diff --git a/.python-version b/.python-version deleted file mode 100644 index db0033b7..00000000 --- a/.python-version +++ /dev/null @@ -1 +0,0 @@ -ensembl_metadata_api diff --git a/.travis.yml b/.travis.yml index b1177099..1b28ddaa 100644 --- a/.travis.yml +++ b/.travis.yml @@ -8,10 +8,14 @@ python: env: - TESTENV=test +services: + - mysql + before_script: - pip install -r requirements-test.txt - pip install . - export PYTHONPATH=$PYTHONPATH:$PWD/src + - mysql -u root -h 127.0.0.1 -e 'CREATE DATABASE ncbi_taxonomy; CREATE DATABASE ensembl_metadata_2020; use ncbi_taxonomy; source tests/ncbi_taxonomy.sql; use ensembl_metadata_2020; source tests/ensembl_metadata_2020.sql;' script: - if [[ "$TESTENV" == "test" ]]; then coverage run -m pytest; fi diff --git a/src/ensembl/production/metadata/api.py b/src/ensembl/production/metadata/api.py index 1598d8a3..ec324f8d 100644 --- a/src/ensembl/production/metadata/api.py +++ b/src/ensembl/production/metadata/api.py @@ -10,37 +10,12 @@ # See the License for the specific language governing permissions and # limitations under the License. import sqlalchemy as db -from sqlalchemy import select -from sqlalchemy.orm import Session, sessionmaker -import pymysql from ensembl.production.metadata.config import get_metadata_uri, get_taxonomy_uri from ensembl.database.dbconnection import DBConnection +from ensembl.ncbi_taxonomy.models import NCBITaxaName, NCBITaxaNode from ensembl.production.metadata.models import * -#Database ORM connection. -class load_database(DBConnection): - """ - Load a database and directly create a session for ORM interaction with the database - """ - def create_session(self, engine): - self._session = Session(engine, future=True) - - def __init__(self, url): - super().__init__(url) - self.create_session(self._engine) - - #Commit any changes to the database and create a new session instance. - def commit(self): - self._session.commit() - self._session.close() - self.create_session(self._engine) - - #rollback any changes made before commiting the session instance. - def rollback(self): - self._session.rollback() - - def check_parameter(param): if param is not None and not isinstance(param, list): param = [param] @@ -51,57 +26,57 @@ class BaseAdaptor: def __init__(self, metadata_uri=None): if metadata_uri is None: metadata_uri = get_metadata_uri() - self.metadata_db = load_database(metadata_uri) + self.metadata_db = DBConnection(metadata_uri) class ReleaseAdaptor(BaseAdaptor): def fetch_releases( - self, - release_id=None, - release_version=None, - current_only=True, - release_type=None, - site_name=None, + self, + release_id=None, + release_version=None, + current_only=True, + release_type=None, + site_name=None, ): release_id = check_parameter(release_id) release_version = check_parameter(release_version) release_type = check_parameter(release_type) site_name = check_parameter(site_name) - release_select = db.select( - EnsemblRelease,EnsemblSite + EnsemblRelease, EnsemblSite ).join(EnsemblRelease.ensembl_site) - #WHERE ensembl_release.release_id = :release_id_1 + # WHERE ensembl_release.release_id = :release_id_1 if release_id is not None: release_select = release_select.filter( EnsemblRelease.release_id.in_(release_id) ) - #WHERE ensembl_release.version = :version_1 + # WHERE ensembl_release.version = :version_1 elif release_version is not None: release_select = release_select.filter( EnsemblRelease.version.in_(release_version) ) - #WHERE ensembl_release.is_current =:is_current_1 + # WHERE ensembl_release.is_current =:is_current_1 elif current_only: release_select = release_select.filter( EnsemblRelease.is_current == 1 ) - #WHERE ensembl_release.release_type = :release_type_1 + # WHERE ensembl_release.release_type = :release_type_1 if release_type is not None: release_select = release_select.filter( EnsemblRelease.release_type.in_(release_type) ) - #WHERE ensembl_site.name = :name_1 + # WHERE ensembl_site.name = :name_1 if site_name is not None: release_select = release_select.filter( EnsemblSite.name.in_(site_name) ) - return self.metadata_db._session.execute(release_select) - + with self.metadata_db.session_scope() as session: + session.expire_on_commit = False + return session.execute(release_select).all() def fetch_releases_for_genome(self, genome_uuid, site_name=None): @@ -118,10 +93,11 @@ def fetch_releases_for_genome(self, genome_uuid, site_name=None): ) release_ids = [] - release_objects = self.metadata_db._session.execute(release_id_select) - for rid in release_objects: - release_ids.append(rid[0]) - release_ids = list(dict.fromkeys(release_ids)) + with self.metadata_db.session_scope() as session: + release_objects = session.execute(release_id_select).all() + for rid in release_objects: + release_ids.append(rid[0]) + release_ids = list(dict.fromkeys(release_ids)) return self.fetch_releases(release_id=release_ids, site_name=site_name) def fetch_releases_for_dataset(self, dataset_uuid, site_name=None): @@ -139,85 +115,85 @@ def fetch_releases_for_dataset(self, dataset_uuid, site_name=None): ) release_ids = [] - release_objects = self.metadata_db._session.execute(release_id_select) - for rid in release_objects: - release_ids.append(rid[0]) - release_ids = list(dict.fromkeys(release_ids)) - + with self.metadata_db.session_scope() as session: + release_objects = session.execute(release_id_select).all() + for rid in release_objects: + release_ids.append(rid[0]) + release_ids = list(dict.fromkeys(release_ids)) return self.fetch_releases(release_id=release_ids, site_name=site_name) class GenomeAdaptor(BaseAdaptor): - taxon_names = {} - def __init__(self, metadata_uri=None, taxonomy_uri=None): super().__init__(metadata_uri) if taxonomy_uri is None: - taxonomy_uri = config.TAXONOMY_URI - self.taxonomy_db = load_database(taxonomy_uri) - self.taxonomy_db_session = Session(self.taxonomy_db, future=True) - - # Cache the taxon names; data is in a separate db, - # which is tricky to fetch elegantly and efficiently otherwise. - taxonomy_ids = self.fetch_taxonomy_ids() - self.taxon_names = self.fetch_taxonomy_names(taxonomy_ids) - - def fetch_taxonomy_ids(self): - organism = db.Table("organism", self.md, autoload_with=self.metadata_db) - taxonomy_id_select = db.select(organism.c.taxonomy_id.distinct()) - taxonomy_ids = [tid for (tid,) in self.metadata_db.execute(taxonomy_id_select)] - return taxonomy_ids - - def fetch_taxonomy_names(self, taxonomy_id): - ncbi_taxa_name = db.Table( - "ncbi_taxa_name", self.md, autoload_with=self.taxonomy_db - ) + taxonomy_uri = get_taxonomy_uri() + self.taxonomy_db = DBConnection(taxonomy_uri) + + def fetch_taxonomy_names(self, taxonomy_ids): taxons = {} - for tid in taxonomy_id: + for tid in taxonomy_ids: names = {"scientific_name": None, "synonym": []} taxons[tid] = names - sci_name_select = db.select( - ncbi_taxa_name.c.taxon_id, ncbi_taxa_name.c.name - ).filter( - ncbi_taxa_name.c.taxon_id.in_(taxonomy_id), - ncbi_taxa_name.c.name_class == "scientific name", - ) - for x in self.taxonomy_db.execute(sci_name_select): - taxons[x.taxon_id]["scientific_name"] = x.name - - synonym_class = [ - "common name", - "equivalent name", - "genbank common name", - "genbank synonym", - "synonym", - ] - synonyms_select = db.select( - ncbi_taxa_name.c.taxon_id, ncbi_taxa_name.c.name - ).filter( - ncbi_taxa_name.c.taxon_id.in_(taxonomy_id), - ncbi_taxa_name.c.name_class.in_(synonym_class), - ) - for x in self.taxonomy_db.execute(synonyms_select): - taxons[x.taxon_id]["synonym"].append(x.name) + for taxon in taxons: + sci_name_select = db.select( + NCBITaxaName.name + ).filter( + NCBITaxaName.taxon_id == taxon, + NCBITaxaName.name_class == "scientific name", + ) + synonym_class = [ + "common name", + "equivalent name", + "genbank common name", + "genbank synonym", + "synonym", + ] + + synonyms_select = db.select( + NCBITaxaName.name + ).filter( + NCBITaxaName.taxon_id == taxon, + NCBITaxaName.name_class.in_(synonym_class), + ) + with self.taxonomy_db.session_scope() as session: + sci_name = session.execute(sci_name_select).one() + taxons[taxon]["scientific_name"] = sci_name[0] + synonyms = session.execute(synonyms_select).all() + for synonym in synonyms: + taxons[taxon]["synonym"].append(synonym[0]) return taxons + def fetch_taxonomy_ids(self, taxonomy_names): + taxids = [] + taxonomy_names = check_parameter(taxonomy_names) + for taxon in taxonomy_names: + taxa_name_select = db.select( + NCBITaxaName.taxon_id + ).filter( + NCBITaxaName.name == taxon + ) + with self.taxonomy_db.session_scope() as session: + taxid = session.execute(taxa_name_select).one() + taxids.append(taxid[0]) + return taxids + def fetch_genomes( - self, - genome_id=None, - genome_uuid=None, - assembly_accession=None, - ensembl_name=None, - taxonomy_id=None, - unreleased_only=False, - site_name=None, - release_type=None, - release_version=None, - current_only=True, + self, + genome_id=None, + genome_uuid=None, + assembly_accession=None, + ensembl_name=None, + taxonomy_id=None, + unreleased_only=False, + site_name=None, + release_type=None, + release_version=None, + current_only=True, ): genome_id = check_parameter(genome_id) genome_uuid = check_parameter(genome_uuid) @@ -225,98 +201,58 @@ def fetch_genomes( ensembl_name = check_parameter(ensembl_name) taxonomy_id = check_parameter(taxonomy_id) - genome = db.Table("genome", self.md, autoload_with=self.metadata_db) - assembly = self.md.tables["assembly"] - organism = self.md.tables["organism"] - - genome_select = ( - db.select( - genome.c.genome_id, - genome.c.genome_uuid, - organism.c.ensembl_name, - organism.c.url_name, - organism.c.display_name, - organism.c.strain, - organism.c.taxonomy_id, - assembly.c.accession.label("assembly_accession"), - assembly.c.name.label("assembly_name"), - assembly.c.ucsc_name.label("assembly_ucsc_name"), - assembly.c.level.label("assembly_level"), - ) - .select_from(genome) - .join(assembly) - .join(organism) - ) + genome_select = db.select( + Genome, Organism, Assembly + ).join(Genome.assembly).join(Genome.organism) if unreleased_only: - genome_release = db.Table( - "genome_release", self.md, autoload_with=self.metadata_db - ) - - genome_select = genome_select.outerjoin(genome_release).filter_by( - genome_id=None + genome_select = genome_select.outerjoin(Genome.genome_releases).filter( + GenomeRelease.genome_id == None ) - elif site_name is not None: - genome_release = db.Table( - "genome_release", self.md, autoload_with=self.metadata_db - ) - release = self.md.tables["ensembl_release"] - site = self.md.tables["ensembl_site"] - - genome_select = ( - genome_select.join(genome_release) - .join(release) - .join(site) - .filter_by(name=site_name) - ) + genome_select = genome_select.join( + Genome.genome_releases).join( + GenomeRelease.ensembl_release).join( + EnsemblRelease.ensembl_site).filter(EnsemblSite.name == site_name) if release_type is not None: - genome_select = genome_select.filter( - release.c.release_type == release_type - ) + genome_select = genome_select.filter(EnsemblRelease.release_type == release_type) if current_only: - genome_select = genome_select.filter(genome_release.c.is_current == 1) + genome_select = genome_select.filter(GenomeRelease.is_current == 1) if release_version is not None: - genome_select = genome_select.filter( - release.c.version <= release_version - ) + genome_select = genome_select.filter(EnsemblRelease.version <= release_version) # These options are in order of decreasing specificity, # and thus the ones later in the list can be redundant. if genome_id is not None: - genome_select = genome_select.filter(genome.c.genome_id.in_(genome_id)) + genome_select = genome_select.filter(Genome.genome_id == genome_id) + elif genome_uuid is not None: - genome_select = genome_select.filter(genome.c.genome_uuid.in_(genome_uuid)) + genome_select = genome_select.filter(Genome.genome_uuid == genome_uuid) + elif assembly_accession is not None: - genome_select = genome_select.filter( - assembly.c.accession.in_(assembly_accession) - ) + genome_select = genome_select.filter(Assembly.accession == assembly_accession) + elif ensembl_name is not None: - genome_select = genome_select.filter( - organism.c.ensembl_name.in_(ensembl_name) - ) + genome_select = genome_select.filter(Organism.ensembl_name == ensembl_name) + elif taxonomy_id is not None: - genome_select = genome_select.filter( - organism.c.taxonomy_id.in_(taxonomy_id) - ) + genome_select = genome_select.filter(Organism.taxonomy_id == taxonomy_id) - for result in self.metadata_db_session.execute(genome_select): - taxon_names = self.taxon_names[result.taxonomy_id] - result_dict = dict(result) - result_dict.update(taxon_names) - yield result_dict + with self.metadata_db.session_scope() as session: + session.expire_on_commit = False + return session.execute(genome_select).all() def fetch_genomes_by_genome_uuid( - self, - genome_uuid, - unreleased_only=False, - site_name=None, - release_type=None, - release_version=None, - current_only=True, + self, + genome_uuid, + unreleased_only=False, + site_name=None, + release_type=None, + release_version=None, + current_only=True, ): return self.fetch_genomes( genome_uuid=genome_uuid, @@ -328,13 +264,13 @@ def fetch_genomes_by_genome_uuid( ) def fetch_genomes_by_assembly_accession( - self, - assembly_accession, - unreleased_only=False, - site_name=None, - release_type=None, - release_version=None, - current_only=True, + self, + assembly_accession, + unreleased_only=False, + site_name=None, + release_type=None, + release_version=None, + current_only=True, ): return self.fetch_genomes( assembly_accession=assembly_accession, @@ -346,13 +282,13 @@ def fetch_genomes_by_assembly_accession( ) def fetch_genomes_by_ensembl_name( - self, - ensembl_name, - unreleased_only=False, - site_name=None, - release_type=None, - release_version=None, - current_only=True, + self, + ensembl_name, + unreleased_only=False, + site_name=None, + release_type=None, + release_version=None, + current_only=True, ): return self.fetch_genomes( ensembl_name=ensembl_name, @@ -364,13 +300,13 @@ def fetch_genomes_by_ensembl_name( ) def fetch_genomes_by_taxonomy_id( - self, - taxonomy_id, - unreleased_only=False, - site_name=None, - release_type=None, - release_version=None, - current_only=True, + self, + taxonomy_id, + unreleased_only=False, + site_name=None, + release_type=None, + release_version=None, + current_only=True, ): return self.fetch_genomes( taxonomy_id=taxonomy_id, @@ -382,44 +318,15 @@ def fetch_genomes_by_taxonomy_id( ) def fetch_genomes_by_scientific_name( - self, - scientific_name, - unreleased_only=False, - site_name=None, - release_type=None, - release_version=None, - current_only=True, + self, + scientific_name, + unreleased_only=False, + site_name=None, + release_type=None, + release_version=None, + current_only=True, ): - taxonomy_ids = [ - t_id - for t_id in self.taxon_names - if self.taxon_names[t_id]["scientific_name"] == scientific_name - ] - - return self.fetch_genomes_by_taxonomy_id( - taxonomy_ids, - unreleased_only=unreleased_only, - site_name=site_name, - release_type=release_type, - release_version=release_version, - current_only=current_only, - ) - - def fetch_genomes_by_synonym( - self, - synonym, - unreleased_only=False, - site_name=None, - release_type=None, - release_version=None, - current_only=True, - ): - taxonomy_ids = [] - for taxon_id in self.taxon_names: - if synonym.casefold() in [ - x.casefold() for x in self.taxon_names[taxon_id]["synonym"] - ]: - taxonomy_ids.append(taxon_id) + taxonomy_ids = self.fetch_taxonomy_ids(scientific_name) return self.fetch_genomes_by_taxonomy_id( taxonomy_ids, @@ -431,57 +338,39 @@ def fetch_genomes_by_synonym( ) def fetch_sequences( - self, - genome_id=None, - genome_uuid=None, - assembly_accession=None, - chromosomal_only=False, + self, + genome_id=None, + genome_uuid=None, + assembly_accession=None, + chromosomal_only=False, ): genome_id = check_parameter(genome_id) genome_uuid = check_parameter(genome_uuid) assembly_accession = check_parameter(assembly_accession) - assembly = db.Table("assembly", self.md, autoload_with=self.metadata_db) - assembly_sequence = db.Table( - "assembly_sequence", self.md, autoload_with=self.metadata_db - ) + seq_select = db.select(AssemblySequence, ) - seq_select = ( - db.select( - assembly_sequence.c.accession, - assembly_sequence.c.name, - assembly_sequence.c.sequence_location, - assembly_sequence.c.length, - assembly_sequence.c.chromosomal, - assembly_sequence.c.sequence_checksum, - assembly_sequence.c.ga4gh_identifier, - ) - .select_from(assembly) - .join( - assembly_sequence, - assembly.c.assembly_id == assembly_sequence.c.assembly_id, - ) - ) if chromosomal_only: - seq_select = seq_select.filter_by(chromosomal=1) + seq_select = seq_select.filter(AssemblySequence.chromosomal == 1) # These options are in order of decreasing specificity, # and thus the ones later in the list can be redundant. if genome_id is not None: - genome = db.Table("genome", self.md, autoload_with=self.metadata_db) - seq_select = seq_select.join(genome).filter( - genome.c.genome_id.in_(genome_id) + seq_select = seq_select.join(AssemblySequence.assembly).join(Assembly.genomes).filter( + Genome.genome_id == genome_id ) + elif genome_uuid is not None: - genome = db.Table("genome", self.md, autoload_with=self.metadata_db) - seq_select = seq_select.join(genome).filter( - genome.c.genome_uuid.in_(genome_uuid) + seq_select = seq_select.join(AssemblySequence.assembly).join(Assembly.genomes).filter( + Genome.genome_uuid == genome_uuid ) + elif assembly_accession is not None: - seq_select = seq_select.filter(assembly.c.accession.in_(assembly_accession)) + seq_select = seq_select.filter(Assembly.accession == assembly_accession) - for result in self.metadata_db_session.execute(seq_select): - yield dict(result) + with self.metadata_db.session_scope() as session: + session.expire_on_commit = False + return session.execute(seq_select).all() def fetch_sequences_by_genome_uuid(self, genome_uuid, chromosomal_only=False): return self.fetch_sequences( @@ -489,7 +378,7 @@ def fetch_sequences_by_genome_uuid(self, genome_uuid, chromosomal_only=False): ) def fetch_sequences_by_assembly_accession( - self, assembly_accession, chromosomal_only=False + self, assembly_accession, chromosomal_only=False ): return self.fetch_sequences( assembly_accession=assembly_accession, chromosomal_only=chromosomal_only diff --git a/src/ensembl/production/metadata/models.py b/src/ensembl/production/metadata/models.py index 336d5e24..d74b8711 100644 --- a/src/ensembl/production/metadata/models.py +++ b/src/ensembl/production/metadata/models.py @@ -19,11 +19,9 @@ from sqlalchemy.ext.declarative import declarative_base from sqlalchemy import create_engine, MetaData, inspect - Base = declarative_base() metadata = Base.metadata - class Assembly(Base): __tablename__ = 'assembly' diff --git a/tests/TEST.db b/tests/TEST.db deleted file mode 100644 index dfd297ad..00000000 Binary files a/tests/TEST.db and /dev/null differ diff --git a/tests/ensembl_metadata_2020.sql b/tests/ensembl_metadata_2020.sql new file mode 100644 index 00000000..3b364a30 --- /dev/null +++ b/tests/ensembl_metadata_2020.sql @@ -0,0 +1,497 @@ +-- noinspection SqlDialectInspectionForFile + +-- noinspection SqlNoDataSourceInspectionForFile + +-- MySQL dump 10.13 Distrib 8.0.30, for Linux (x86_64) +-- +-- Host: localhost Database: ensembl_metadata_2020 +-- ------------------------------------------------------ +-- Server version 8.0.30-0ubuntu0.22.04.1 + +/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */; +/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */; +/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */; +/*!50503 SET NAMES utf8 */; +/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */; +/*!40103 SET TIME_ZONE='+00:00' */; +/*!40014 SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0 */; +/*!40014 SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0 */; +/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='NO_AUTO_VALUE_ON_ZERO' */; +/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */; + +-- +-- Current Database: `ensembl_metadata_2020` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `ensembl_metadata_2020` /*!40100 DEFAULT CHARACTER SET utf8 COLLATE utf8_general_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `ensembl_metadata_2020`; + +-- +-- Table structure for table `assembly` +-- + +DROP TABLE IF EXISTS `assembly`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8 */; +CREATE TABLE `assembly` ( + `assembly_id` int NOT NULL AUTO_INCREMENT, + `ucsc_name` varchar(16) DEFAULT NULL, + `accession` varchar(16) NOT NULL, + `level` varchar(32) NOT NULL, + `name` varchar(128) NOT NULL, + `accession_body` varchar(32) DEFAULT NULL, + `assembly_default` varchar(32) DEFAULT NULL, + `tolid` varchar(32) DEFAULT NULL, + `created` datetime DEFAULT NULL, + `ensembl_name` varchar(255) DEFAULT NULL, + PRIMARY KEY (`assembly_id`), + UNIQUE KEY `accession` (`accession`), + UNIQUE KEY `tol_id_key` (`tolid`), + UNIQUE KEY `assembly_ensembl_name_uindex` (`ensembl_name`) +) ENGINE=InnoDB AUTO_INCREMENT=9 DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Dumping data for table `assembly` +-- + +LOCK TABLES `assembly` WRITE; +/*!40000 ALTER TABLE `assembly` DISABLE KEYS */; +INSERT INTO `assembly` VALUES (1,NULL,'GCA_000005845.2','chromosome','ASM584v2',NULL,NULL,NULL,'2022-06-21 10:18:12',NULL),(2,NULL,'GCA_000002985.3','chromosome','WBcel235',NULL,NULL,NULL,'2022-06-21 10:18:12',NULL),(3,'hg38','GCA_000001405.28','chromosome','GRCh38.p13',NULL,NULL,NULL,'2022-06-21 10:18:12','grch38'),(4,NULL,'GCA_000002765.2','chromosome','ASM276v2',NULL,NULL,NULL,'2022-06-21 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(`assembly_sequence_id`), + UNIQUE KEY `assembly_sequence_assembly_id_accession_5f3e5119_uniq` (`assembly_id`,`accession`), + KEY `assembly_sequence_assembly_id_2a84ddcb` (`assembly_id`), + CONSTRAINT `assembly_sequence_assembly_id_2a84ddcb_fk_assembly_assembly_id` FOREIGN KEY (`assembly_id`) REFERENCES `assembly` (`assembly_id`) +) ENGINE=InnoDB AUTO_INCREMENT=256 DEFAULT CHARSET=latin1 ROW_FORMAT=COMPACT; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Dumping data for table `assembly_sequence` +-- + +LOCK TABLES `assembly_sequence` WRITE; +/*!40000 ALTER TABLE `assembly_sequence` DISABLE KEYS */; +INSERT INTO `assembly_sequence` VALUES 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08:24:42.000000',12,'InterPro2GO mapping'),(262,'a7434722-93e7-11ec-a39d-005056b38ce3',17,'interproscan','5.48-83.0','2022-01-26 17:59:38.000000',2,'InterProScan'),(263,'a74347a0-93e7-11ec-a39d-005056b38ce3',17,'interproscan','5.48-83.0','2022-01-26 18:43:00.000000',4,'InterProScan'),(264,'a7434811-93e7-11ec-a39d-005056b38ce3',17,'interproscan','5.48-83.0','2022-01-27 07:59:56.000000',9,'InterProScan'),(265,'a7434889-93e7-11ec-a39d-005056b38ce3',17,'interproscan','5.48-83.0','2022-01-27 08:03:06.000000',10,'InterProScan'),(266,'a74348f4-93e7-11ec-a39d-005056b38ce3',17,'interproscan','5.48-83.0','2022-01-27 08:24:42.000000',12,'InterProScan'),(267,'a7434963-93e7-11ec-a39d-005056b38ce3',18,'ena_repeat_dispersed','2020-01-22','2022-01-26 17:46:20.000000',1,'Dispersed repeats (ENA)'),(268,'a74349d2-93e7-11ec-a39d-005056b38ce3',18,'ena_repeat_tandem','2020-01-21','2022-01-26 17:46:20.000000',1,'Tandem repeats 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(ENA)'),(277,'a7434d79-93e7-11ec-a39d-005056b38ce3',18,'ena_repeat','2020-01-21','2022-01-26 17:46:20.000000',1,'Repeats (ENA)'),(278,'a7434dda-93e7-11ec-a39d-005056b38ce3',18,'ena_repeat','2020-01-21','2022-01-26 17:46:20.000000',1,'Repeats (ENA)'),(279,'a7434ea2-93e7-11ec-a39d-005056b38ce3',18,'ena_repeat_tandem','2020-01-21','2022-01-26 17:46:20.000000',1,'Tandem repeats (ENA)'),(280,'a7434f12-93e7-11ec-a39d-005056b38ce3',18,'ena_repeat','2020-01-21','2022-01-26 17:46:20.000000',1,'Repeats (ENA)'),(281,'a7434f7b-93e7-11ec-a39d-005056b38ce3',18,'ena_repeat','2020-01-21','2022-01-26 17:46:20.000000',1,'Repeats (ENA)'),(282,'a7434fdf-93e7-11ec-a39d-005056b38ce3',18,'ena_repeat_tandem','2020-01-21','2022-01-26 17:46:20.000000',1,'Tandem repeats (ENA)'),(283,'a7435043-93e7-11ec-a39d-005056b38ce3',18,'ena_repeat','2020-01-21','2022-01-26 17:46:20.000000',1,'Repeats (ENA)'),(284,'a74350a5-93e7-11ec-a39d-005056b38ce3',18,'ena_repeat','2020-01-21','2022-01-26 17:46:20.000000',1,'Repeats (ENA)'),(285,'a7435108-93e7-11ec-a39d-005056b38ce3',18,'ena_repeat','2020-01-21','2022-01-26 17:46:20.000000',1,'Repeats (ENA)'),(286,'a743516a-93e7-11ec-a39d-005056b38ce3',18,'ena_repeat','2020-01-21','2022-01-26 17:46:20.000000',1,'Repeats (ENA)'),(287,'a74351c9-93e7-11ec-a39d-005056b38ce3',18,'ena_repeat','2020-01-21','2022-01-26 17:46:20.000000',1,'Repeats (ENA)'),(288,'a7435227-93e7-11ec-a39d-005056b38ce3',18,'ena_repeat','2020-01-21','2022-01-26 17:46:20.000000',1,'Repeats (ENA)'),(289,'a7435285-93e7-11ec-a39d-005056b38ce3',18,'ena_repeat','2020-01-21','2022-01-26 17:46:20.000000',1,'Repeats (ENA)'),(290,'a74352e9-93e7-11ec-a39d-005056b38ce3',18,'ena_repeat','2020-01-21','2022-01-26 17:46:20.000000',1,'Repeats (ENA)'),(291,'a743534b-93e7-11ec-a39d-005056b38ce3',18,'ena_repeat','2020-01-21','2022-01-26 17:46:20.000000',1,'Repeats (ENA)'),(292,'a74353ac-93e7-11ec-a39d-005056b38ce3',18,'ena_repeat_tandem','2020-01-21','2022-01-26 17:46:20.000000',1,'Tandem repeats (ENA)'),(293,'a743540e-93e7-11ec-a39d-005056b38ce3',18,'ena_repeat','2020-01-21','2022-01-26 17:46:20.000000',1,'Repeats (ENA)'),(294,'a743546e-93e7-11ec-a39d-005056b38ce3',18,'ena_repeat','2020-01-21','2022-01-26 17:46:20.000000',1,'Repeats (ENA)'),(295,'a74354d1-93e7-11ec-a39d-005056b38ce3',18,'ena_repeat','2020-01-21','2022-01-26 17:46:20.000000',1,'Repeats (ENA)'),(296,'a7435531-93e7-11ec-a39d-005056b38ce3',18,'ena_repeat','2020-01-21','2022-01-26 17:46:20.000000',1,'Repeats (ENA)'),(297,'a74355a5-93e7-11ec-a39d-005056b38ce3',18,'dust','1','2022-01-26 17:59:38.000000',2,'Low complexity (Dust)'),(298,'a743560f-93e7-11ec-a39d-005056b38ce3',18,'repeatmask','1','2022-01-26 17:59:38.000000',2,'Repeats'),(299,'a7435673-93e7-11ec-a39d-005056b38ce3',18,'trf','1','2022-01-26 17:59:38.000000',2,'Tandem repeats (TRF)'),(300,'a74356e2-93e7-11ec-a39d-005056b38ce3',18,'dust','1','2022-01-26 18:43:00.000000',4,'Low complexity 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REdat'),(309,'a7435b35-93e7-11ec-a39d-005056b38ce3',18,'repeatmask_repbase','4.0.5','2022-01-27 08:24:42.000000',12,'Repeats: Repbase'),(310,'a7435be8-93e7-11ec-a39d-005056b38ce3',18,'tallymer','2018-11-05','2022-01-27 08:24:42.000000',12,'Repeats: Tallymer'),(311,'a7435c52-93e7-11ec-a39d-005056b38ce3',18,'trf','4.0','2022-01-27 08:24:42.000000',12,'Tandem repeats (TRF)'),(312,'a7435cc3-93e7-11ec-a39d-005056b38ce3',6,'grc_alignment_import','GRCh38.p2','2022-02-22 13:59:29.000000',6,'GRC alignment import'),(313,'a7435d4e-93e7-11ec-a39d-005056b38ce3',6,'human_est','Jan 31 12:35','2022-02-22 13:59:29.000000',6,'Human ESTs'),(314,'a7435e01-93e7-11ec-a39d-005056b38ce3',7,'ccds_import','24042014','2022-02-22 13:59:29.000000',6,'CCDS set'),(315,'a7435e81-93e7-11ec-a39d-005056b38ce3',7,'cls_all_anchored','GSE93848','2022-02-22 13:59:29.000000',6,'All Capture Long-Seq (anchored)'),(316,'a7435ef3-93e7-11ec-a39d-005056b38ce3',7,'cls_all_unanchored','GSE93848','2022-02-22 13:59:29.000000',6,'All Capture Long-Seq'),(317,'a7435f61-93e7-11ec-a39d-005056b38ce3',7,'cls_brain_anchored','GSE93848','2022-02-22 13:59:29.000000',6,'Brain Capture Long-Seq (anchored)'),(318,'a7435fd2-93e7-11ec-a39d-005056b38ce3',7,'cls_brain_unanchored','GSE93848','2022-02-22 13:59:29.000000',6,'Brain Capture Long-Seq'),(319,'a743603e-93e7-11ec-a39d-005056b38ce3',7,'cls_heart_anchored','GSE93848','2022-02-22 13:59:29.000000',6,'Heart Capture Long-Seq (anchored)'),(320,'a74360a8-93e7-11ec-a39d-005056b38ce3',7,'cls_heart_unanchored','GSE93848','2022-02-22 13:59:29.000000',6,'Heart Capture Long-Seq'),(321,'a743610c-93e7-11ec-a39d-005056b38ce3',7,'cls_hela_anchored','GSE93848','2022-02-22 13:59:29.000000',6,'HeLa Capture Long-Seq (anchored)'),(322,'a7436176-93e7-11ec-a39d-005056b38ce3',7,'cls_hela_unanchored','GSE93848','2022-02-22 13:59:29.000000',6,'HeLa Capture Long-Seq'),(323,'a74361dd-93e7-11ec-a39d-005056b38ce3',7,'cls_k562_anchored','GSE93848','2022-02-22 13:59:29.000000',6,'K562 Capture Long-Seq 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import'),(331,'a743652e-93e7-11ec-a39d-005056b38ce3',7,'aligned_tgac','2017-09-12','2022-02-22 13:59:29.000000',14,'Genes aligned from TGACv1 with Exonerate'),(332,'a74365a8-93e7-11ec-a39d-005056b38ce3',7,'iwgsc_low_conf','2017-10-30','2022-02-22 13:59:29.000000',14,'Genes annotated with low confidence by IWGSC'),(333,'a7436625-93e7-11ec-a39d-005056b38ce3',7,'gene_rnaseq','2014-05-07','2022-02-22 13:59:29.000000',7,'RNA-seq gene models'),(334,'a743669c-93e7-11ec-a39d-005056b38ce3',19,'datafiles_bamcov','2014-06-23','2022-02-22 13:59:29.000000',7,'BAM coverage files'),(526,'50e192ea-948d-11ec-a39d-005056b38ce3',1,'assembly',NULL,'2022-02-22 16:50:48.000000',16,'GCA_000001405.14'),(527,'50e198e3-948d-11ec-a39d-005056b38ce3',22,'assembly',NULL,'2022-02-22 16:50:48.000000',16,'GCA_000001405.14'),(529,'546e8ed4-948d-11ec-a39d-005056b38ce3',7,'gene_core',NULL,'2022-02-22 16:50:48.000000',16,'2010-07-Ensembl/2013-09'),(530,'546e9178-948d-11ec-a39d-005056b38ce3',28,'gene_core',NULL,'2022-02-22 16:50:48.000000',16,'2010-07-Ensembl/2013-09'),(595,'76ff0f75-948d-11ec-a39d-005056b38ce3',2,'rnacentral_checksum','1','2022-01-26 18:43:00.000000',4,'RNAcentral'),(596,'76ff1535-948d-11ec-a39d-005056b38ce3',2,'uniparc_checksum','1','2022-01-26 18:43:00.000000',4,'UniParc'),(597,'76ff1831-948d-11ec-a39d-005056b38ce3',3,'xref_alignment','2009-06-01','2022-01-26 18:43:00.000000',4,'Alignment-based cross-references'),(598,'76ff18e3-948d-11ec-a39d-005056b38ce3',3,'xref_alignment','2014-06-18','2022-01-26 18:43:00.000000',4,'Alignment-based cross-references'),(599,'76ff198c-948d-11ec-a39d-005056b38ce3',4,'xref_dependent','2009-06-01','2022-01-26 18:43:00.000000',4,'Dependent cross-references'),(600,'76ff1a08-948d-11ec-a39d-005056b38ce3',4,'xref_dependent','2021-01-08','2022-01-26 18:43:00.000000',4,'Dependent cross-references'),(601,'76ff1a95-948d-11ec-a39d-005056b38ce3',5,'xref_direct','2014-06-13','2022-01-26 18:43:00.000000',4,'Direct 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+/*!40000 ALTER TABLE `ncbi_taxa_node` ENABLE KEYS */; +UNLOCK TABLES; +/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */; + +/*!40101 SET SQL_MODE=@OLD_SQL_MODE */; +/*!40014 SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS */; +/*!40014 SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS */; +/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */; +/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */; +/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; +/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; + +-- Dump completed on 2022-10-30 9:14:23 diff --git a/tests/test_api.py b/tests/test_api.py index c708bba7..33b115e9 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -15,27 +15,86 @@ from os.path import dirname from ensembl.production.metadata.api import * -DB_NAME = 'sqlite:///' + dirname(__file__) + '/TEST.db' +DB_NAME = 'mysql://root:@127.0.0.1:3306/ensembl_metadata_2020' +TX_NAME = 'mysql://root:@127.0.0.1:3306/ncbi_taxonomy' + def test_load_database(): DB_TEST = ReleaseAdaptor(DB_NAME) assert DB_TEST, "DB should not be empty" + def test_fetch_releases(): conn = ReleaseAdaptor(DB_NAME) - TEST = conn.fetch_releases(release_id=1).one() - #Test the one to many connection - assert TEST.EnsemblSite.name == '2020-map' - #Test the direct access. - assert TEST.EnsemblRelease.label == '2020 MAP 7 species' + TEST = conn.fetch_releases(release_id=1) + # Test the one to many connection + assert TEST[0].EnsemblSite.name == '2020-map' + # Test the direct access. + assert TEST[0].EnsemblRelease.label == '2020 MAP 7 species' + -#currently only have one release, so the testing is not comprehensive +# currently only have one release, so the testing is not comprehensive def test_fetch_releases_for_genome(): conn = ReleaseAdaptor(DB_NAME) - TEST = conn.fetch_releases_for_genome('a733574a-93e7-11ec-a39d-005056b38ce3').one() - assert TEST.EnsemblSite.name == '2020-map' + TEST = conn.fetch_releases_for_genome('a733574a-93e7-11ec-a39d-005056b38ce3') + assert TEST[0].EnsemblSite.name == '2020-map' + def test_fetch_releases_for_dataset(): conn = ReleaseAdaptor(DB_NAME) - TEST = conn.fetch_releases_for_dataset('76ffa505-948d-11ec-a39d-005056b38ce3').one() - assert TEST.EnsemblSite.name == '2020-map' \ No newline at end of file + TEST = conn.fetch_releases_for_dataset('76ffa505-948d-11ec-a39d-005056b38ce3') + assert TEST[0].EnsemblSite.name == '2020-map' + + +def test_fetch_taxonomy_names(): + conn = GenomeAdaptor(metadata_uri=DB_NAME, taxonomy_uri=TX_NAME) + TEST = conn.fetch_taxonomy_names(taxonomy_ids=(6239, 511145)) + assert TEST[511145]['scientific_name'] == 'Escherichia coli str. K-12 substr. MG1655' + + +def test_fetch_taxonomy_ids(): + conn = GenomeAdaptor(metadata_uri=DB_NAME, taxonomy_uri=TX_NAME) + TEST = conn.fetch_taxonomy_ids(taxonomy_names='Caenorhabditis elegans') + assert TEST[0] == 6239 + + +def test_fetch_genomes(): + conn = GenomeAdaptor(metadata_uri=DB_NAME, taxonomy_uri=TX_NAME) + TEST = conn.fetch_genomes() + assert TEST[0].Organism.scientific_name == 'Escherichia coli str. K-12 substr. MG1655 str. K12' + + +def test_fetch_genomes_by_genome_uuid(): + conn = GenomeAdaptor(metadata_uri=DB_NAME, taxonomy_uri=TX_NAME) + TEST = conn.fetch_genomes_by_genome_uuid('a733550b-93e7-11ec-a39d-005056b38ce3') + assert TEST[0].Organism.scientific_name == 'Caenorhabditis elegans' + + +def test_fetch_genomes_by_assembly_accession(): + conn = GenomeAdaptor(metadata_uri=DB_NAME, taxonomy_uri=TX_NAME) + TEST = conn.fetch_genomes_by_assembly_accession('GCA_000005845.2') + assert TEST[0].Organism.scientific_name == 'Escherichia coli str. K-12 substr. MG1655 str. K12' + + +def test_fetch_genomes_by_ensembl_name(): + conn = GenomeAdaptor(metadata_uri=DB_NAME, taxonomy_uri=TX_NAME) + TEST = conn.fetch_genomes_by_ensembl_name('caenorhabditis_elegans') + assert TEST[0].Organism.scientific_name == 'Caenorhabditis elegans' + + +def test_fetch_genomes_by_taxonomy_id(): + conn = GenomeAdaptor(metadata_uri=DB_NAME, taxonomy_uri=TX_NAME) + TEST = conn.fetch_genomes_by_taxonomy_id(6239) + assert TEST[0].Organism.scientific_name == 'Caenorhabditis elegans' + + +def test_fetch_genomes_by_scientific_name(): + conn = GenomeAdaptor(metadata_uri=DB_NAME, taxonomy_uri=TX_NAME) + TEST = conn.fetch_genomes_by_scientific_name('Caenorhabditis elegans') + assert TEST[0].Organism.scientific_name == 'Caenorhabditis elegans' + + +def test_fetch_sequences(): + conn = GenomeAdaptor(metadata_uri=DB_NAME, taxonomy_uri=TX_NAME) + TEST = conn.fetch_sequences() + assert TEST[0].AssemblySequence.accession == 'CM000663.2'