def test_premature_commit():
with projecttest_context(set_up_project_stage='uniprot'):
try:
Commit()
raise Exception('Premature commit was not supposed to be successful!')
except DatabaseException:
pass
def test_gather_uniprot_using_network():
with projecttest_context(set_up_project_stage='init'):
GatherUniProt(
uniprot_query='mnemonic:ABL1_HUMAN',
uniprot_domain_regex='^Protein kinase(?!; truncated)(?!; inactive)',
)
first_uniprot_entry = models.UniProtEntry.query.first()
first_uniprot_domain = models.UniProtDomain.query.first()
first_target_domain = models.UniProtDomain.query.filter_by(
is_target_domain=True).first()
assert first_uniprot_entry.entry_name == 'ABL1_HUMAN'
assert first_uniprot_domain.domain_id == 0
assert first_target_domain.target_id == 'ABL1_HUMAN_D0'
assert first_target_domain.domain_id == 2
first_pdb_entry = models.PDBEntry.query.first()
assert first_pdb_entry.chains.first() is not None
all_pdb_entries = models.PDBEntry.query.all()
assert '1OPL' in [pdb_entry.pdb_id for pdb_entry in all_pdb_entries]
first_pdb_chain = models.PDBChain.query.first()
assert first_pdb_chain.uniprot_domain.domain_id == 1
first_uniprot_isoform = models.UniProtIsoform.query.first()
assert first_uniprot_isoform.uniprot_entry.entry_name == 'ABL1_HUMAN'
assert first_uniprot_isoform.is_canonical
assert first_uniprot_isoform.ensembl_transcripts.first(
).transcript_id == 'ENST00000318560'
def test_gather_pdb():
with projecttest_context(set_up_project_stage='uniprot'):
pdb_and_sifts_structure_files_dir = get_installed_resource_filepath(
os.path.join('resources', 'structures'))
GatherPDB(structure_dirs=pdb_and_sifts_structure_files_dir)
first_pdb_chain = models.PDBChain.query.first()
assert first_pdb_chain.observed_seq_aln_exp is not None
def test_gather_pdb():
with projecttest_context(set_up_project_stage='uniprot'):
pdb_and_sifts_structure_files_dir = get_installed_resource_filepath(
os.path.join('resources', 'structures')
)
GatherPDB(structure_dirs=pdb_and_sifts_structure_files_dir)
first_pdb_chain = models.PDBChain.query.first()
assert first_pdb_chain.observed_seq_aln_exp is not None
def test_premature_commit():
with projecttest_context(set_up_project_stage='uniprot'):
try:
Commit()
raise Exception(
'Premature commit was not supposed to be successful!')
except DatabaseException:
pass
def test_gather_ncbi_gene():
with projecttest_context(set_up_project_stage="uniprot"):
GatherNCBIGene(use_existing_gene2pubmed=True)
first_ncbi_gene_row = models.NCBIGeneEntry.query.first()
assert isinstance(first_ncbi_gene_row, models.NCBIGeneEntry)
assert first_ncbi_gene_row.gene_id == 25
first_publication_row = models.NCBIGenePublication.query.first()
assert isinstance(first_publication_row, models.NCBIGenePublication)
assert first_publication_row.pmid == 1281542
def test_gather_ncbi_gene():
with projecttest_context(set_up_project_stage='uniprot'):
GatherNCBIGene(use_existing_gene2pubmed=True)
first_ncbi_gene_row = models.NCBIGeneEntry.query.first()
assert isinstance(first_ncbi_gene_row, models.NCBIGeneEntry)
assert first_ncbi_gene_row.gene_id == 25
first_publication_row = models.NCBIGenePublication.query.first()
assert isinstance(first_publication_row, models.NCBIGenePublication)
assert first_publication_row.pmid == 1281542
def test_gather_cbioportal_using_network():
with projecttest_context(set_up_project_stage='uniprot'):
GatherCbioportalData()
first_mutation_row = models.CbioportalMutation.query.first()
first_mutation_in_domain_row = models.CbioportalMutation.query.filter_by(
in_uniprot_domain=True).first()
assert isinstance(first_mutation_row, models.CbioportalMutation)
assert isinstance(first_mutation_in_domain_row.oncotator_aa_pos, int)
assert first_mutation_in_domain_row.uniprot_domain.description == 'SH2'
def test_gather_cbioportal_using_network():
with projecttest_context(set_up_project_stage='uniprot'):
GatherCbioportalData()
first_mutation_row = models.CbioportalMutation.query.first()
first_mutation_in_domain_row = models.CbioportalMutation.query.filter_by(
in_uniprot_domain=True
).first()
assert isinstance(first_mutation_row, models.CbioportalMutation)
assert isinstance(first_mutation_in_domain_row.oncotator_aa_pos, int)
assert first_mutation_in_domain_row.uniprot_domain.description == 'SH2'
def test_gather_cbioportal():
with projecttest_context(set_up_project_stage='uniprot'):
GatherCbioportalData(use_existing_cbioportal_data=True, use_existing_oncotator_data=True)
first_mutation_row = models.CbioportalMutation.query.first()
assert first_mutation_row is not None
first_mutation_in_domain_row = models.CbioportalMutation.query.filter_by(
in_uniprot_domain=True
).first()
assert first_mutation_in_domain_row is not None
assert isinstance(first_mutation_in_domain_row.oncotator_aa_pos, int)
assert first_mutation_in_domain_row.uniprot_domain.description == 'SH2'
def test_gather_uniprot_no_domain_regex():
with projecttest_context(set_up_project_stage='init'):
GatherUniProt(uniprot_query='mnemonic:ABL1_HUMAN',
use_existing_data=True)
first_uniprot_entry = models.UniProtEntry.query.first()
first_uniprot_domain = models.UniProtDomain.query.first()
assert first_uniprot_entry.entry_name == 'ABL1_HUMAN'
assert first_uniprot_domain.domain_id == 0
assert len(
models.UniProtDomain.query.filter_by(
is_target_domain=True).all()) == 0
def test_gather_cbioportal():
with projecttest_context(set_up_project_stage='uniprot'):
GatherCbioportalData(use_existing_cbioportal_data=True,
use_existing_oncotator_data=True)
first_mutation_row = models.CbioportalMutation.query.first()
assert first_mutation_row is not None
first_mutation_in_domain_row = models.CbioportalMutation.query.filter_by(
in_uniprot_domain=True).first()
assert first_mutation_in_domain_row is not None
assert isinstance(first_mutation_in_domain_row.oncotator_aa_pos, int)
assert first_mutation_in_domain_row.uniprot_domain.description == 'SH2'
def test_gather_uniprot_no_domain_regex():
with projecttest_context(set_up_project_stage='init'):
GatherUniProt(
uniprot_query='mnemonic:ABL1_HUMAN',
use_existing_data=True
)
first_uniprot_entry = models.UniProtEntry.query.first()
first_uniprot_domain = models.UniProtDomain.query.first()
assert first_uniprot_entry.entry_name == 'ABL1_HUMAN'
assert first_uniprot_domain.domain_id == 0
assert len(models.UniProtDomain.query.filter_by(is_target_domain=True).all()) == 0
def test_init_project():
with projecttest_context(set_up_project_stage='blank'):
InitProject(db_name='test', project_path=os.getcwd())
assert os.path.exists(project_config_filename)
assert os.path.exists(database_filename)
assert os.path.exists(external_data_dirpath)
assert os.path.exists(wsgi_filename)
assert os.path.exists(manual_overrides_filename)
assert app.config.get('SQLALCHEMY_DATABASE_URI') is not None
crawldata_row = models.CrawlData.query.first()
assert crawldata_row is not None
assert crawldata_row.current_crawl_number == 0
datestamps_row = models.DateStamps.query.first()
assert datestamps_row is not None
assert datestamps_row.crawl_number == 0
def test_gather_uniprot_using_network():
with projecttest_context(set_up_project_stage='init'):
GatherUniProt(
uniprot_query='mnemonic:ABL1_HUMAN',
uniprot_domain_regex='^Protein kinase(?!; truncated)(?!; inactive)',
)
first_uniprot_entry = models.UniProtEntry.query.first()
first_uniprot_domain = models.UniProtDomain.query.first()
first_target_domain = models.UniProtDomain.query.filter_by(is_target_domain=True).first()
assert first_uniprot_entry.entry_name == 'ABL1_HUMAN'
assert first_uniprot_domain.domain_id == 0
assert first_target_domain.target_id == 'ABL1_HUMAN_D0'
assert first_target_domain.domain_id == 2
first_pdb_entry = models.PDBEntry.query.first()
assert first_pdb_entry.chains.first() is not None
all_pdb_entries = models.PDBEntry.query.all()
assert '1OPL' in [pdb_entry.pdb_id for pdb_entry in all_pdb_entries]
first_pdb_chain = models.PDBChain.query.first()
assert first_pdb_chain.uniprot_domain.domain_id == 1
first_uniprot_isoform = models.UniProtIsoform.query.first()
assert first_uniprot_isoform.uniprot_entry.entry_name == 'ABL1_HUMAN'
assert first_uniprot_isoform.is_canonical
assert first_uniprot_isoform.ensembl_transcripts.first().transcript_id == 'ENST00000318560'
def test_gather_bindingdb():
with projecttest_context(set_up_project_stage='uniprot'):
GatherBindingDB(use_existing_bindingdb_data=True)
first_bioassay_row = models.BindingDBBioassay.query.first()
assert isinstance(first_bioassay_row, models.BindingDBBioassay)
assert first_bioassay_row.target_name == 'ABL1'
def test_projecttest_context():
with projecttest_context() as temp_dir:
assert os.path.exists(temp_dir)
def test_gather_pdb_using_network():
with projecttest_context(set_up_project_stage='uniprot'):
GatherPDB()
first_pdb_chain = models.PDBChain.query.first()
assert first_pdb_chain.observed_seq_aln_exp is not None
def test_gather_chembl_target():
with projecttest_context(set_up_project_stage='uniprot'):
GatherChemblTarget()
def test_commit():
with projecttest_context(set_up_project_stage='cbioportal'):
Commit()
crawl_data_row = models.CrawlData.query.first()
assert crawl_data_row.safe_crawl_number == 0
def test_commit():
with projecttest_context(set_up_project_stage='cbioportal'):
Commit()
crawl_data_row = models.CrawlData.query.first()
assert crawl_data_row.safe_crawl_number == 0
def test_gather_pdb_using_network():
with projecttest_context(set_up_project_stage='uniprot'):
GatherPDB()
first_pdb_chain = models.PDBChain.query.first()
assert first_pdb_chain.observed_seq_aln_exp is not None