diff --git a/requirements_web.txt b/requirements_web.txt index c5a89daf..ad338535 100644 --- a/requirements_web.txt +++ b/requirements_web.txt @@ -1,7 +1,5 @@ # biothings -biothings[web_extra]==0.9.1 -elasticsearch==6.3.1 -elasticsearch-dsl==6.3.1 +git+git://github.com/biothings/biothings.api@0.10.x#egg=biothings[web_extra] # for sentry monitoring raven diff --git a/src/config_hub.py b/src/config_hub.py index c6d005ff..4605f919 100644 --- a/src/config_hub.py +++ b/src/config_hub.py @@ -1,6 +1,9 @@ # ######### # # HUB VARS # # ######### # +from biothings import ConfigurationError, ConfigurationDefault, ConfigurationValue +from biothings.utils.loggers import setup_default_log +import logging import os import copy @@ -14,11 +17,12 @@ EVENT_COLLECTION = 'event' # for launched/running commands in shell # define valid sources to get chrom from, and for each, name of the chrom field -CHROM_FIELDS = {'cadd':'chrom', 'clinvar':'chrom', 'cosmic':'chrom', 'dbnsfp':'chrom', - 'dbsnp':'chrom', 'docm':'chrom', 'evs':'chrom', 'exac':'chrom'} +CHROM_FIELDS = {'cadd': 'chrom', 'clinvar': 'chrom', 'cosmic': 'chrom', 'dbnsfp': 'chrom', + 'dbsnp': 'chrom', 'docm': 'chrom', 'evs': 'chrom', 'exac': 'chrom'} HG38_FIELDS = ['clinvar.hg38', 'dbnsfp.hg38', 'evs.hg38'] -HG19_FIELDS = ['clinvar.hg19', 'cosmic.hg19', 'dbnsfp.hg19', 'dbsnp.hg19', 'docm.hg19', 'evs.hg19', 'grasp.hg19'] +HG19_FIELDS = ['clinvar.hg19', 'cosmic.hg19', 'dbnsfp.hg19', + 'dbsnp.hg19', 'docm.hg19', 'evs.hg19', 'grasp.hg19'] # Max length for vcf.alt and vcf.ref fields (must be less than 32k as a keyword field in ElasticSearch) # otherwise, Elasticsearch will raise an error like this: @@ -72,145 +76,145 @@ # Pre-prod/test ES definitions INDEX_CONFIG = { - "build_config_key" : "assembly", # used to select proper idxr/syncer - "indexer_select": { - # default - None : "hub.dataindex.indexer.VariantIndexer", - # when there's a cold_collection definition - "build_config.cold_collection" : "hub.dataindex.indexer.ColdHotVariantIndexer", - }, - "env" : { - "prod" : { - "host" : ":9200", - "indexer" : { - "args" : { - "timeout" : 300, - "retry_on_timeout" : True, - "max_retries" : 10, - }, + "build_config_key": "assembly", # used to select proper idxr/syncer + "indexer_select": { + # default + None: "hub.dataindex.indexer.VariantIndexer", + # when there's a cold_collection definition + "build_config.cold_collection": "hub.dataindex.indexer.ColdHotVariantIndexer", + }, + "env": { + "prod": { + "host": ":9200", + "indexer": { + "args": { + "timeout": 300, + "retry_on_timeout": True, + "max_retries": 10, }, - "index" : [ - # keys match build_config_key value - {"index": "myvariant_current_hg19", "doc_type": "variant", "hg19": True}, - {"index": "myvariant_current_hg38", "doc_type": "variant", "hg38": True}, - ], - }, - "local" : { - "host" : "localhost:9200", - "indexer" : { - "args" : { - "timeout" : 300, - "retry_on_timeout" : True, - "max_retries" : 10, - }, + }, + "index": [ + # keys match build_config_key value + {"index": "myvariant_current_hg19", "doc_type": "variant", "hg19": True}, + {"index": "myvariant_current_hg38", "doc_type": "variant", "hg38": True}, + ], + }, + "local": { + "host": "localhost:9200", + "indexer": { + "args": { + "timeout": 300, + "retry_on_timeout": True, + "max_retries": 10, }, - "index" : [ - # "hg19/hg38" are flags used to filter compatible index from the UI - {"index": "myvariant_current_hg19", "doc_type": "variant", "hg19": True}, - {"index": "myvariant_current_hg38", "doc_type": "variant", "hg38": True}, - ], - }, }, - } + "index": [ + # "hg19/hg38" are flags used to filter compatible index from the UI + {"index": "myvariant_current_hg19", "doc_type": "variant", "hg19": True}, + {"index": "myvariant_current_hg38", "doc_type": "variant", "hg38": True}, + ], + }, + }, +} # Snapshot environment configuration SNAPSHOT_CONFIG = { - "env" : { - "prod" : { - "cloud" : { - "type" : "aws", # default, only one supported by now - "access_key" : None, - "secret_key" : None, - }, - "repository" : { - "name" : "variant_repository-$(Y)", - "type" : "s3", - "settings" : { - "bucket" : "", - "base_path" : "myvariant.info/$(Y)", # per year - "region" : "us-west-2", - }, - "acl" : "private", - }, - "indexer" : { - # reference to INDEX_CONFIG - "env" : "local", - }, - # when creating a snapshot, how long should we wait before querying ES - # to check snapshot status/completion ? (in seconds) - "monitor_delay" : 60 * 5, + "env": { + "prod": { + "cloud": { + "type": "aws", # default, only one supported by now + "access_key": None, + "secret_key": None, + }, + "repository": { + "name": "variant_repository-$(Y)", + "type": "s3", + "settings": { + "bucket": "", + "base_path": "myvariant", + "region": "us-west-2", }, - "demo" : { - "cloud" : { - "type" : "aws", # default, only one supported by now - "access_key" : None, - "secret_key" : None, - }, - "repository" : { - "name" : "variant_repository-demo-$(Y)", - "type" : "s3", - "settings" : { - "bucket" : "", - "base_path" : "myvariant.info/$(Y)", # per year - "region" : "us-west-2", - }, - "acl" : "public", - }, - "indexer" : { - # reference to INDEX_CONFIG - "env" : "local", - }, - # when creating a snapshot, how long should we wait before querying ES - # to check snapshot status/completion ? (in seconds) - "monitor_delay" : 10, - } - } + "acl": "private", + }, + "indexer": { + # reference to INDEX_CONFIG + "env": "local", + }, + # when creating a snapshot, how long should we wait before querying ES + # to check snapshot status/completion ? (in seconds) + "monitor_delay": 60 * 5, + }, + "demo": { + "cloud": { + "type": "aws", # default, only one supported by now + "access_key": None, + "secret_key": None, + }, + "repository": { + "name": "variant_repository-demo-$(Y)", + "type": "s3", + "settings": { + "bucket": "", + "base_path": "myvariant.info/$(Y)", # per year + "region": "us-west-2", + }, + "acl": "public", + }, + "indexer": { + # reference to INDEX_CONFIG + "env": "local", + }, + # when creating a snapshot, how long should we wait before querying ES + # to check snapshot status/completion ? (in seconds) + "monitor_delay": 10, } + } +} # Release configuration # Each root keys define a release environment (test, prod, ...) RELEASE_CONFIG = { - "env" : { - "prod-hg19" : { - "cloud" : { - "type" : "aws", # default, only one supported by now - "access_key" : None, - "secret_key" : None, - }, - "release" : { - "bucket" : "", - "region" : "us-west-2", - "folder" : "myvariant.info-hg19", - "auto" : True, # automatically generate release-note ? - }, - "diff" : { - "bucket" : "", - "folder" : "myvariant.info-hg19", - "region" : "us-west-2", - "auto" : True, # automatically generate diff ? Careful if lots of changes - }, - }, - "demo-hg19": { - "cloud" : { - "type" : "aws", # default, only one supported by now - "access_key" : None, - "secret_key" : None, - }, - "release" : { - "bucket" : "", - "region" : "us-west-2", - "folder" : "myvariant.info-demo_hg19", - "auto" : True, # automatically generate release-note ? - }, - "diff" : { - "bucket" : "", - "folder" : "myvariant.info-demo_hg19", - "region" : "us-west-2", - "auto" : True, # automatically generate diff ? Careful if lots of changes - }, - } - } + "env": { + "prod-hg19": { + "cloud": { + "type": "aws", # default, only one supported by now + "access_key": None, + "secret_key": None, + }, + "release": { + "bucket": "", + "region": "us-west-2", + "folder": "myvariant.info-hg19", + "auto": True, # automatically generate release-note ? + }, + "diff": { + "bucket": "", + "folder": "myvariant.info-hg19", + "region": "us-west-2", + "auto": True, # automatically generate diff ? Careful if lots of changes + }, + }, + "demo-hg19": { + "cloud": { + "type": "aws", # default, only one supported by now + "access_key": None, + "secret_key": None, + }, + "release": { + "bucket": "", + "region": "us-west-2", + "folder": "myvariant.info-demo_hg19", + "auto": True, # automatically generate release-note ? + }, + "diff": { + "bucket": "", + "folder": "myvariant.info-demo_hg19", + "region": "us-west-2", + "auto": True, # automatically generate diff ? Careful if lots of changes + }, } + } +} # fir hg38 it's almost the same @@ -236,7 +240,7 @@ ################################################################################ # The format is a dictionary of 'username': 'cryptedpassword' # Generate crypted passwords with 'openssl passwd -crypt' -HUB_PASSWD = {"guest":"9RKfd8gDuNf0Q"} +HUB_PASSWD = {"guest": "9RKfd8gDuNf0Q"} # cached data (it None, caches won't be used at all) CACHE_FOLDER = None @@ -273,8 +277,6 @@ #AUTOHUB_INDEXER_FACTORY = "biothings.hub.dataindex.indexer.DynamicIndexerFactory" #AUTOHUB_ES_HOST = "localhost:9200" -import logging -from biothings.utils.loggers import setup_default_log ######################################## # APP-SPECIFIC CONFIGURATION VARIABLES # @@ -289,35 +291,38 @@ # any other variables in this file as required. Variables defined as ValueError() exceptions # *must* be defined # -from biothings.utils.configuration import ConfigurationError, ConfigurationDefault, ConfigurationValue # Individual source database connection DATA_SRC_SERVER = ConfigurationError("Define hostname for source database") DATA_SRC_PORT = ConfigurationError("Define port for source database") DATA_SRC_DATABASE = ConfigurationError("Define name for source database") -DATA_SRC_SERVER_USERNAME = ConfigurationError("Define username for source database connection (or None if not needed)") -DATA_SRC_SERVER_PASSWORD = ConfigurationError("Define password for source database connection (or None if not needed)") +DATA_SRC_SERVER_USERNAME = ConfigurationError( + "Define username for source database connection (or None if not needed)") +DATA_SRC_SERVER_PASSWORD = ConfigurationError( + "Define password for source database connection (or None if not needed)") # Target (merged collection) database connection DATA_TARGET_SERVER = ConfigurationError("Define hostname for target database (merged collections)") DATA_TARGET_PORT = ConfigurationError("Define port for target database (merged collections)") DATA_TARGET_DATABASE = ConfigurationError("Define name for target database (merged collections)") -DATA_TARGET_SERVER_USERNAME = ConfigurationError("Define username for target database connection (or None if not needed)") -DATA_TARGET_SERVER_PASSWORD = ConfigurationError("Define password for target database connection (or None if not needed)") +DATA_TARGET_SERVER_USERNAME = ConfigurationError( + "Define username for target database connection (or None if not needed)") +DATA_TARGET_SERVER_PASSWORD = ConfigurationError( + "Define password for target database connection (or None if not needed)") HUB_DB_BACKEND = ConfigurationError("Define Hub DB connection") # Internal backend. Default to mongodb # For now, other options are: mongodb, sqlite3, elasticsearch -#HUB_DB_BACKEND = { +# HUB_DB_BACKEND = { # "module" : "biothings.utils.sqlite3", # "sqlite_db_foder" : "./db", # } -#HUB_DB_BACKEND = { +# HUB_DB_BACKEND = { # "module" : "biothings.utils.mongo", # "uri" : "mongodb://localhost:27017", # #"uri" : "mongodb://user:passwd@localhost:27017", # mongodb std URI # } -#HUB_DB_BACKEND = { +# HUB_DB_BACKEND = { # "module" : "biothings.utils.es", # "host" : "localhost:9200", # } @@ -325,36 +330,37 @@ #ES_HOST = ConfigurationError("Define ElasticSearch host used for index creation (eg localhost:9200)") # Path to a folder to store all downloaded files, logs, caches, etc... -DATA_ARCHIVE_ROOT = ConfigurationError("Define path to folder which will contain all downloaded data, cache files, etc...") +DATA_ARCHIVE_ROOT = ConfigurationError( + "Define path to folder which will contain all downloaded data, cache files, etc...") # Path to a folder to store all 3rd party parsers, dumpers, etc... DATA_PLUGIN_FOLDER = ConfigurationDefault( - default="./plugins", - desc="Define path to folder which will contain all 3rd party parsers, dumpers, etc...") + default="./plugins", + desc="Define path to folder which will contain all 3rd party parsers, dumpers, etc...") # Path to folder containing diff files DIFF_PATH = ConfigurationDefault( - default=ConfigurationValue("""os.path.join(DATA_ARCHIVE_ROOT,"diff")"""), - desc="Define path to folder which will contain output files from diff") + default=ConfigurationValue("""os.path.join(DATA_ARCHIVE_ROOT,"diff")"""), + desc="Define path to folder which will contain output files from diff") # Path to folder containing release note files RELEASE_PATH = ConfigurationDefault( - default=ConfigurationValue("""os.path.join(DATA_ARCHIVE_ROOT,"release")"""), - desc="Define path to folder which will contain release files") + default=ConfigurationValue("""os.path.join(DATA_ARCHIVE_ROOT,"release")"""), + desc="Define path to folder which will contain release files") # this dir must be created manually LOG_FOLDER = ConfigurationDefault( - default=ConfigurationValue("""os.path.join(DATA_ARCHIVE_ROOT,"logs")"""), - desc="Define path to folder which will contain log files") + default=ConfigurationValue("""os.path.join(DATA_ARCHIVE_ROOT,"logs")"""), + desc="Define path to folder which will contain log files") -IDS_S3_BUCKET = ConfigurationDefault( - default="myvariant-ids", - desc="Define a bucket name to upload myvariant _ids to") +IDS_S3_BUCKET = ConfigurationDefault( + default="myvariant-ids", + desc="Define a bucket name to upload myvariant _ids to") # default hub logger logger = ConfigurationDefault( - default=logging, - desc="Provide a default hub logger instance (use setup_default_log(name,log_folder)") + default=logging, + desc="Provide a default hub logger instance (use setup_default_log(name,log_folder)") ACTIVE_DATASOURCES = [ # auto-updated @@ -385,4 +391,4 @@ # generated resources 'hub.dataload.sources.snpeff', - ] +] diff --git a/src/config_web.py b/src/config_web.py index c96f38af..8bf701cb 100644 --- a/src/config_web.py +++ b/src/config_web.py @@ -1,17 +1,20 @@ -# -*- coding: utf-8 -*- import copy import re -from biothings.web.settings.default import (ANNOTATION_KWARGS, APP_LIST, - QUERY_KWARGS) +from biothings.web.settings.default import ( + ANNOTATION_KWARGS, APP_LIST, QUERY_KWARGS) # ***************************************************************************** # Elasticsearch variables # ***************************************************************************** -ES_HOST = 'es6.biothings.io:9200' -ES_INDEX = 'myvariant_current_hg19' -ES_DOC_TYPE = 'variant' +ES_HOST = 'es7.biothings.io:443' +ES_ARGS = { + 'timeout': 120, + 'aws': True +} ES_INDICES = { + None: 'myvariant_current_hg19', + 'variant': 'myvariant_current_hg19', 'hg19': 'myvariant_current_hg19', 'hg38': 'myvariant_current_hg38' } @@ -21,8 +24,9 @@ # ***************************************************************************** API_VERSION = 'v1' APP_LIST = [ - (r'/v1/variant/(chr.{1,2}):(?!g\.)[g\.]{0,2}(\d+.*)', 'tornado.web.RedirectHandler', {'url': '/v1/variant/{0}:g.{1}'}), - *APP_LIST, + (r'/v1/variant/(chr.{1,2}):(?!g\.)[g\.]{0,2}(\d+.*)', + 'tornado.web.RedirectHandler', {'url': '/v1/variant/{0}:g.{1}'}), + *APP_LIST, # default handlers (r"/{pre}/metadata/fields/?", 'web.handlers.MVMetadataFieldHandler'), (r"/{pre}/metadata/?", 'web.handlers.MVMetadataSourceHandler'), (r"/{pre}/{ver}/metadata/fields/?", 'web.handlers.MVMetadataFieldHandler'), @@ -38,18 +42,18 @@ # Analytics & Tracking # ***************************************************************************** -GA_ACTION_QUERY_GET = 'query_get' -GA_ACTION_QUERY_POST = 'query_post' -GA_ACTION_ANNOTATION_GET = 'variant_get' -GA_ACTION_ANNOTATION_POST = 'variant_post' -GA_TRACKER_URL = 'MyVariant.info' URL_BASE = 'http://myvariant.info' # for logo on format=html HTML_OUT_HEADER_IMG = "/static/favicon.ico" # for title line on format=html -HTML_OUT_TITLE = """

MyVariant.info - Variant Annotation as a Service

""" +HTML_OUT_TITLE = """ +

+ + MyVariant.info - Variant Annotation as a Service + +

""" METADATA_DOCS_URL = "http://docs.myvariant.info/en/latest/doc/data.html" QUERY_DOCS_URL = "http://docs.myvariant.info/en/latest/doc/variant_query_service.html" @@ -58,20 +62,27 @@ # kwargs for status check get STATUS_CHECK = { 'id': 'chr1:g.218631822G>A', - 'index': 'myvariant_current_hg19', - 'doc_type': 'variant' + 'index': 'myvariant_current_hg19' } # ***************************************************************************** # User Input Control # ***************************************************************************** -ANNOTATION_ID_REGEX_LIST = [(re.compile(r'rs[0-9]+', re.I), 'dbsnp.rsid'), - (re.compile(r'rcv[0-9\.]+', re.I), 'clinvar.rcv.accession'), - (re.compile(r'var_[0-9]+', re.I), 'uniprot.humsavar.ftid')] +ANNOTATION_ID_REGEX_LIST = [ + (re.compile(r'rs[0-9]+', re.I), 'dbsnp.rsid'), + (re.compile(r'rcv[0-9\.]+', re.I), 'clinvar.rcv.accession'), + (re.compile(r'var_[0-9]+', re.I), 'uniprot.humsavar.ftid') +] ANNOTATION_DEFAULT_SCOPES = ['_id', 'clingen.caid'] # typedef for assembly parameter -ASSEMBLY_TYPEDEF = {'assembly': {'type': str, 'default': 'hg19', 'enum': ('hg19', 'hg38'), 'group': ('esqb', 'es')}} +ASSEMBLY_TYPEDEF = { + 'assembly': { + 'type': str, + 'default': 'hg19', + 'enum': ('hg19', 'hg38') + } +} ANNOTATION_KWARGS = copy.deepcopy(ANNOTATION_KWARGS) ANNOTATION_KWARGS['*'].update(ASSEMBLY_TYPEDEF) diff --git a/src/hub/dataindex/indexer.py b/src/hub/dataindex/indexer.py index beff77ee..e32cfb42 100644 --- a/src/hub/dataindex/indexer.py +++ b/src/hub/dataindex/indexer.py @@ -1,56 +1,64 @@ -import os, time +import time import asyncio import config -import biothings.hub.dataindex.indexer as indexer +from biothings.hub.dataindex.indexer import Indexer, IndexManager, ColdHotIndexer from biothings.hub.dataexport.ids import export_ids, upload_ids from biothings.utils.hub_db import get_src_build from biothings.utils.es import ESIndexer from utils.stats import update_stats -class BaseVariantIndexer(indexer.Indexer): - - def enrich_final_mapping(self,final_mapping): - # enrich with myvariant specific stuff - final_mapping["properties"]["chrom"] = { - 'analyzer': 'string_lowercase', - 'type': 'text'} - final_mapping["properties"]["observed"] = { - "type": "boolean"} - final_mapping["properties"]["_seqhashed"] = { - "type" : "object", - "properties" : { - "_flag": { - "type" : "boolean" - } - } - } +class BaseVariantIndexer(Indexer): - return final_mapping + def __init__(self, build_doc, indexer_env, target_name, index_name): + super().__init__(build_doc, indexer_env, target_name, index_name) - def get_index_creation_settings(self): - settings = super(BaseVariantIndexer,self).get_index_creation_settings() - settings.setdefault("mapping",{}).setdefault("total_fields",{})["limit"] = 2000 - return settings + self.es_index_mappings["properties"]["chrom"] = { + 'analyzer': 'string_lowercase', + 'type': 'text' + } + self.es_index_mappings["properties"]["observed"] = { + "type": "boolean" + } + self.es_index_mappings["properties"]["_seqhashed"] = { + "type": "object", + "properties": { + "_flag": { + "type": "boolean" + } + } + } + self.es_index_settings["mapping"] = { + "total_fields": { + "limit": 2000 + } + } + self.assembly = build_doc["build_config"]["assembly"] - def post_index(self, target_name, index_name, job_manager, steps=["index","post"], batch_size=10000, ids=None, mode=None): - # TODO: not tested yet + @asyncio.coroutine + def post_index(self): + # Migrated from Sebastian's commit 1a7b7a + # It was orginally marked "Not Tested Yet". self.logger.info("Sleeping for a bit while index is being fully updated...") - time.sleep(3*60) - idxer = ESIndexer(index=index_name,doc_type=self.doc_type,es_host=self.host) - self.logger.info("Updating 'stats' by querying index '%s'" % index_name) - assembly = self.build_config["assembly"] - return update_stats(idxer,assembly) + yield from time.sleep(3*60) + idxer = ESIndexer( + index=self.es_index_name, + doc_type=self.doc_type, + es_host=self.es_client_args.get('hosts')) + self.logger.info("Updating 'stats' by querying index '%s'" % self.es_index_name) + return update_stats(idxer, self.assembly) + +class MyVariantIndexerManager(IndexManager): -class MyVariantIndexerManager(indexer.IndexManager): + # New Hub Command def post_publish(self, snapshot, index, *args, **kwargs): # assuming build name == index name, and assuming demo index has # "demo" in its name... # assuming full index, not demo, guess name now - bdoc = get_src_build().find_one({"_id" : index}) + bdoc = get_src_build().find_one({"_id": index}) assert bdoc, "Can't find build doc associated with index '%s' (should be named the same)" % index ids_file = export_ids(index) if "hg19" in index or "hg19" in snapshot: @@ -59,15 +67,15 @@ def post_publish(self, snapshot, index, *args, **kwargs): redir = "hg38_ids.xz" if "demo" in index or "demo" in snapshot: redir = "demo_%s" % redir - upload_ids(ids_file, redir, - s3_bucket=config.IDS_S3_BUCKET, - aws_key=config.AWS_KEY, - aws_secret=config.AWS_SECRET) + upload_ids(ids_file, redir, + s3_bucket=config.IDS_S3_BUCKET, + aws_key=config.AWS_KEY, + aws_secret=config.AWS_SECRET) + class VariantIndexer(BaseVariantIndexer): pass -class ColdHotVariantIndexer(indexer.ColdHotIndexer,BaseVariantIndexer): + +class ColdHotVariantIndexer(ColdHotIndexer, BaseVariantIndexer): pass - - diff --git a/src/index.py b/src/index.py index 78012262..531099b6 100644 --- a/src/index.py +++ b/src/index.py @@ -1,13 +1,16 @@ from tornado.web import StaticFileHandler, RedirectHandler -from biothings.web.index_base import main +from biothings.web.launcher import main from web.beacon.handlers import BeaconHandler, BeaconInfoHandler if __name__ == "__main__": main([ - (r"/", RedirectHandler, {"url": "/standalone", "permanent": False}), # override default frontpage - (r"/demo/?()", StaticFileHandler, {"path": "docs/demo", "default_filename": "index.html"}), - (r"/standalone/?()", StaticFileHandler, {"path": "docs/standalone", "default_filename": "index.html"}), + # override default frontpage + (r"/", RedirectHandler, {"url": "/standalone", "permanent": False}), + (r"/demo/?()", StaticFileHandler, + {"path": "docs/demo", "default_filename": "index.html"}), + (r"/standalone/?()", StaticFileHandler, + {"path": "docs/standalone", "default_filename": "index.html"}), (r"/beacon/query?", BeaconHandler), (r"/beacon/info", BeaconInfoHandler), ]) diff --git a/src/tests/__init__.py b/src/tests/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/src/tests/app/config.py b/src/tests/app/config.py new file mode 100644 index 00000000..0061f222 --- /dev/null +++ b/src/tests/app/config.py @@ -0,0 +1,47 @@ + +""" + Config file to run tests for MyVariant.info +""" +import os as _os +import importlib.util as _imp_util + +CONFIG_FILE_NAME = "config_web.py" + +# find the path of the config file +_cfg_path = _os.path.abspath(_os.path.join(_os.path.curdir, CONFIG_FILE_NAME)) +while True: + if _os.path.exists(_cfg_path): + break + _new_path = _os.path.abspath(_os.path.join( + _os.path.join(_os.path.dirname(_cfg_path), _os.path.pardir), + CONFIG_FILE_NAME) + ) + if _new_path == _cfg_path: + raise Exception(f"no config file {CONFIG_FILE_NAME} found") + else: + _cfg_path = _new_path + +# load config file using path +_spec = _imp_util.spec_from_file_location("parent_config", _cfg_path) +_config = _imp_util.module_from_spec(_spec) +_spec.loader.exec_module(_config) + +# put the config variables into the module namespace +for _k, _v in _config.__dict__.items(): + if not _k.startswith('_'): + globals()[_k] = _v + +# cleanup +del CONFIG_FILE_NAME + +# override default +ES_HOST = 'localhost:9200' +ES_INDICES = { + None: 'mvtest_hg19', + 'variant': 'mvtest_hg19', + 'hg19': 'mvtest_hg19', + 'hg38': 'mvtest_hg38' +} +ES_ARGS = { + 'timeout': 120, +} diff --git a/src/tests/app/test_data/mv_app_test/mvtest_hg19.json b/src/tests/app/test_data/mv_app_test/mvtest_hg19.json new file mode 100644 index 00000000..02fd0029 --- /dev/null +++ b/src/tests/app/test_data/mv_app_test/mvtest_hg19.json @@ -0,0 +1 @@ +{"aliases": {"myvariant_current": {}, "myvariant_current_hg19": {}}, "mappings": {"dynamic": "false", "_meta": {"build_date": "2021-04-22T16:05:10.429385-07:00", "biothing_type": "variant", "stats": {"total": 973301265, "hg19": 938911912, "vcf": 939474331, "observed": 803819895}, "src": {"cosmic": {"note": "COSMIC v68 was imported from UCSC database dump. 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{"primate": 1.0, "primate_rankscore": 0.97212}}, "siphy_29way": {"pi": {"a": 0.0, "c": 0.0, "g": 0.0, "t": 1.0}, "logodds": 15.2145, "logodds_rankscore": 0.72943}, "bayesdel": {"add_af": {"score": 0.338381, "rankscore": 0.85723, "pred": "D"}, "no_af": {"score": 0.248285, "rankscore": 0.85535, "pred": "D"}}, "clinpred": {"score": 0.982197165489197, "rankscore": 0.74348, "pred": "D"}, "list-s2": {"score": ["0.964204", "0.960654", "0.962904", "0.963004", "0.960654", "0.959504", "0.964204", "0.962904", "0.963004", "0.963804", "0.964204", "0.963754", "0.966803", "0.960654", "0.963004"], "rankscore": 0.87909, "pred": ["D", "D", "D", "D", "D", "D", "D", "D", "D", "D", "D", "D", "D", "D", "D"]}, "clinvar": {"clinvar_id": 11534, "clinsig": "Likely_pathogenic", "trait": ["FG_syndrome_4", "Mental_retardation_and_microcephaly_with_pontine_and_cerebellar_hypoplasia"], "review": ["criteria_provided", "_single_submitter"], "hgvs": "NC_000023.11:g.41542717T>C", "omim": [300422, 300749], "medgen": ["C1845546", "C2677903"], "orphanet": "ORPHA163937", "var_source": ["OMIM_Allelic_Variant:300172.0005", "UniProtKB_(protein):O14936#VAR_062998"]}, "hgvsc": ["c.2078A>G", "c.2006A>G", "c.2111A>G", "c.860A>G", "c.2147A>G", "c.2129A>G", "c.494A>G", "c.2075A>G", "c.2093A>G", "c.1451A>G", "c.2042A>G", "c.905A>G", "c.2060A>G"], "hgvsp": ["p.Asp692Gly", "p.Asp687Gly", "p.Asp681Gly", "p.Asp704Gly", "p.Asp710Gly", "p.Asp302Gly", "p.D710G", "p.Asp698Gly", "p.Asp693Gly", "p.D698G", "p.Asp165Gly", "p.Asp716Gly", "p.Asp669Gly", "p.Asp484Gly", "p.Asp287Gly", "p.D681G", "p.D687G"]}, "dbsnp": {"gene": {"name": "calcium/calmodulin dependent serine protein kinase", "is_pseudo": false, "rnas": [{"codon_aligned_transcript_change": {"seq_id": "NM_001126054.2", "position": 2104, "deleted_sequence": "GAT", "inserted_sequence": "GAT"}, "protein": {"variant": {"spdi": {"seq_id": "NP_001119526.1", "position": 686, "deleted_sequence": "D", "inserted_sequence": "D"}}}, "hgvs": "NM_001126054.2:c.2060=", "refseq": "NM_001126054.2", "so": [{"name": "coding_sequence_variant", "accession": "SO:0001580"}], "protein_product": {"refseq": "NP_001119526.1"}}, {"codon_aligned_transcript_change": {"seq_id": "NM_001126055.2", "position": 2086, "deleted_sequence": "GAT", "inserted_sequence": "GAT"}, "protein": {"variant": {"spdi": {"seq_id": "NP_001119527.1", "position": 680, "deleted_sequence": "D", "inserted_sequence": "D"}}}, "hgvs": "NM_001126055.2:c.2042=", "refseq": "NM_001126055.2", "so": [{"name": "coding_sequence_variant", "accession": "SO:0001580"}], "protein_product": {"refseq": "NP_001119527.1"}}, {"codon_aligned_transcript_change": {"seq_id": "NM_001367721.1", "position": 2693, "deleted_sequence": "GAT", "inserted_sequence": "GAT"}, "protein": {"variant": {"spdi": {"seq_id": "NP_001354650.1", "position": 709, "deleted_sequence": "D", "inserted_sequence": "D"}}}, "hgvs": "NM_001367721.1:c.2129=", "refseq": "NM_001367721.1", "so": [{"name": "coding_sequence_variant", "accession": "SO:0001580"}], "protein_product": {"refseq": "NP_001354650.1"}}, {"codon_aligned_transcript_change": {"seq_id": "NM_003688.3", "position": 2173, "deleted_sequence": "GAT", "inserted_sequence": "GAT"}, "protein": {"variant": {"spdi": {"seq_id": "NP_003679.2", "position": 709, "deleted_sequence": "D", "inserted_sequence": "D"}}}, "hgvs": "NM_003688.3:c.2129=", "refseq": "NM_003688.3", "so": [{"name": "coding_sequence_variant", "accession": "SO:0001580"}], "protein_product": {"refseq": "NP_003679.2"}}, {"codon_aligned_transcript_change": {"seq_id": "XM_005272686.4", "position": 2646, "deleted_sequence": "GAT", "inserted_sequence": "GAT"}, "protein": {"variant": {"spdi": {"seq_id": "XP_005272743.1", "position": 703, "deleted_sequence": "D", "inserted_sequence": "D"}}}, "hgvs": "XM_005272686.4:c.2111=", "refseq": "XM_005272686.4", "so": [{"name": "coding_sequence_variant", "accession": "SO:0001580"}], "protein_product": {"refseq": "XP_005272743.1"}}, {"codon_aligned_transcript_change": {"seq_id": "XM_006724566.3", "position": 2541, "deleted_sequence": "GAT", "inserted_sequence": "GAT"}, "protein": {"variant": {"spdi": {"seq_id": "XP_006724629.1", "position": 668, "deleted_sequence": "D", "inserted_sequence": "D"}}}, "hgvs": "XM_006724566.3:c.2006=", "refseq": "XM_006724566.3", "so": [{"name": "coding_sequence_variant", "accession": "SO:0001580"}], "protein_product": {"refseq": "XP_006724629.1"}}, {"codon_aligned_transcript_change": {"seq_id": "XM_011543993.2", "position": 2225, "deleted_sequence": "GAT", "inserted_sequence": "GAT"}, "protein": {"variant": {"spdi": {"seq_id": "XP_011542295.1", "position": 709, "deleted_sequence": "D", "inserted_sequence": "D"}}}, "hgvs": "XM_011543993.2:c.2129=", "refseq": "XM_011543993.2", "so": [{"name": "coding_sequence_variant", "accession": "SO:0001580"}], "protein_product": {"refseq": "XP_011542295.1"}}, {"codon_aligned_transcript_change": {"seq_id": "XM_011543994.2", "position": 2189, "deleted_sequence": "GAT", "inserted_sequence": "GAT"}, "protein": {"variant": {"spdi": {"seq_id": "XP_011542296.1", "position": 697, "deleted_sequence": "D", "inserted_sequence": "D"}}}, "hgvs": "XM_011543994.2:c.2093=", "refseq": "XM_011543994.2", "so": [{"name": "coding_sequence_variant", "accession": "SO:0001580"}], "protein_product": {"refseq": "XP_011542296.1"}}, {"codon_aligned_transcript_change": {"seq_id": "XM_011543995.2", "position": 2156, "deleted_sequence": "GAT", "inserted_sequence": "GAT"}, "protein": {"variant": {"spdi": {"seq_id": "XP_011542297.1", "position": 686, "deleted_sequence": "D", "inserted_sequence": "D"}}}, "hgvs": "XM_011543995.2:c.2060=", "refseq": "XM_011543995.2", "so": [{"name": "coding_sequence_variant", "accession": "SO:0001580"}], "protein_product": {"refseq": "XP_011542297.1"}}, {"codon_aligned_transcript_change": {"seq_id": "XM_011543996.2", "position": 2120, "deleted_sequence": "GAT", "inserted_sequence": "GAT"}, "protein": {"variant": {"spdi": {"seq_id": "XP_011542298.1", "position": 674, "deleted_sequence": "D", "inserted_sequence": "D"}}}, "hgvs": "XM_011543996.2:c.2024=", "refseq": "XM_011543996.2", "so": [{"name": "coding_sequence_variant", "accession": "SO:0001580"}], "protein_product": {"refseq": "XP_011542298.1"}}, {"codon_aligned_transcript_change": {"seq_id": "XM_011543997.3", "position": 1882, "deleted_sequence": "GAT", "inserted_sequence": "GAT"}, "protein": {"variant": {"spdi": {"seq_id": "XP_011542299.1", "position": 518, "deleted_sequence": "D", "inserted_sequence": "D"}}}, "hgvs": "XM_011543997.3:c.1556=", "refseq": "XM_011543997.3", "so": [{"name": "coding_sequence_variant", "accession": "SO:0001580"}], "protein_product": {"refseq": "XP_011542299.1"}}, {"codon_aligned_transcript_change": {"seq_id": "XM_024452473.1", "position": 1764, "deleted_sequence": "GAT", "inserted_sequence": "GAT"}, "protein": {"variant": {"spdi": {"seq_id": "XP_024308241.1", "position": 483, "deleted_sequence": "D", "inserted_sequence": "D"}}}, "hgvs": "XM_024452473.1:c.1451=", "refseq": "XM_024452473.1", "so": [{"name": "coding_sequence_variant", "accession": "SO:0001580"}], "protein_product": {"refseq": "XP_024308241.1"}}], "strand": "-", "geneid": 8573, "symbol": "CASK"}, "hg38": {"start": 41542717, "end": 41542717}, "vartype": "snv", "rsid": "rs137852818", "dbsnp_build": 154, "citations": 19377476, "chrom": "X", "ref": "T", "alt": "C"}, "hg38": {"start": 41542717, "end": 41542717}, "snpeff": {"ann": [{"gene_id": "CASK", "hgvs_p": "p.Asp710Gly", "cds": {"length": "2766", "position": "2129"}, "rank": "22", "feature_type": "transcript", "genename": "CASK", "effect": "missense_variant", "cdna": {"length": "8296", "position": "2175"}, "protein": {"length": "921", "position": "710"}, "transcript_biotype": "protein_coding", "putative_impact": "MODERATE", "hgvs_c": "c.2129A>G", "total": "27", "feature_id": "NM_003688.3"}, {"gene_id": "CASK", "hgvs_p": "p.Asp687Gly", "cds": {"length": "2697", "position": "2060"}, "rank": "21", "feature_type": "transcript", "genename": "CASK", "effect": "missense_variant", "cdna": {"length": "8227", "position": "2106"}, "protein": {"length": "898", "position": "687"}, "transcript_biotype": "protein_coding", "putative_impact": "MODERATE", "hgvs_c": "c.2060A>G", "total": "26", "feature_id": "NM_001126054.2"}, {"gene_id": "CASK", "hgvs_p": "p.Asp681Gly", "cds": {"length": "2694", "position": "2042"}, "rank": "20", "feature_type": "transcript", "genename": "CASK", "effect": "missense_variant", "cdna": {"length": "8224", "position": "2088"}, "protein": {"length": "897", "position": "681"}, "transcript_biotype": "protein_coding", "putative_impact": "MODERATE", "hgvs_c": "c.2042A>G", "total": "25", "feature_id": "NM_001126055.2"}]}, "vcf": {"position": "41542717", "ref": "T", "alt": "C"}, "chrom": "X", "clinvar": {"allele_id": 26573, "chrom": "X", "omim": "300172.0005", "hg19": {"start": 41401970, "end": 41401970}, "hg38": {"start": 41542717, "end": 41542717}, "type": "single nucleotide variant", "gene": {"id": "8573", "symbol": "CASK"}, "rcv": [{"preferred_name": "NM_001367721.1(CASK):c.2129A>G (p.Asp710Gly)", "accession": "RCV000012290", "clinical_significance": "Pathogenic", "number_submitters": 1, "review_status": "no assertion criteria provided", "last_evaluated": "2009-05-01", "origin": "germline", "conditions": {"name": "FG syndrome 4 (FGS4)", "synonyms": ["MENTAL RETARDATION, X-LINKED, WITH NYSTAGMUS", "MENTAL RETARDATION, X-LINKED, WITHOUT NYSTAGMUS", "X-Linked Intellectual Disability with or without Nystagmus"], "identifiers": {"mondo": "MONDO:0010318", "medgen": "C1845546", "omim": "300422"}}}, {"preferred_name": "NM_001367721.1(CASK):c.2129A>G (p.Asp710Gly)", "accession": "RCV000760252", "clinical_significance": "Likely pathogenic", "number_submitters": 1, "review_status": "criteria provided, single submitter", "last_evaluated": "2017-03-08", "origin": "maternal", "conditions": [{"name": "Mental retardation and microcephaly with pontine and cerebellar hypoplasia (MICPCH)", "synonyms": ["MICPCH SYNDROME", "MENTAL RETARDATION, X-LINKED, SYNDROMIC, NAJM TYPE", "Intellectual Disability and Microcephaly with Pontine and Cerebellar Hypoplasia"], "identifiers": {"mondo": "MONDO:0010417", "medgen": "C2677903", "orphanet": "163937", "omim": "300749"}}, {"name": "FG syndrome 4 (FGS4)", "synonyms": ["MENTAL RETARDATION, X-LINKED, WITH NYSTAGMUS", "MENTAL RETARDATION, X-LINKED, WITHOUT NYSTAGMUS", "X-Linked Intellectual Disability with or without Nystagmus"], "identifiers": {"mondo": "MONDO:0010318", "medgen": "C1845546", "omim": "300422"}}]}], "rsid": "rs137852818", "cytogenic": "Xp11.4", "hgvs": {"genomic": ["NC_000023.10:g.41401970T>C", "NC_000023.11:g.41542717T>C", "NG_016754.1:g.385318A>G", "NG_016754.2:g.385318A>G"], "coding": ["NM_001126054.2:c.2060A>G", "NM_001126055.2:c.2042A>G", "NM_001367721.1:c.2129A>G", "NM_003688.3:c.2129A>G"]}, "ref": "T", "alt": "C", "variant_id": 11534}, "uniprot": {"humsavar": {"ftid": "VAR_062998", "swiss_prot_ac": "O14936", "disease_name": "Mentalretardation and microcephaly with pontine and cerebellar hypoplasia (MICPCH) [MIM:300749]", "type_of_variant": "Disease"}}} diff --git a/src/tests/app/test_local.py b/src/tests/app/test_local.py new file mode 100644 index 00000000..ef9e8a41 --- /dev/null +++ b/src/tests/app/test_local.py @@ -0,0 +1,141 @@ +from time import sleep +from urllib.parse import urljoin + +from biothings.tests.web import BiothingsWebAppTest + + +class TestMetadataAssemblyAware(BiothingsWebAppTest): + TEST_DATA_DIR_NAME = 'mv_app_test' + + def test_metadata_source_assembly(self): + metadata_url = f'{self.prefix}/' + 'metadata/fields' + res_default = self.request(metadata_url) + res_hg19 = self.request(metadata_url, params={'assembly': 'hg19'}) + res_hg38 = self.request(metadata_url, params={'assembly': 'hg38'}) + assert res_default.json() == res_hg19.json() + assert res_hg19.json() != res_hg38.json() # I am not certain this will hold true + + def test_metadata_field_assembly(self): + metadata_url = f'{self.prefix}/' + 'metadata' + res_default = self.request(metadata_url) + res_hg19 = self.request(metadata_url, params={'assembly': 'hg19'}) + res_hg38 = self.request(metadata_url, params={'assembly': 'hg38'}) + assert res_default.json() == res_hg19.json() + assert res_hg19.json() != res_hg38.json() # I am not certain this will hold true + + +class TestAnnotationFields(BiothingsWebAppTest): + TEST_DATA_DIR_NAME = 'mv_app_test' + + def test_id_variant(self): + variant = 'chr8:g.7194707G>A' + res = self.request('variant', data={'id': variant}) + assert res.json()['_id'] == variant + + def test_id_hg19(self): + variant = 'chr8:g.7194707G>A' + res = self.request('hg19', data={'id': variant}) + assert res.json()['_id'] == variant + + def test_id_hg38(self): + variant = 'chrX:g.30718532C>T' + res = self.request('hg38', data={'id': variant}) + assert res.json()['_id'] == variant + + def test_clingen_caid(self): + # FIXME: this field is not found + pass + + def test_rsid(self): + variant = 'rs771931171' + res = self.request('variant', data={'id': variant}) + assert self.value_in_result(variant, res.json(), 'dbsnp.rsid', + case_insensitive=True) + + def test_rsid_ci(self): + variant = 'rS771931171' + res = self.request('variant', data={'id': variant}) + assert self.value_in_result(variant, res.json(), 'dbsnp.rsid', + case_insensitive=True) + + def test_rcv_id(self): + variant = 'RCV000665743' + res = self.request('variant', data={'id': variant}) + assert self.value_in_result(variant, res.json(), 'clinvar.rcv.accession', + case_insensitive=True) + def test_rcv_id_ci(self): + variant = 'rCv000665743' + res = self.request('variant', data={'id': variant}) + assert self.value_in_result(variant, res.json(), 'clinvar.rcv.accession', + case_insensitive=True) + + def test_ftid(self): + # also tests using hg38 as an argument to assembly + variant = 'VAR_062998' + res = self.request('variant', data={'id': variant, 'assembly': 'hg38'}) + assert self.value_in_result(variant, res.json(), 'uniprot.humsavar.ftid', + case_insensitive=True) + + def test_ftid_ci(self): + variant = 'var_062998' + res = self.request('variant', data={'id': variant, 'assembly': 'hg38'}) + assert self.value_in_result(variant, res.json(), 'uniprot.humsavar.ftid', + case_insensitive=True) + + +class TestRedirecdt(BiothingsWebAppTest): + def test_redir_1_expected(self): + # Not entirely sure what this is supposed to do + res = self.request('/v1/variant/chr8:7194707G>A', expect=301, + allow_redirects=False) + assert res.headers['location'] == '/v1/variant/chr8:g.7194707G>A' + + def test_redir_2(self): + res = self.request('/v1/variant/chr99:..1test', expect=301, + allow_redirects=False) + assert res.headers['location'] == '/v1/variant/chr99:g.1test' + + def test_redir_3(self): + res = self.request('/v1/variant/chr1:gg1test', expect=301, + allow_redirects=False) + assert res.headers['location'] == '/v1/variant/chr1:g.1test' + + def test_redir_4(self): + res = self.request('/v1/variant/chrTM:.g1test', expect=301, + allow_redirects=False) + assert res.headers['location'] == '/v1/variant/chrTM:g.1test' + + def test_redir_not(self): + # we don't have ES for this test class, expect 500 + self.request('/v1/variant/chr8:g.7194707G>A', expect=500, + allow_redirects=False) + + +class TestLicenseXfrm(BiothingsWebAppTest): + TEST_DATA_DIR_NAME = 'mv_app_test' + + def test_exac_nontcga(self): + res = self.request('variant', data={'id': 'chr8:g.7194707G>A'}) + assert '_license' in res.json()['exac_nontcga'] + + def test_gnomad_exome(self): + res = self.request('variant', data={'id': 'chr8:g.7194707G>A'}) + assert '_license' in res.json()['gnomad_exome'] + + def test_gnomad_genome(self): + res = self.request('variant', data={'id': 'chr8:g.7194707G>A'}) + assert '_license' in res.json()['gnomad_genome'] + + +class TestBeaconEndpoints(BiothingsWebAppTest): + pass + # FIXME: document the endpoint and implement tests + # for /beacon/*, handlers in web.beacon.handlers + + +class TestGenomicIntervalQuery(BiothingsWebAppTest): + TEST_DATA_DIR_NAME = 'mv_app_test' + + pass + # TODO: Write tests along with the correct implementation + # the data is already enough to write the tests diff --git a/src/tests/test_annotation.py b/src/tests/data/test_annotation.py similarity index 96% rename from src/tests/test_annotation.py rename to src/tests/data/test_annotation.py index 768552b5..7ef0e239 100644 --- a/src/tests/test_annotation.py +++ b/src/tests/data/test_annotation.py @@ -2,10 +2,12 @@ MyVariant Data-Aware Tests ''' -from biothings.tests.web import BiothingsTestCase +from biothings.tests.web import BiothingsDataTest -class TestMyvariant(BiothingsTestCase): +class TestMyvariant(BiothingsDataTest): + prefix = 'v1' + host = 'myvariant.info' # override def query(self, *args, **kwargs): diff --git a/src/tests/test_others.py b/src/tests/data/test_others.py similarity index 83% rename from src/tests/test_others.py rename to src/tests/data/test_others.py index 3bdc7bdf..bd4f47f0 100644 --- a/src/tests/test_others.py +++ b/src/tests/data/test_others.py @@ -1,14 +1,12 @@ -''' - MyVariant Data-Aware Tests -''' -import os -import time + from pprint import pformat -from biothings.tests.web import BiothingsTestCase +from biothings.tests.web import BiothingsDataTest -class TestMyvariant(BiothingsTestCase): +class TestMyvariant(BiothingsDataTest): + prefix = 'v1' + host = 'myvariant.info' def check_index_count(self, assembly): # when run individually @@ -18,7 +16,7 @@ def check_index_count(self, assembly): meta = self.request(f"{assembly}/metadata").json() results = {} for src_name in meta["src"]: - #if src_name == "cadd": + # if src_name == "cadd": # continue if src_name == "snpeff": continue # not a root src, counts always different @@ -30,7 +28,8 @@ def check_index_count(self, assembly): subsrc = subsrc.rstrip("s") # plural in meta, singular in docs meta_cnt = meta["src"][src_name]["stats"][stat] try: - res = self.request("query?q=_exists_:%s&size=0&assembly=%s" % (subsrc, assembly)).json() + res = self.request("query?q=_exists_:%s&size=0&assembly=%s" % + (subsrc, assembly)).json() except: print(f'Query error for ("{subsrc}", "{assembly}")') raise @@ -45,7 +44,6 @@ def check_index_count(self, assembly): errs[src]["diff"] = mc - ic assert len(errs) == 0, "Some counts don't match metadata:\n%s" % pformat(errs) - def test_300_metadata(self): self.request("metadata").content @@ -61,11 +59,6 @@ def test_301_fields(self): assert 'wellderly' in res assert 'clinvar' in res - def test_310_status(self): - self.request(self.host + '/status') - # (testing failing status would require actually loading tornado app from there - # and deal with config params...) - def test_320_index_count_hg19(self): self.check_index_count("hg19") diff --git a/src/tests/test_query.py b/src/tests/data/test_query.py similarity index 98% rename from src/tests/test_query.py rename to src/tests/data/test_query.py index 8c1d653d..b324a10d 100644 --- a/src/tests/test_query.py +++ b/src/tests/data/test_query.py @@ -1,13 +1,10 @@ -''' - MyVariant Data-Aware Tests -''' -import os -from pprint import pformat -from biothings.tests.web import BiothingsTestCase +from biothings.tests.web import BiothingsDataTest -class TestMyvariant(BiothingsTestCase): +class TestMyvariant(BiothingsDataTest): + prefix = 'v1' + host = 'myvariant.info' # override def query(self, *args, **kwargs): @@ -66,7 +63,8 @@ def test_129_query(self): self.query(q='snpeff.ann.genename:BTK', morethan=8000) def test_130_query(self): - self.query(q='_exists_:wellderly AND cadd.polyphen.cat:possibly_damaging', fields='wellderly,cadd.polyphen') + self.query(q='_exists_:wellderly AND cadd.polyphen.cat:possibly_damaging', + fields='wellderly,cadd.polyphen') def test_131_query_jsonld(self): pass # feature removed in biothings 0.7.0 diff --git a/src/web/handlers.py b/src/web/handlers.py index 8e76660c..49a557d0 100644 --- a/src/web/handlers.py +++ b/src/web/handlers.py @@ -1,19 +1,20 @@ from tornado.web import RequestHandler -from biothings.web.handlers.es import (MetadataFieldHandler, - MetadataSourceHandler) +from biothings.web.handlers import ( + MetadataFieldHandler, + MetadataSourceHandler) class AssemblyAwareMixin(RequestHandler): - + def prepare(self): super().prepare() - self.biothing_type = self.args.es.assembly + self.biothing_type = self.args.assembly -class MVMetadataFieldHandler(AssemblyAwareMixin, MetadataFieldHandler): +class MVMetadataFieldHandler(AssemblyAwareMixin, MetadataFieldHandler): pass -class MVMetadataSourceHandler(AssemblyAwareMixin, MetadataSourceHandler): +class MVMetadataSourceHandler(AssemblyAwareMixin, MetadataSourceHandler): pass diff --git a/src/web/pipeline.py b/src/web/pipeline.py index df901d4f..bd241f9a 100644 --- a/src/web/pipeline.py +++ b/src/web/pipeline.py @@ -1,12 +1,13 @@ import re -from biothings.utils.web.es_dsl import AsyncSearch -from biothings.web.pipeline import ESQueryBuilder, ESQueryBackend +from elasticsearch_dsl import Search +from biothings.web.query import ESQueryBuilder, AsyncESQueryBackend INTERVAL_PATTERN = re.compile( r'(?P.+(?P[Aa][Nn][Dd]))*(?P\s*chr(?P[1-9xXyYmM][0-9tT]?):(?P[0-9,]+)-(?P[0-9,]+)\s*)(?P(?P[Aa][Nn][Dd]).+)*') -SNP_PATTERN = re.compile(r'(?P.+(?P[Aa][Nn][Dd]))*(?P\s*chr(?P[1-9xXyYmM][0-9tT]?):(?P(?P[0-9,]+))\s*)(?P(?P[Aa][Nn][Dd]).+)*') +SNP_PATTERN = re.compile( + r'(?P.+(?P[Aa][Nn][Dd]))*(?P\s*chr(?P[1-9xXyYmM][0-9tT]?):(?P(?P[0-9,]+))\s*)(?P(?P[Aa][Nn][Dd]).+)*') PATTERNS = [INTERVAL_PATTERN, SNP_PATTERN] @@ -33,7 +34,7 @@ def default_string_query(self, q, options): match = self._parse_interval_query(q) if match: # interval query - search = AsyncSearch() + search = Search() if match['query']: search = search.query("query_string", query=match['query']) search = search.filter('match', chrom=match['chr']) @@ -47,12 +48,12 @@ def default_string_query(self, q, options): return search -class MVQueryBackend(ESQueryBackend): +class MVQueryBackend(AsyncESQueryBackend): - def execute(self, query, options): + def execute(self, query, **options): # override index to query - if options.assembly == 'hg38': - options.biothing_type = 'hg38' + if options.get('assembly') == 'hg38': + options['biothing_type'] = 'hg38' - return super().execute(query, options) + return super().execute(query, **options)