiochris.models.data.PluginInstanceData.previous_id": {"fullname": "aiochris.models.data.PluginInstanceData.previous_id", "modulename": "aiochris.models.data", "qualname": "PluginInstanceData.previous_id", "kind": "variable", "doc": "

FS plugins will not produce a previous_id value\n(even though they will return \"previous\": null)

\n", "annotation": ": Optional[int]", "default_value": " = None"}, "aiochris.models.data.PluginInstanceData.size": {"fullname": "aiochris.models.data.PluginInstanceData.size", "modulename": "aiochris.models.data", "qualname": "PluginInstanceData.size", "kind": "variable", "doc": "

IDK what it is the size of.

\n\n

This field shows up when the plugin instance is maybe done,\nbut not when the plugin instance is created.

\n", "annotation": ": Optional[int]", "default_value": " = None"}, "aiochris.models.data.PluginInstanceData.template": {"fullname": "aiochris.models.data.PluginInstanceData.template", "modulename": "aiochris.models.data", "qualname": "PluginInstanceData.template", "kind": "variable", "doc": "

Present only when getting a plugin instance.

\n", "annotation": ": Optional[dict]", "default_value": " = None"}, "aiochris.models.data.FeedData": {"fullname": "aiochris.models.data.FeedData", "modulename": "aiochris.models.data", "qualname": "FeedData", "kind": "class", "doc": "

\n", "bases": "aiochris.link.linked.LinkedModel"}, "aiochris.models.data.FeedData.__init__": {"fullname": "aiochris.models.data.FeedData.__init__", "modulename": "aiochris.models.data", "qualname": "FeedData.__init__", "kind": "function", "doc": "

\n", "signature": "(\ts: aiohttp.client.ClientSession,\tmax_search_requests: int,\turl: aiochris.types.FeedUrl,\tid: aiochris.types.FeedId,\tcreation_date: datetime.datetime,\tmodification_date: datetime.datetime,\tname: str,\tcreator_username: aiochris.types.Username,\tcreated_jobs: int,\twaiting_jobs: int,\tscheduled_jobs: int,\tstarted_jobs: int,\tregistering_jobs: int,\tfinished_jobs: int,\terrored_jobs: int,\tcancelled_jobs: int,\towner: list[aiochris.types.UserUrl],\tnote: aiochris.types.NoteUrl,\ttags: aiochris.types.TagsUrl,\ttaggings: aiochris.types.TaggingsUrl,\tcomments: aiochris.types.CommentsUrl,\tfiles: aiochris.types.FilesUrl,\tplugin_instances: aiochris.types.PluginInstancesUrl)"}, "aiochris.models.data.FeedNoteData": {"fullname": "aiochris.models.data.FeedNoteData", "modulename": "aiochris.models.data", "qualname": "FeedNoteData", "kind": "class", "doc": "

\n", "bases": "aiochris.link.linked.LinkedModel"}, "aiochris.models.data.FeedNoteData.__init__": {"fullname": "aiochris.models.data.FeedNoteData.__init__", "modulename": "aiochris.models.data", "qualname": "FeedNoteData.__init__", "kind": "function", "doc": "

\n", "signature": "(\ts: aiohttp.client.ClientSession,\tmax_search_requests: int,\turl: aiochris.types.FeedUrl,\tid: aiochris.types.NoteId,\ttitle: str,\tcontent: str,\tfeed: aiochris.types.FeedUrl)"}, "aiochris.models.logged_in": {"fullname": "aiochris.models.logged_in", "modulename": "aiochris.models.logged_in", "kind": "module", "doc": "

Subclasses of classes from aiochris.models.data which are returned\nfrom an aiochris.client.authed.AuthenticatedClient.\nThese classes may have read-write functionality on the ChRIS API.

\n"}, "aiochris.models.logged_in.User": {"fullname": "aiochris.models.logged_in.User", "modulename": "aiochris.models.logged_in", "qualname": "User", "kind": "class", "doc": "

\n", "bases": "aiochris.models.data.UserData, aiochris.link.linked.LinkedModel"}, "aiochris.models.logged_in.User.__init__": {"fullname": "aiochris.models.logged_in.User.__init__", "modulename": "aiochris.models.logged_in", "qualname": "User.__init__", "kind": "function", "doc": "

\n", "signature": "(\ts: aiohttp.client.ClientSession,\tmax_search_requests: int,\turl: aiochris.types.UserUrl,\tid: aiochris.types.UserId,\tusername: aiochris.types.Username,\temail: str)"}, "aiochris.models.logged_in.File": {"fullname": "aiochris.models.logged_in.File", "modulename": "aiochris.models.logged_in", "qualname": "File", "kind": "class", "doc": "

A file in CUBE.

\n", "bases": "aiochris.link.linked.LinkedModel"}, "aiochris.models.logged_in.File.__init__": {"fullname": "aiochris.models.logged_in.File.__init__", "modulename": "aiochris.models.logged_in", "qualname": "File.__init__", "kind": "function", "doc": "

\n", "signature": "(\ts: aiohttp.client.ClientSession,\tmax_search_requests: int,\turl: str,\tfname: aiochris.types.FileFname,\tfsize: int,\tfile_resource: aiochris.types.FileResourceUrl)"}, "aiochris.models.logged_in.File.parent": {"fullname": "aiochris.models.logged_in.File.parent", "modulename": "aiochris.models.logged_in", "qualname": "File.parent", "kind": "variable", "doc": "

Get the parent (directory) of a file.

\n\n
Examples
\n\n
\n
assert file.fname == 'chris/feed_4/pl-dircopy_7/data/hello-world.txt'\nassert file.parent == 'chris/feed_4/pl-dircopy_7/data'\n
\n
\n", "annotation": ": str"}, "aiochris.models.logged_in.PACSFile": {"fullname": "aiochris.models.logged_in.PACSFile", "modulename": "aiochris.models.logged_in", "qualname": "PACSFile", "kind": "class", "doc": "

A file from a PACS server which was pushed into ChRIS.\nA PACSFile is usually a DICOM file.

\n\n

See https://github.com/FNNDSC/ChRIS_ultron_backEnd/blob/a1bf499144df79622eb3f8a459cdb80d8e34cb04/chris_backend/pacsfiles/models.py#L16-L33

\n", "bases": "File"}, "aiochris.models.logged_in.PACSFile.__init__": {"fullname": "aiochris.models.logged_in.PACSFile.__init__", "modulename": "aiochris.models.logged_in", "qualname": "PACSFile.__init__", "kind": "function", "doc": "

\n", "signature": "(\ts: aiohttp.client.ClientSession,\tmax_search_requests: int,\turl: str,\tfname: aiochris.types.FileFname,\tfsize: int,\tfile_resource: aiochris.types.FileResourceUrl,\tPatientID: str,\tPatientName: str,\tPatientBirthDate: str,\tPatientAge: int,\tPatientSex: str,\tStudyDate: str,\tAccessionNumber: str,\tModality: str,\tProtocolName: str,\tStudyInstanceUID: str,\tStudyDescription: str,\tSeriesInstanceUID: str,\tSeriesDescription: str,\tpacs_identifier: str)"}, "aiochris.models.logged_in.PluginInstance": {"fullname": "aiochris.models.logged_in.PluginInstance", "modulename": "aiochris.models.logged_in", "qualname": "PluginInstance", "kind": "class", "doc": "

\n", "bases": "aiochris.models.data.PluginInstanceData"}, "aiochris.models.logged_in.PluginInstance.__init__": {"fullname": "aiochris.models.logged_in.PluginInstance.__init__", "modulename": "aiochris.models.logged_in", "qualname": "PluginInstance.__init__", "kind": "function", "doc": "

\n", "signature": "(\ts: aiohttp.client.ClientSession,\tmax_search_requests: int,\turl: aiochris.types.PluginInstanceUrl,\tid: aiochris.types.PluginInstanceId,\ttitle: str,\tcompute_resource_name: aiochris.types.ComputeResourceName,\tplugin_id: aiochris.types.PluginId,\tplugin_name: aiochris.types.PluginName,\tplugin_version: aiochris.types.PluginVersion,\tplugin_type: aiochris.enums.PluginType,\tpipeline_inst: Optional[int],\tfeed_id: aiochris.types.FeedId,\tstart_date: datetime.datetime,\tend_date: datetime.datetime,\toutput_path: aiochris.types.CubeFilePath,\tstatus: aiochris.enums.Status,\tsummary: str,\traw: str,\towner_username: aiochris.types.Username,\tcpu_limit: int,\tmemory_limit: int,\tnumber_of_workers: int,\tgpu_limit: int,\terror_code: aiochris.types.CUBEErrorCode,\tprevious: Optional[aiochris.types.PluginInstanceUrl],\tfeed: aiochris.types.FeedUrl,\tplugin: aiochris.types.PluginUrl,\tdescendants: aiochris.types.DescendantsUrl,\tfiles: aiochris.types.FilesUrl,\tparameters: aiochris.types.PluginInstanceParametersUrl,\tcompute_resource: aiochris.types.ComputeResourceUrl,\tsplits: aiochris.types.SplitsUrl,\tprevious_id: Optional[int] = None,\tsize: Optional[int] = None,\ttemplate: Optional[dict] = None)"}, "aiochris.models.logged_in.PluginInstance.get_feed": {"fullname": "aiochris.models.logged_in.PluginInstance.get_feed", "modulename": "aiochris.models.logged_in", "qualname": "PluginInstance.get_feed", "kind": "function", "doc": "

Get the feed this plugin instance belongs to.

\n", "signature": "(self) -> aiochris.models.logged_in.Feed:", "funcdef": "async def"}, "aiochris.models.logged_in.PluginInstance.get": {"fullname": "aiochris.models.logged_in.PluginInstance.get", "modulename": "aiochris.models.logged_in", "qualname": "PluginInstance.get", "kind": "function", "doc": "

Get this plugin's state (again).

\n", "signature": "(self) -> aiochris.models.logged_in.PluginInstance:", "funcdef": "async def"}, "aiochris.models.logged_in.PluginInstance.set": {"fullname": "aiochris.models.logged_in.PluginInstance.set", "modulename": "aiochris.models.logged_in", "qualname": "PluginInstance.set", "kind": "function", "doc": "

Set the title or status of this plugin instance.

\n", "signature": "(\tself,\ttitle: Optional[str] = None,\tstatus: Optional[str] = None) -> aiochris.models.logged_in.PluginInstance:", "funcdef": "async def"}, "aiochris.models.logged_in.PluginInstance.delete": {"fullname": "aiochris.models.logged_in.PluginInstance.delete", "modulename": "aiochris.models.logged_in", "qualname": "PluginInstance.delete", "kind": "function", "doc": "

Delete this plugin instance.

\n", "signature": "(self) -> None:", "funcdef": "async def"}, "aiochris.models.logged_in.PluginInstance.wait": {"fullname": "aiochris.models.logged_in.PluginInstance.wait", "modulename": "aiochris.models.logged_in", "qualname": "PluginInstance.wait", "kind": "function", "doc": "

Wait until this plugin instance finishes (or some other desired status).

\n\n
Parameters
\n\n
    \n
  • status: Statuses to wait for
    • \n
  • timeout: Number of seconds to wait for before giving up
    • \n
  • interval: Number of seconds to wait between checking on status
    • \n
\n\n
Returns
\n\n
    \n
  • Returns the number of seconds elapsed and the last state of the plugin instance.
    • \n

  • This function will return for one of two reasons (either the plugin instance finished,):

    • \n

  • or this function timed out. Make sure you check the plugin instance's final status!

    • \n
\n", "signature": "(\tself,\tstatus: Union[aiochris.enums.Status, Sequence[aiochris.enums.Status]] = (<Status.finishedSuccessfully: 'finishedSuccessfully'>, <Status.finishedWithError: 'finishedWithError'>, <Status.cancelled: 'cancelled'>),\ttimeout: float = 300,\tinterval: float = 5) -> tuple[float, aiochris.models.logged_in.PluginInstance]:", "funcdef": "async def"}, "aiochris.models.logged_in.FeedNote": {"fullname": "aiochris.models.logged_in.FeedNote", "modulename": "aiochris.models.logged_in", "qualname": "FeedNote", "kind": "class", "doc": "

\n", "bases": "aiochris.models.data.FeedNoteData"}, "aiochris.models.logged_in.FeedNote.__init__": {"fullname": "aiochris.models.logged_in.FeedNote.__init__", "modulename": "aiochris.models.logged_in", "qualname": "FeedNote.__init__", "kind": "function", "doc": "

\n", "signature": "(\ts: aiohttp.client.ClientSession,\tmax_search_requests: int,\turl: aiochris.types.FeedUrl,\tid: aiochris.types.NoteId,\ttitle: str,\tcontent: str,\tfeed: aiochris.types.FeedUrl)"}, "aiochris.models.logged_in.FeedNote.get_feed": {"fullname": "aiochris.models.logged_in.FeedNote.get_feed", "modulename": "aiochris.models.logged_in", "qualname": "FeedNote.get_feed", "kind": "function", "doc": "

Get the feed this note belongs to.

\n", "signature": "(self) -> aiochris.models.logged_in.Feed:", "funcdef": "async def"}, "aiochris.models.logged_in.FeedNote.set": {"fullname": "aiochris.models.logged_in.FeedNote.set", "modulename": "aiochris.models.logged_in", "qualname": "FeedNote.set", "kind": "function", "doc": "

Change this note.

\n", "signature": "(\tself,\ttitle: Optional[str] = None,\tcontent: Optional[str] = None) -> aiochris.models.logged_in.FeedNote:", "funcdef": "async def"}, "aiochris.models.logged_in.Feed": {"fullname": "aiochris.models.logged_in.Feed", "modulename": "aiochris.models.logged_in", "qualname": "Feed", "kind": "class", "doc": "

A feed of a logged in user.

\n", "bases": "aiochris.models.data.FeedData"}, "aiochris.models.logged_in.Feed.__init__": {"fullname": "aiochris.models.logged_in.Feed.__init__", "modulename": "aiochris.models.logged_in", "qualname": "Feed.__init__", "kind": "function", "doc": "

\n", "signature": "(\ts: aiohttp.client.ClientSession,\tmax_search_requests: int,\turl: aiochris.types.FeedUrl,\tid: aiochris.types.FeedId,\tcreation_date: datetime.datetime,\tmodification_date: datetime.datetime,\tname: str,\tcreator_username: aiochris.types.Username,\tcreated_jobs: int,\twaiting_jobs: int,\tscheduled_jobs: int,\tstarted_jobs: int,\tregistering_jobs: int,\tfinished_jobs: int,\terrored_jobs: int,\tcancelled_jobs: int,\towner: list[aiochris.types.UserUrl],\tnote: aiochris.types.NoteUrl,\ttags: aiochris.types.TagsUrl,\ttaggings: aiochris.types.TaggingsUrl,\tcomments: aiochris.types.CommentsUrl,\tfiles: aiochris.types.FilesUrl,\tplugin_instances: aiochris.types.PluginInstancesUrl)"}, "aiochris.models.logged_in.Feed.set": {"fullname": "aiochris.models.logged_in.Feed.set", "modulename": "aiochris.models.logged_in", "qualname": "Feed.set", "kind": "function", "doc": "

Change the name or the owner of this feed.

\n\n
Parameters
\n\n
    \n
  • name: new name for this feed
    • \n
  • owner: new owner for this feed
    • \n
\n", "signature": "(\tself,\tname: Optional[str] = None,\towner: Union[str, aiochris.types.Username, NoneType] = None) -> aiochris.models.logged_in.Feed:", "funcdef": "async def"}, "aiochris.models.logged_in.Feed.get_note": {"fullname": "aiochris.models.logged_in.Feed.get_note", "modulename": "aiochris.models.logged_in", "qualname": "Feed.get_note", "kind": "function", "doc": "

\n", "signature": "(self) -> aiochris.models.logged_in.FeedNote:", "funcdef": "async def"}, "aiochris.models.logged_in.Plugin": {"fullname": "aiochris.models.logged_in.Plugin", "modulename": "aiochris.models.logged_in", "qualname": "Plugin", "kind": "class", "doc": "

A ChRIS plugin. Create a plugin instance of this plugin to run it.

\n", "bases": "aiochris.models.public.PublicPlugin"}, "aiochris.models.logged_in.Plugin.__init__": {"fullname": "aiochris.models.logged_in.Plugin.__init__", "modulename": "aiochris.models.logged_in", "qualname": "Plugin.__init__", "kind": "function", "doc": "

\n", "signature": "(\ts: aiohttp.client.ClientSession,\tmax_search_requests: int,\turl: aiochris.types.PluginUrl,\tid: aiochris.types.PluginId,\tname: aiochris.types.PluginName,\tversion: aiochris.types.PluginVersion,\tdock_image: aiochris.types.ImageTag,\tpublic_repo: str,\tcompute_resources: aiochris.types.ComputeResourceUrl,\tparameters: aiochris.types.PluginParametersUrl,\tplugin_type: aiochris.enums.PluginType,\tinstances: aiochris.types.ApiUrl)"}, "aiochris.models.logged_in.Plugin.create_instance": {"fullname": "aiochris.models.logged_in.Plugin.create_instance", "modulename": "aiochris.models.logged_in", "qualname": "Plugin.create_instance", "kind": "function", "doc": "

Create a plugin instance, i.e. \"run\" this plugin.

\n\n

Parameters common to all plugins are described below.\nNot all valid parameters are listed, since each plugin's parameters are different.\nSome plugins have required parameters too.\nTo list all possible parameters, make a GET request to the specific plugin's instances link.

\n\n
Parameters
\n\n
    \n
  • previous (chris.models.data.PluginInstanceData):\nPrevious plugin instance
    • \n
  • previous_id (int):\nPrevious plugin instance ID number (conflicts with previous)
    • \n
  • compute_resource_name (Optional[str]):\nName of compute resource to use
    • \n
  • memory_limit (Optional[str]):\nMemory limit. Format is xMi or xGi where x is an integer.
    • \n
  • cpu_limit (Optional[str]):\nCPU limit. Format is xm for x is an integer in millicores.
    • \n
  • gpu_limit (Optional[int]):\nGPU limit.
    • \n
\n", "signature": "(\tself,\tprevious: Optional[aiochris.models.logged_in.PluginInstance] = None,\t**kwargs) -> aiochris.models.logged_in.PluginInstance:", "funcdef": "async def"}, "aiochris.models.public": {"fullname": "aiochris.models.public", "modulename": "aiochris.models.public", "kind": "module", "doc": "

Read-only models for CUBE resources.

\n"}, "aiochris.models.public.ComputeResource": {"fullname": "aiochris.models.public.ComputeResource", "modulename": "aiochris.models.public", "qualname": "ComputeResource", "kind": "class", "doc": "

\n"}, "aiochris.models.public.ComputeResource.__init__": {"fullname": "aiochris.models.public.ComputeResource.__init__", "modulename": "aiochris.models.public", "qualname": "ComputeResource.__init__", "kind": "function", "doc": "

\n", "signature": "(\turl: aiochris.types.ApiUrl,\tid: aiochris.types.ComputeResourceId,\tcreation_date: str,\tmodification_date: str,\tname: aiochris.types.ComputeResourceName,\tcompute_url: aiochris.types.PfconUrl,\tcompute_auth_url: str,\tdescription: str,\tmax_job_exec_seconds: int)"}, "aiochris.models.public.PluginParameter": {"fullname": "aiochris.models.public.PluginParameter", "modulename": "aiochris.models.public", "qualname": "PluginParameter", "kind": "class", "doc": "

Information about a parameter (a command-line option/flag) of a plugin.

\n", "bases": "aiochris.link.linked.LinkedModel"}, "aiochris.models.public.PluginParameter.__init__": {"fullname": "aiochris.models.public.PluginParameter.__init__", "modulename": "aiochris.models.public", "qualname": "PluginParameter.__init__", "kind": "function", "doc": "

\n", "signature": "(\ts: aiohttp.client.ClientSession,\tmax_search_requests: int,\turl: aiochris.types.PluginParameterUrl,\tid: aiochris.types.ParameterGlobalId,\tname: aiochris.types.ParameterName,\ttype: Union[str, int, float, bool],\toptional: bool,\tdefault: Union[str, int, float, bool, NoneType],\tflag: str,\tshort_flag: str,\taction: Literal['store', 'store_true', 'store_false'],\thelp: str,\tui_exposed: bool,\tplugin: aiochris.types.PluginUrl)"}, "aiochris.models.public.PublicPlugin": {"fullname": "aiochris.models.public.PublicPlugin", "modulename": "aiochris.models.public", "qualname": "PublicPlugin", "kind": "class", "doc": "

A ChRIS plugin.

\n", "bases": "aiochris.link.linked.LinkedModel"}, "aiochris.models.public.PublicPlugin.__init__": {"fullname": "aiochris.models.public.PublicPlugin.__init__", "modulename": "aiochris.models.public", "qualname": "PublicPlugin.__init__", "kind": "function", "doc": "

\n", "signature": "(\ts: aiohttp.client.ClientSession,\tmax_search_requests: int,\turl: aiochris.types.PluginUrl,\tid: aiochris.types.PluginId,\tname: aiochris.types.PluginName,\tversion: aiochris.types.PluginVersion,\tdock_image: aiochris.types.ImageTag,\tpublic_repo: str,\tcompute_resources: aiochris.types.ComputeResourceUrl,\tparameters: aiochris.types.PluginParametersUrl,\tplugin_type: aiochris.enums.PluginType)"}, "aiochris.models.public.PublicPlugin.get_compute_resources": {"fullname": "aiochris.models.public.PublicPlugin.get_compute_resources", "modulename": "aiochris.models.public", "qualname": "PublicPlugin.get_compute_resources", "kind": "function", "doc": "

Get the compute resources this plugin is registered to.

\n", "signature": "(\tself) -> aiochris.util.search.Search[aiochris.models.public.ComputeResource]:", "funcdef": "def"}, "aiochris.models.public.PublicPlugin.get_parameters": {"fullname": "aiochris.models.public.PublicPlugin.get_parameters", "modulename": "aiochris.models.public", "qualname": "PublicPlugin.get_parameters", "kind": "function", "doc": "

Get the parameters of this plugin.

\n", "signature": "(\tself) -> aiochris.util.search.Search[aiochris.models.public.PluginParameter]:", "funcdef": "def"}, "aiochris.models.public.PublicPlugin.print_help": {"fullname": "aiochris.models.public.PublicPlugin.print_help", "modulename": "aiochris.models.public", "qualname": "PublicPlugin.print_help", "kind": "function", "doc": "

Display the help messages for this plugin's parameters.

\n", "signature": "(self, out: <class 'TextIO'> = <_io.StringIO object>) -> None:", "funcdef": "async def"}, "aiochris.types": {"fullname": "aiochris.types", "modulename": "aiochris.types", "kind": "module", "doc": "

NewTypes for ChRIS models.

\n"}, "aiochris.types.Username": {"fullname": "aiochris.types.Username", "modulename": "aiochris.types", "qualname": "Username", "kind": "variable", "doc": "

ChRIS user account username

\n", "default_value": " = aiochris.types.Username"}, "aiochris.types.Password": {"fullname": "aiochris.types.Password", "modulename": "aiochris.types", "qualname": "Password", "kind": "variable", "doc": "

ChRIS user account password

\n", "default_value": " = aiochris.types.Password"}, "aiochris.types.ChrisURL": {"fullname": "aiochris.types.ChrisURL", "modulename": "aiochris.types", "qualname": "ChrisURL", "kind": "variable", "doc": "

ChRIS backend API base URL

\n", "default_value": " = aiochris.types.ChrisURL"}, "aiochris.types.ApiUrl": {"fullname": "aiochris.types.ApiUrl", "modulename": "aiochris.types", "qualname": "ApiUrl", "kind": "variable", "doc": "

Any CUBE URL which I am too lazy to be more specific about.

\n", "default_value": " = aiochris.types.ApiUrl"}, "aiochris.types.ResourceId": {"fullname": "aiochris.types.ResourceId", "modulename": "aiochris.types", "qualname": "ResourceId", "kind": "variable", "doc": "

ID number which I am too lazy to be more specific about.

\n", "default_value": " = aiochris.types.ResourceId"}, "aiochris.types.PluginName": {"fullname": "aiochris.types.PluginName", "modulename": "aiochris.types", "qualname": "PluginName", "kind": "variable", "doc": "

Name of a ChRIS plugin

\n", "default_value": " = aiochris.types.PluginName"}, "aiochris.types.ImageTag": {"fullname": "aiochris.types.ImageTag", "modulename": "aiochris.types", "qualname": "ImageTag", "kind": "variable", "doc": "

OCI image tag (informally, a Docker Image name)

\n", "default_value": " = aiochris.types.ImageTag"}, "aiochris.types.PluginVersion": {"fullname": "aiochris.types.PluginVersion", "modulename": "aiochris.types", "qualname": "PluginVersion", "kind": "variable", "doc": "

Version string of a ChRIS plugin

\n", "default_value": " = aiochris.types.PluginVersion"}, "aiochris.types.PluginUrl": {"fullname": "aiochris.types.PluginUrl", "modulename": "aiochris.types", "qualname": "PluginUrl", "kind": "variable", "doc": "

URL of a ChRIS plugin.

\n\n

Examples

\n\n\n", "default_value": " = aiochris.types.PluginUrl"}, "aiochris.types.AdminUrl": {"fullname": "aiochris.types.AdminUrl", "modulename": "aiochris.types", "qualname": "AdminUrl", "kind": "variable", "doc": "

A admin resource URL ending with /chris-admin/api/v1/

\n", "default_value": " = aiochris.types.AdminUrl"}, "aiochris.types.NoteId": {"fullname": "aiochris.types.NoteId", "modulename": "aiochris.types", "qualname": "NoteId", "kind": "variable", "doc": "

A feed note's ID number.

\n", "default_value": " = aiochris.types.NoteId"}, "aiochris.types.NoteUrl": {"fullname": "aiochris.types.NoteUrl", "modulename": "aiochris.types", "qualname": "NoteUrl", "kind": "variable", "doc": "

A feed's note URL.

\n\n

Examples

\n\n\n", "default_value": " = aiochris.types.NoteUrl"}, "aiochris.util": {"fullname": "aiochris.util", "modulename": "aiochris.util", "kind": "module", "doc": "

\n"}, "aiochris.util.search": {"fullname": "aiochris.util.search", "modulename": "aiochris.util.search", "kind": "module", "doc": "

\n"}, "aiochris.util.search.Search": {"fullname": "aiochris.util.search.Search", "modulename": "aiochris.util.search", "qualname": "Search", "kind": "class", "doc": "

Abstraction over paginated collection responses from CUBE.\nSearch objects are returned by methods for search endpoints of the CUBE API.\nIt is an asynchronous iterable\nwhich produces items from responses that return multiple results.\nHTTP requests are fired as-neede, they happen in the background during iteration.\nNo request is made before the first time a Search object is called.

\n\n
\n\n
Pagination is handled internally and automatically.
\n\n

The query parameters limit and offset can be explicitly given, but they shouldn't.

\n\n
\n\n
Examples
\n\n

Use an async for loop to print the name of every feed:

\n\n
\n
all_feeds = chris.search_feeds()  # returns a Search[Feed]\nasync for feed in all_feeds:\n    print(feed.name)\n
\n
\n", "bases": "typing.Generic[~T], typing.AsyncIterable[~T]"}, "aiochris.util.search.Search.__init__": {"fullname": "aiochris.util.search.Search.__init__", "modulename": "aiochris.util.search", "qualname": "Search.__init__", "kind": "function", "doc": "

\n", "signature": "(\tbase_url: str,\tparams: dict[str, typing.Any],\tclient: aiochris.link.linked.Linked,\tItem: Type[~T],\tmax_requests: int = 100,\tsubpath: str = 'search/')"}, "aiochris.util.search.Search.first": {"fullname": "aiochris.util.search.Search.first", "modulename": "aiochris.util.search", "qualname": "Search.first", "kind": "function", "doc": "

Get the first item.

\n\n
See also
\n\n

get_only : similar use, but more strict

\n", "signature": "(self) -> Optional[~T]:", "funcdef": "async def"}, "aiochris.util.search.Search.get_only": {"fullname": "aiochris.util.search.Search.get_only", "modulename": "aiochris.util.search", "qualname": "Search.get_only", "kind": "function", "doc": "

Get the only item from a search with one result.

\n\n
Examples
\n\n

This method is very commonly used for getting \"one thing\" from CUBE.

\n\n
\n
await chris.search_plugins(name_exact="pl-dircopy", version="2.1.1").get_only()\n
\n
\n\n

In the example above, a search for plugins given (name_exact, version)\nis guaranteed to return either 0 or 1 result.

\n\n
Raises
\n\n
    \n
  • aiochris.util.search.NoneSearchError: If this search is empty.
    • \n
  • aiochris.util.search.ManySearchError: If this search has more than one item and allow_multiple is False
    • \n
\n\n
See also
\n\n

first : does the same thing but without checks.

\n\n
Parameters
\n\n
    \n
  • allow_multiple (bool):\nif True, do not raise ManySearchError if count > 1
    • \n
\n", "signature": "(self, allow_multiple=False) -> ~T:", "funcdef": "async def"}, "aiochris.util.search.Search.count": {"fullname": "aiochris.util.search.Search.count", "modulename": "aiochris.util.search", "qualname": "Search.count", "kind": "function", "doc": "

Get the number of items in this collection search.

\n\n
Examples
\n\n

count is useful for rendering a progress bar. TODO example with files

\n", "signature": "(self) -> int:", "funcdef": "async def"}, "aiochris.util.search.acollect": {"fullname": "aiochris.util.search.acollect", "modulename": "aiochris.util.search", "qualname": "acollect", "kind": "function", "doc": "

Simple helper to convert a Search to a list.

\n\n

Using this function is not recommended unless you can assume the collection is small.

\n", "signature": "(async_iterable: AsyncIterable[~T]) -> list[~T]:", "funcdef": "async def"}, "aiochris.util.search.TooMuchPaginationError": {"fullname": "aiochris.util.search.TooMuchPaginationError", "modulename": "aiochris.util.search", "qualname": "TooMuchPaginationError", "kind": "class", "doc": "

Specified maximum number of requests exceeded while retrieving results from a paginated resource.

\n", "bases": "aiochris.errors.BaseClientError"}, "aiochris.util.search.GetOnlyError": {"fullname": "aiochris.util.search.GetOnlyError", "modulename": "aiochris.util.search", "qualname": "GetOnlyError", "kind": "class", "doc": "

Search does not have exactly one result.

\n", "bases": "aiochris.errors.BaseClientError"}, "aiochris.util.search.NoneSearchError": {"fullname": "aiochris.util.search.NoneSearchError", "modulename": "aiochris.util.search", "qualname": "NoneSearchError", "kind": "class", "doc": "

A search expected to have at least one element, has none.

\n", "bases": "GetOnlyError"}, "aiochris.util.search.ManySearchError": {"fullname": "aiochris.util.search.ManySearchError", "modulename": "aiochris.util.search", "qualname": "ManySearchError", "kind": "class", "doc": "

A search expected to have only one result, has several.

\n", "bases": "GetOnlyError"}}, "docInfo": {"aiochris": {"qualname": 0, "fullname": 1, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 2652}, "aiochris.AnonChrisClient": {"qualname": 1, "fullname": 2, "annotation": 0, "default_value": 0, "signature": 0, "bases": 10, "doc": 23}, "aiochris.AnonChrisClient.from_url": {"qualname": 3, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 114, "bases": 0, "doc": 21}, "aiochris.AnonChrisClient.search_plugins": {"qualname": 3, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 59, "bases": 0, "doc": 24}, "aiochris.ChrisClient": {"qualname": 1, "fullname": 2, "annotation": 0, "default_value": 0, "signature": 0, "bases": 10, "doc": 18}, "aiochris.ChrisClient.create_user": {"qualname": 3, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 174, "bases": 0, "doc": 3}, "aiochris.ChrisAdminClient": {"qualname": 1, "fullname": 2, "annotation": 0, "default_value": 0, "signature": 0, "bases": 10, "doc": 23}, "aiochris.ChrisAdminClient.register_plugin_from_store": {"qualname": 5, "fullname": 6, "annotation": 0, "default_value": 0, "signature": 82, "bases": 0, "doc": 10}, "aiochris.ChrisAdminClient.add_plugin": {"qualname": 3, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 133, "bases": 0, "doc": 509}, "aiochris.ChrisAdminClient.create_compute_resource": {"qualname": 4, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 219, "bases": 0, "doc": 8}, "aiochris.Search": {"qualname": 1, "fullname": 2, "annotation": 0, "default_value": 0, "signature": 0, "bases": 4, "doc": 197}, "aiochris.Search.__init__": {"qualname": 3, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 130, "bases": 0, "doc": 3}, "aiochris.Search.first": {"qualname": 2, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 22, "bases": 0, "doc": 23}, "aiochris.Search.get_only": {"qualname": 3, "fullname": 4, "annotation": 0, "default_value": 0, 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1}}, "df": 4}}}}}, "l": {"docs": {}, "df": 0, "l": {"docs": {"aiochris": {"tf": 1}, "aiochris.client.authed.AuthenticatedClient.upload_file": {"tf": 1}, "aiochris.client.authed.AuthenticatedClient.username": {"tf": 1}, "aiochris.client.base.BaseChrisClient.new": {"tf": 1}, "aiochris.models.data.PluginInstanceData.previous_id": {"tf": 1.4142135623730951}, "aiochris.models.logged_in.PluginInstance.wait": {"tf": 1}}, "df": 6}}}, "o": {"docs": {}, "df": 0, "r": {"docs": {}, "df": 0, "k": {"docs": {}, "df": 0, "s": {"docs": {"aiochris": {"tf": 1.4142135623730951}}, "df": 1}, "i": {"docs": {}, "df": 0, "n": {"docs": {}, "df": 0, "g": {"docs": {"aiochris": {"tf": 1}}, "df": 1}}}}, "l": {"docs": {}, "df": 0, "d": {"docs": {"aiochris.models.logged_in.File.parent": {"tf": 1}}, "df": 1}}}, "u": {"docs": {}, "df": 0, "l": {"docs": {}, "df": 0, "d": {"docs": {"aiochris.client.authed.AuthenticatedClient.from_chrs": {"tf": 1}}, "df": 1}}}}, "a": {"docs": {}, "df": 0, "y": {"docs": {"aiochris": {"tf": 1}}, "df": 1}, "l": {"docs": {}, "df": 0, "k": {"docs": {}, "df": 0, "t": {"docs": {}, "df": 0, "h": {"docs": {}, "df": 0, "r": {"docs": {}, "df": 0, "o": {"docs": {}, "df": 0, "u": {"docs": {}, "df": 0, "g": {"docs": {}, "df": 0, "h": {"docs": {"aiochris": {"tf": 1}}, "df": 1}}}}}}}}}, "n": {"docs": {}, "df": 0, "t": {"docs": {"aiochris.client.authed.AuthenticatedClient.from_chrs": {"tf": 1}}, "df": 1}}, "s": {"docs": {"aiochris.models.logged_in.PACSFile": {"tf": 1}}, "df": 1}, "i": {"docs": {}, "df": 0, "t": {"docs": {"aiochris.models.logged_in.PluginInstance.wait": {"tf": 2}}, "df": 1}}}, "e": {"docs": {"aiochris": {"tf": 1}}, "df": 1, "l": {"docs": {}, "df": 0, "l": {"docs": {"aiochris.client.base.BaseChrisClient.new": {"tf": 1}}, "df": 1}}}, "r": {"docs": {}, "df": 0, "i": {"docs": {}, "df": 0, "t": {"docs": {}, "df": 0, "e": {"docs": {"aiochris.client.authed.AuthenticatedClient.from_chrs": {"tf": 1}, "aiochris.models.logged_in": {"tf": 1}}, "df": 2}}}}}, "j": {"docs": {}, "df": 0, "u": {"docs": {}, "df": 0, "p": {"docs": {}, "df": 0, "y": {"docs": {}, "df": 0, "t": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "r": {"docs": {"aiochris": {"tf": 1.4142135623730951}, "aiochris.client.authed.AuthenticatedClient.from_chrs": {"tf": 1.4142135623730951}}, "df": 2}}}}}, "s": {"docs": {}, "df": 0, "t": {"docs": {"aiochris.ChrisAdminClient.add_plugin": {"tf": 1}, "aiochris.client.admin.ChrisAdminClient.add_plugin": {"tf": 1}}, "df": 2}}}, "s": {"docs": {}, "df": 0, "o": {"docs": {}, "df": 0, "n": {"docs": {"aiochris.ChrisAdminClient.add_plugin": {"tf": 1.4142135623730951}, "aiochris.client.admin.ChrisAdminClient.add_plugin": {"tf": 1.4142135623730951}}, "df": 2}}}, "o": {"docs": {}, "df": 0, "b": {"docs": {"aiochris.models.data.PluginInstanceData": {"tf": 1}}, "df": 1, "s": {"docs": {"aiochris.client.authed.AuthenticatedClient.upload_file": {"tf": 1.4142135623730951}}, "df": 1}}}}, "k": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "p": {"docs": {"aiochris": {"tf": 1}}, "df": 1}}, "y": {"docs": {}, "df": 0, "r": {"docs": {}, "df": 0, "i": {"docs": {}, "df": 0, "n": {"docs": {}, "df": 0, "g": {"docs": {"aiochris.client.from_chrs.ChrsLogin.to_keyring_username": {"tf": 1}, "aiochris.client.from_chrs.ChrsKeyringError": {"tf": 1}}, "df": 2}}}}}}}, "y": {"docs": {}, "df": 0, "o": {"docs": {}, "df": 0, "u": {"docs": {"aiochris": {"tf": 1.7320508075688772}, "aiochris.AnonChrisClient.search_plugins": {"tf": 1}, "aiochris.ChrisAdminClient.add_plugin": {"tf": 1}, "aiochris.acollect": {"tf": 1}, "aiochris.client.admin.ChrisAdminClient.add_plugin": {"tf": 1}, "aiochris.client.anon.AnonChrisClient.search_plugins": {"tf": 1}, "aiochris.client.authed.AuthenticatedClient.from_chrs": {"tf": 1.4142135623730951}, "aiochris.client.base.BaseChrisClient.new": {"tf": 1}, "aiochris.models.logged_in.PluginInstance.wait": {"tf": 1}, "aiochris.util.search.acollect": {"tf": 1}}, "df": 10, "r": {"docs": {"aiochris": {"tf": 1}, "aiochris.client.authed.AuthenticatedClient.from_chrs": {"tf": 1}}, "df": 2}}}}, "x": {"docs": {"aiochris.models.logged_in.Plugin.create_instance": {"tf": 2.23606797749979}}, "df": 1}}}}, "pipeline": ["trimmer"], "_isPrebuiltIndex": true}; + + // mirrored in build-search-index.js (part 1) + // Also split on html tags. this is a cheap heuristic, but good enough. + elasticlunr.tokenizer.setSeperator(/[\s\-.;&_'"=,()]+|<[^>]*>/); + + let searchIndex; + if (docs._isPrebuiltIndex) { + console.info("using precompiled search index"); + searchIndex = elasticlunr.Index.load(docs); + } else { + console.time("building search index"); + // mirrored in build-search-index.js (part 2) + searchIndex = elasticlunr(function () { + this.pipeline.remove(elasticlunr.stemmer); + this.pipeline.remove(elasticlunr.stopWordFilter); + this.addField("qualname"); + this.addField("fullname"); + this.addField("annotation"); + this.addField("default_value"); + this.addField("signature"); + this.addField("bases"); + this.addField("doc"); + this.setRef("fullname"); + }); + for (let doc of docs) { + searchIndex.addDoc(doc); + } + console.timeEnd("building search index"); + } + + return (term) => searchIndex.search(term, { + fields: { + qualname: {boost: 4}, + fullname: {boost: 2}, + annotation: {boost: 2}, + default_value: {boost: 2}, + signature: {boost: 2}, + bases: {boost: 2}, + doc: {boost: 1}, + }, + expand: true + }); +})(); \ No newline at end of file