Added pop column

pepdbagent/db_utils.py

@@ -1,19 +1,17 @@
 import datetime
 import logging
-from typing import Any, Optional, List
+from typing import Optional, List
 
 from sqlalchemy import (
     BigInteger,
     FetchedValue,
-    PrimaryKeyConstraint,
     Result,
     Select,
     String,
     event,
     select,
     TIMESTAMP,
     ForeignKey,
-    ForeignKeyConstraint,
     UniqueConstraint,
 )
 from sqlalchemy.dialects.postgresql import JSON
@@ -92,6 +90,7 @@ class Projects(Base):
         onupdate=deliver_update_date, default=deliver_update_date
     )
     pep_schema: Mapped[Optional[str]]
+    pop: Mapped[Optional[bool]] = mapped_column(default=False)
     samples_mapping: Mapped[List["Samples"]] = relationship(
         back_populates="sample_mapping", cascade="all, delete-orphan"
     )

pepdbagent/models.py

@@ -1,9 +1,6 @@
 # file with pydantic models
-import datetime
 from typing import List, Optional, Union
-
-import peppy
-from pydantic import BaseModel, Extra, Field, validator
+from pydantic import BaseModel, Extra, Field, validator, ConfigDict, field_validator
 
 
 class AnnotationModel(BaseModel):
@@ -21,12 +18,14 @@ class AnnotationModel(BaseModel):
     submission_date: Optional[str]
     digest: Optional[str]
     pep_schema: Optional[str]
+    pop: Optional[bool] = False
 
-    class Config:
-        allow_population_by_field_name = True
-        validate_assignment = True
+    model_config = ConfigDict(
+        validate_assignment=True,
+        populate_by_name=True,
+    )
 
-    @validator("is_private")
+    @field_validator("is_private")
     def is_private_should_be_bool(cls, v):
         if not isinstance(v, bool):
             return False
@@ -71,20 +70,20 @@ class UpdateItems(BaseModel):
     Model used for updating individual items in db
     """
 
-    name: Optional[str]
-    description: Optional[str]
-    tag: Optional[str]
-    is_private: Optional[bool]
-    pep_schema: Optional[str]
-    digest: Optional[str]
-    config: Optional[dict]
-    samples: Optional[List[dict]]
-    subsamples: Optional[List[List[dict]]]
-    description: Optional[str]
-
-    class Config:
-        arbitrary_types_allowed = True
-        extra = Extra.forbid
+    name: Optional[str] = None
+    description: Optional[str] = None
+    tag: Optional[str] = None
+    is_private: Optional[bool] = None
+    pep_schema: Optional[str] = None
+    digest: Optional[str] = None
+    config: Optional[dict] = None
+    samples: Optional[List[dict]] = None
+    subsamples: Optional[List[List[dict]]] = None
+
+    model_config = ConfigDict(
+        arbitrary_types_allowed=True,
+        extra="forbid",
+    )
 
     @property
     def number_of_samples(self) -> Union[int, None]:
@@ -99,37 +98,35 @@ class UpdateModel(BaseModel):
     Model used for updating individual items and creating sql string in the code
     """
 
-    config: Optional[dict]
+    config: Optional[dict] = None
     name: Optional[str] = None
     tag: Optional[str] = None
-    private: Optional[bool] = Field(alias="is_private")
-    digest: Optional[str]
-    number_of_samples: Optional[int]
-    pep_schema: Optional[str]
+    private: Optional[bool] = Field(alias="is_private", default=None)
+    digest: Optional[str] = None
+    number_of_samples: Optional[int] = None
+    pep_schema: Optional[str] = None
     description: Optional[str] = ""
     # last_update_date: Optional[datetime.datetime] = datetime.datetime.now(datetime.timezone.utc)
 
-    @validator("tag", "name")
+    @field_validator("tag", "name")
     def value_must_not_be_empty(cls, v):
         if "" == v:
             return None
         return v
 
-    @validator("tag", "name")
+    @field_validator("tag", "name")
     def value_must_be_lowercase(cls, v):
         if v:
             return v.lower()
         return v
 
-    @validator("tag", "name")
+    @field_validator("tag", "name")
     def value_should_not_contain_question(cls, v):
         if "?" in v:
             return ValueError("Question mark (?) is prohibited in name and tag.")
         return v
 
-    class Config:
-        extra = Extra.forbid
-        allow_population_by_field_name = True
+    model_config = ConfigDict(populate_by_name=True, extra="forbid")
 
 
 class NamespaceInfo(BaseModel):

pepdbagent/modules/annotation.py

@@ -2,8 +2,7 @@
 from datetime import datetime
 from typing import List, Literal, Optional, Union
 
-from sqlalchemy import Engine, and_, func, or_, select
-from sqlalchemy.exc import IntegrityError
+from sqlalchemy import and_, func, or_, select
 from sqlalchemy.sql.selectable import Select
 
 from pepdbagent.const import (
@@ -189,6 +188,7 @@ def _get_single_annotation(
             Projects.last_update_date,
             Projects.digest,
             Projects.pep_schema,
+            Projects.pop,
         ).where(
             and_(
                 Projects.name == name,
@@ -214,6 +214,7 @@ def _get_single_annotation(
                 last_update_date=str(query_result.last_update_date),
                 digest=query_result.digest,
                 pep_schema=query_result.pep_schema,
+                pop=query_result.pop,
             )
             _LOGGER.info(f"Annotation of the project '{namespace}/{name}:{tag}' has been found!")
             return annot
@@ -307,6 +308,7 @@ def _get_projects(
             Projects.last_update_date,
             Projects.digest,
             Projects.pep_schema,
+            Projects.pop,
         ).select_from(Projects)
 
         statement = self._add_condition(
@@ -337,6 +339,7 @@ def _get_projects(
                     last_update_date=str(result.last_update_date),
                     digest=result.digest,
                     pep_schema=result.pep_schema,
+                    pop=result.pop,
                 )
             )
         return results_list
@@ -445,7 +448,7 @@ def _add_date_filter_if_provided(
             return statement
         else:
             if filter_by:
-                _LOGGER.warning(f"filter_start_date was not provided, skipping filter...")
+                _LOGGER.warning("filter_start_date was not provided, skipping filter...")
             return statement
 
     def get_project_number_in_namespace(

pepdbagent/modules/project.py

@@ -4,14 +4,20 @@
 from typing import Union, List, NoReturn
 
 import peppy
-from sqlalchemy import Engine, and_, delete, insert, or_, select, update
+from sqlalchemy import and_, delete, select
 from sqlalchemy.exc import IntegrityError, NoResultFound
 from sqlalchemy.orm import Session
 from sqlalchemy import Select
 
 from peppy.const import SAMPLE_RAW_DICT_KEY, SUBSAMPLE_RAW_LIST_KEY, CONFIG_KEY
 
-from pepdbagent.const import *
+from pepdbagent.const import (
+    DEFAULT_TAG,
+    DESCRIPTION_KEY,
+    NAME_KEY,
+    PKG_NAME,
+)
+
 from pepdbagent.db_utils import Projects, Samples, Subsamples, BaseEngine
 from pepdbagent.exceptions import ProjectNotFoundError, ProjectUniqueNameError
 from pepdbagent.models import UpdateItems, UpdateModel
@@ -200,6 +206,7 @@ def create(
         tag: str = DEFAULT_TAG,
         description: str = None,
         is_private: bool = False,
+        pop: bool = False,
         pep_schema: str = None,
         overwrite: bool = False,
         update_only: bool = False,
@@ -215,6 +222,7 @@ def create(
         :param tag: tag (or version) of the project.
         :param is_private: boolean value if the project should be visible just for user that creates it.
         :param pep_schema: assign PEP to a specific schema. [DefaultL: None]
+        :param pop: if project is a pep of peps (POP) [Default: False]
         :param overwrite: if project exists overwrite the project, otherwise upload it.
             [Default: False - project won't be overwritten if it exists in db]
         :param update_only: if project exists overwrite it, otherwise do nothing.  [Default: False]
@@ -232,7 +240,7 @@ def create(
         elif proj_dict[CONFIG_KEY][NAME_KEY]:
             proj_name = proj_dict[CONFIG_KEY][NAME_KEY].lower()
         else:
-            raise ValueError(f"Name of the project wasn't provided. Project will not be uploaded.")
+            raise ValueError("Name of the project wasn't provided. Project will not be uploaded.")
 
         proj_dict[CONFIG_KEY][NAME_KEY] = proj_name
 
@@ -251,6 +259,7 @@ def create(
                 private=is_private,
                 pep_schema=pep_schema,
                 description=description,
+                pop=pop,
             )
             return None
         else:
@@ -268,6 +277,7 @@ def create(
                     last_update_date=datetime.datetime.now(datetime.timezone.utc),
                     pep_schema=pep_schema,
                     description=description,
+                    pop=pop,
                 )
 
                 self._add_samples_to_project(new_prj, proj_dict[SAMPLE_RAW_DICT_KEY])
@@ -299,9 +309,9 @@ def create(
 
                 else:
                     raise ProjectUniqueNameError(
-                        f"Namespace, name and tag already exists. Project won't be "
-                        f"uploaded. Solution: Set overwrite value as True"
-                        f" (project will be overwritten), or change tag!"
+                        "Namespace, name and tag already exists. Project won't be "
+                        "uploaded. Solution: Set overwrite value as True"
+                        " (project will be overwritten), or change tag!"
                     )
 
     def _overwrite(
@@ -315,6 +325,7 @@ def _overwrite(
         private: bool = False,
         pep_schema: str = None,
         description: str = "",
+        pop: bool = False,
     ) -> None:
         """
         Update existing project by providing all necessary information.
@@ -328,6 +339,7 @@ def _overwrite(
         :param private: boolean value if the project should be visible just for user that creates it.
         :param pep_schema: assign PEP to a specific schema. [DefaultL: None]
         :param description: project description
+        :param pop: if project is a pep of peps, simply POP [Default: False]
         :return: None
         """
         proj_name = proj_name.lower()
@@ -414,6 +426,7 @@ def update(
                     update_dict["subsamples"] = project_dict[SUBSAMPLE_RAW_LIST_KEY]
 
                 update_values = UpdateItems(**update_dict)
+                # update_values = UpdateItems(tag="ff")
 
             update_values = self.__create_update_dict(update_values)
 
@@ -476,64 +489,64 @@ def __create_update_dict(update_values: UpdateItems) -> dict:
             updating values
         :return: unified update dict
         """
-        update_final = UpdateModel()
+        update_final = UpdateModel.model_construct()
 
         if update_values.name is not None:
             if update_values.config is not None:
                 update_values.config[NAME_KEY] = update_values.name
             update_final = UpdateModel(
                 name=update_values.name,
-                **update_final.dict(exclude_unset=True),
+                **update_final.model_dump(exclude_unset=True),
             )
 
         if update_values.description is not None:
             if update_values.config is not None:
                 update_values.config[DESCRIPTION_KEY] = update_values.description
             update_final = UpdateModel(
                 description=update_values.description,
-                **update_final.dict(exclude_unset=True),
+                **update_final.model_dump(exclude_unset=True),
             )
         if update_values.config is not None:
             update_final = UpdateModel(
-                config=update_values.config, **update_final.dict(exclude_unset=True)
+                config=update_values.config, **update_final.model_dump(exclude_unset=True)
             )
             name = update_values.config.get(NAME_KEY)
             description = update_values.config.get(DESCRIPTION_KEY)
             if name:
                 update_final = UpdateModel(
                     name=name,
-                    **update_final.dict(exclude_unset=True, exclude={NAME_KEY}),
+                    **update_final.model_dump(exclude_unset=True, exclude={NAME_KEY}),
                 )
             if description:
                 update_final = UpdateModel(
                     description=description,
-                    **update_final.dict(exclude_unset=True, exclude={DESCRIPTION_KEY}),
+                    **update_final.model_dump(exclude_unset=True, exclude={DESCRIPTION_KEY}),
                 )
 
         if update_values.tag is not None:
             update_final = UpdateModel(
-                tag=update_values.tag, **update_final.dict(exclude_unset=True)
+                tag=update_values.tag, **update_final.model_dump(exclude_unset=True)
             )
 
         if update_values.is_private is not None:
             update_final = UpdateModel(
                 is_private=update_values.is_private,
-                **update_final.dict(exclude_unset=True),
+                **update_final.model_dump(exclude_unset=True),
             )
 
         if update_values.pep_schema is not None:
             update_final = UpdateModel(
                 pep_schema=update_values.pep_schema,
-                **update_final.dict(exclude_unset=True),
+                **update_final.model_dump(exclude_unset=True),
             )
 
         if update_values.number_of_samples is not None:
             update_final = UpdateModel(
                 number_of_samples=update_values.number_of_samples,
-                **update_final.dict(exclude_unset=True),
+                **update_final.model_dump(exclude_unset=True),
             )
 
-        return update_final.dict(exclude_unset=True, exclude_none=True)
+        return update_final.model_dump(exclude_unset=True, exclude_none=True)
 
     def exists(
         self,
@@ -565,7 +578,7 @@ def exists(
             return False
 
     @staticmethod
-    def _add_samples_to_project(projects_sa: Projects, samples: List[dict]) -> NoReturn:
+    def _add_samples_to_project(projects_sa: Projects, samples: List[dict]) -> None:
         """
         Add samples to the project sa object. (With commit this samples will be added to the 'samples table')
         :param projects_sa: Projects sa object, in open session
@@ -575,6 +588,8 @@ def _add_samples_to_project(projects_sa: Projects, samples: List[dict]) -> NoRet
         for row_number, sample in enumerate(samples):
             projects_sa.samples_mapping.append(Samples(sample=sample, row_number=row_number))
 
+        return None
+
     @staticmethod
     def _add_subsamples_to_project(
         projects_sa: Projects, subsamples: List[List[dict]]

pepdbagent/utils.py

@@ -7,7 +7,7 @@
 import ubiquerg
 from peppy.const import SAMPLE_RAW_DICT_KEY
 
-from .exceptions import IncorrectDateFormat, RegistryPathError
+from .exceptions import RegistryPathError
 
 
 def is_valid_registry_path(rpath: str) -> bool: