def _process_sub_type(self, sub_type):
self.logger.info("Loading Phenotype Data: %s", sub_type.get_data_provider())
filepath = sub_type.get_filepath()
data = JSONFile().get_data(filepath)
self.logger.info("Finished Loading Phenotype Data: %s", sub_type.get_data_provider())
if data is None:
self.logger.warning("No Data found for %s skipping", sub_type.get_data_provider())
return
commit_size = self.data_type_config.get_neo4j_commit_size()
batch_size = self.data_type_config.get_neo4j_commit_size()
data_provider = sub_type.get_data_provider()
self.logger.info("subtype: " + data_provider)
query_template_list = [
[self.execute_gene_query_template, commit_size,
"phenotype_gene_data_" + sub_type.get_data_provider() + ".csv"],
[self.execute_allele_query_template, commit_size,
"phenotype_allele_data_" + sub_type.get_data_provider() + ".csv"],
[self.execute_agm_query_template, commit_size,
"phenotype_agm_data_" + sub_type.get_data_provider() + ".csv"],
[self.execute_pges_allele_query_template, commit_size,
"phenotype_pges_allele_data_" + sub_type.get_data_provider() + ".csv"],
[self.execute_pges_agm_query_template, commit_size,
"phenotype_pges_agm_data_" + sub_type.get_data_provider() + ".csv"]
]
# Obtain the generator
generators = self.get_generators(data, batch_size)
query_and_file_list = self.process_query_params(query_template_list)
CSVTransactor.save_file_static(generators, query_and_file_list)
Neo4jTransactor.execute_query_batch(query_and_file_list)
self.error_messages("Phenotype-{}: ".format(sub_type.get_data_provider()))
def _process_sub_type(self, sub_type):
self.logger.info("Loading Transcript Data: %s", sub_type.get_data_provider())
commit_size = self.data_type_config.get_neo4j_commit_size()
batch_size = self.data_type_config.get_generator_batch_size()
filepath = sub_type.get_filepath()
# This needs to be in this format (template, param1, params2) others will be ignored
query_template_list = [
[self.transcript_alternate_id_query_template, commit_size,
"transcript_gff3ID_data_" + sub_type.get_data_provider() + ".csv"],
[self.transcript_query_template, commit_size,
"transcript_data_" + sub_type.get_data_provider() + ".csv"],
[self.chromosomes_query_template, commit_size,
"transcript_data_chromosome_" + sub_type.get_data_provider() + ".csv"],
[self.genomic_locations_query_template, commit_size,
"transcript_genomic_locations_" + sub_type.get_data_provider() + ".csv"],
[self.exon_query_template, commit_size,
"exon_data_" + sub_type.get_data_provider() + ".csv"],
[self.exon_genomic_locations_template, commit_size,
"exon_genomic_location_data_" + sub_type.get_data_provider() + ".csv"]
]
# Obtain the generator
generators = self.get_generators(filepath, batch_size)
query_and_file_list = self.process_query_params(query_template_list)
CSVTransactor.save_file_static(generators, query_and_file_list)
Neo4jTransactor.execute_query_batch(query_and_file_list)
def _process_sub_type(self, sub_type, query_tracking_list):
self.logger.info("Loading GOAnnot Data: %s",
sub_type.get_data_provider())
filepath = sub_type.get_file_to_download()
filepath = os.path.join('tmp/', filepath)
self.logger.info("goannot path: %s", filepath)
file = open(filepath, "r")
self.logger.info("Finished Loading GOAnnot Data: %s",
sub_type.get_data_provider())
# This order is the same as the lists yielded from the get_generators function.
# A list of tuples.
commit_size = self.data_type_config.get_neo4j_commit_size()
batch_size = self.data_type_config.get_generator_batch_size()
generators = self.get_generators(\
file,
ETLHelper.go_annot_prefix_lookup(sub_type.get_data_provider()),
batch_size)
query_template_list = [
[
self.main_query_template, commit_size,
"go_annot_" + sub_type.get_data_provider() + ".csv"
],
]
query_and_file_list = self.process_query_params(query_template_list)
CSVTransactor.save_file_static(generators, query_and_file_list)
for item in query_and_file_list:
query_tracking_list.append(item)
def _process_sub_type(self, sub_type):
data_provider = sub_type.get_data_provider()
self.logger.info(data_provider)
if data_provider == 'DOID':
data_provider = 'DO'
self.logger.debug("Starting isa_partof_ Closure for: %s",
data_provider)
query_list = [
[
self.insert_isa_partof_closure_query_template, "100000",
"isa_partof_closure_" + data_provider + ".csv", data_provider,
data_provider
],
]
generators = self.get_closure_terms(data_provider)
query_and_file_list = self.process_query_params(query_list)
CSVTransactor.save_file_static(generators, query_and_file_list)
Neo4jTransactor.execute_query_batch(query_and_file_list)
self.error_messages("Closure-{}: ".format(data_provider))
self.logger.debug("Finished isa_partof Closure for: %s", data_provider)
def _process_sub_type(self, sub_type):
self.logger.info("Loading ECOMAP Ontology Data: %s",
sub_type.get_data_provider())
commit_size = self.data_type_config.get_neo4j_commit_size()
batch_size = self.data_type_config.get_generator_batch_size()
filepath = sub_type.get_filepath()
# This needs to be in this format (template, param1, params2) others will be ignored
query_template_list = [
[
self.eco_query_template, commit_size,
"ecomap_data_" + sub_type.get_data_provider() + ".csv"
],
]
# Obtain the generator
generators = self.get_generators(filepath, batch_size)
query_and_file_list = self.process_query_params(query_template_list)
CSVTransactor.save_file_static(generators, query_and_file_list)
Neo4jTransactor.execute_query_batch(query_and_file_list)
self.error_messages("Ecomap-{}: ".format(sub_type.get_data_provider()))
self.logger.info("Finished Loading ECOMAP Data: %s",
sub_type.get_data_provider())
def _load_and_process_data(self):
filepath = self.data_type_config.get_single_filepath()
commit_size = self.data_type_config.get_neo4j_commit_size()
batch_size = self.data_type_config.get_generator_batch_size()
generators = self.get_generators(filepath, batch_size)
query_template_list = [
[self.do_query_template, commit_size, "do_term_data.csv"],
[self.doterm_isas_query_template, commit_size, "do_isas_data.csv"],
[
self.doterm_synonyms_query_template, commit_size,
"do_synonyms_data.csv"
], [self.xrefs_query_template, commit_size, "do_xrefs_data.csv"],
[
self.doterm_alt_ids_query_template, commit_size,
"do_alt_ids_data.csv"
]
]
query_and_file_list = self.process_query_params(query_template_list)
CSVTransactor.save_file_static(generators, query_and_file_list)
Neo4jTransactor.execute_query_batch(query_and_file_list)
self.error_messages("DO-?: ")
def _load_and_process_data(self):
for sub_type in self.data_type_config.get_sub_type_objects():
species_encoded = urllib.parse.quote_plus(\
ETLHelper.species_lookup_by_data_provider(sub_type.get_data_provider()))
commit_size = self.data_type_config.get_neo4j_commit_size()
#batch_size = self.data_type_config.get_generator_batch_size()
batch_size = 100000
generators = self.get_generators(sub_type, batch_size,
species_encoded)
query_template_list = [
[
self.geo_xref_query_template, commit_size,
"geo_xref_data_" + sub_type.get_data_provider() + ".csv"
],
]
query_and_file_list = self.process_query_params(
query_template_list)
CSVTransactor.save_file_static(generators, query_and_file_list)
Neo4jTransactor.execute_query_batch(query_and_file_list)
def _process_sub_type(self, sub_type):
self.logger.info("Loading Sequence Targeting Reagent Data: %s",
sub_type.get_data_provider())
filepath = sub_type.get_filepath()
self.logger.info(filepath)
data = JSONFile().get_data(filepath)
self.logger.info(
"Finished Loading Sequence Targeting Reagent Data: %s",
sub_type.get_data_provider())
if data is None:
self.logger.warning("No Data found for %s skipping",
sub_type.get_data_provider())
return
# This order is the same as the lists yielded from the get_generators function.
# A list of tuples.
commit_size = self.data_type_config.get_neo4j_commit_size()
batch_size = self.data_type_config.get_generator_batch_size()
# This needs to be in this format (template, param1, params2) others will be ignored
query_template_list = [
[
self.agm_query_template, commit_size,
"agm_data_" + sub_type.get_data_provider() + ".csv"
],
[
self.agm_secondary_ids_query_template, commit_size,
"agm_secondary_ids_" + sub_type.get_data_provider() + ".csv"
],
[
self.agm_synonyms_query_template, commit_size,
"agm_synonyms_" + sub_type.get_data_provider() + ".csv"
],
[
self.agm_components_query_template, commit_size,
"agm_components_" + sub_type.get_data_provider() + ".csv"
],
[
self.agm_sqtrs_query_template, commit_size,
"agm_sqtrs_" + sub_type.get_data_provider() + ".csv"
],
[
self.agm_backgrounds_query_template, commit_size,
"agm_backgrounds_" + sub_type.get_data_provider() + ".csv"
]
]
# Obtain the generator
generators = self.get_generators(data, sub_type.get_data_provider(),
batch_size)
query_and_file_list = self.process_query_params(query_template_list)
CSVTransactor.save_file_static(generators, query_and_file_list)
Neo4jTransactor.execute_query_batch(query_and_file_list)
self.error_messages("AGM-{}: ".format(sub_type.get_data_provider()))
def _load_and_process_data(self):
filepath = self.data_type_config.get_single_filepath()
generators = self.get_generators(filepath)
query_template_list = [[self.main_query_template, 10000, "mi_term_data.csv"]]
query_and_file_list = self.process_query_params(query_template_list)
CSVTransactor.save_file_static(generators, query_and_file_list)
Neo4jTransactor.execute_query_batch(query_and_file_list)
def _load_and_process_data(self):
filepath = 'https://raw.githubusercontent.com/alliance-genome/agr_schemas/master/ingest/species/species.yaml'
generators = self.get_generators(filepath)
query_template_list = [[self.main_query_template, 10000, "species_data.csv"]]
query_and_file_list = self.process_query_params(query_template_list)
CSVTransactor.save_file_static(generators, query_and_file_list)
Neo4jTransactor.execute_query_batch(query_and_file_list)
def _process_sub_type(self, sub_type):
logger.info("Loading HTP metadata Data: %s" %
sub_type.get_data_provider())
filepath = sub_type.get_filepath()
logger.info(filepath)
data = JSONFile().get_data(filepath)
logger.info("Finished Loading HTP metadata Data: %s" %
sub_type.get_data_provider())
if data is None:
logger.warn("No Data found for %s skipping" %
sub_type.get_data_provider())
return
# This order is the same as the lists yielded from the get_generators function.
# A list of tuples.
commit_size = self.data_type_config.get_neo4j_commit_size()
batch_size = self.data_type_config.get_generator_batch_size()
# This needs to be in this format (template, param1, params2) others will be ignored
query_list = [
[
HTPMetaDatasetETL.htp_dataset_query_template, commit_size,
"htp_metadataset_" + sub_type.get_data_provider() + ".csv"
],
[
HTPMetaDatasetETL.htp_category_tags_query_template,
commit_size,
"htp_metadataset_tags_" + sub_type.get_data_provider() + ".csv"
],
[
HTPMetaDatasetETL.htp_dataset_pub_query_template, commit_size,
"htp_metadataset_publications_" +
sub_type.get_data_provider() + ".csv"
],
[
HTPMetaDatasetETL.htpdataset_xrefs_template, commit_size,
"htp_metadataset_xrefs_" + sub_type.get_data_provider() +
".csv"
],
[
HTPMetaDatasetETL.htp_secondaryIds_query_template, commit_size,
"htp_metadataset_secondaryIds_" +
sub_type.get_data_provider() + ".csv"
],
]
# Obtain the generator
generators = self.get_generators(data, batch_size)
query_and_file_list = self.process_query_params(query_list)
CSVTransactor.save_file_static(generators, query_and_file_list)
Neo4jTransactor.execute_query_batch(query_and_file_list)
def _load_and_process_data(self):
self.logger.info("Starting Expression Ribbon Data")
query_template_list = [[
self.insert_ribonless_ebes_query_template, "30000",
"expression_ribbonless_ebes" + ".csv"
]]
generators = self.get_ribbon_terms()
query_and_file_list = self.process_query_params(query_template_list)
CSVTransactor.save_file_static(generators, query_and_file_list)
Neo4jTransactor.execute_query_batch(query_and_file_list)
self.logger.info("Finished Expression Ribbon Data")
def _process_sub_type(self, sub_type):
self.logger.info("Loading Generic Ontology Data: %s",
sub_type.get_data_provider())
filepath = sub_type.get_filepath()
# This order is the same as the lists yielded from the get_generators function.
# A list of tuples.
commit_size = self.data_type_config.get_neo4j_commit_size()
batch_size = self.data_type_config.get_generator_batch_size()
ont_type = sub_type.get_data_provider()
# This needs to be in this format (template, param1, params2) others will be ignored
query_template_list = [
[
self.generic_ontology_term_query_template, 600000,
"generic_ontology_term_" + ont_type + ".csv", ont_type
],
[
self.generic_ontology_isas_query_template, commit_size,
"generic_ontology_isas_" + ont_type + ".csv", ont_type,
ont_type
],
[
self.generic_ontology_partofs_query_template, commit_size,
"generic_ontology_partofs_" + ont_type + ".csv", ont_type,
ont_type
],
[
self.generic_ontology_synonyms_query_template, 400000,
"generic_ontology_synonyms_" + ont_type + ".csv", ont_type
],
[
self.generic_ontology_altids_query_template, commit_size,
"generic_ontology_altids_" + ont_type + ".csv", ont_type
],
]
# Obtain the generator
generators = self.get_generators(filepath, batch_size)
query_and_file_list = self.process_query_params(query_template_list)
CSVTransactor.save_file_static(generators, query_and_file_list)
Neo4jTransactor.execute_query_batch(query_and_file_list)
self.logger.info("Finished Loading Generic Ontology Data: %s",
sub_type.get_data_provider())
def _process_sub_type(self, sub_type, sub_types, query_tracking_list):
self.logger.info("Loading Orthology Data: %s",
sub_type.get_data_provider())
filepath = sub_type.get_filepath()
# data = JSONFile().get_data(filepath)
commit_size = self.data_type_config.get_neo4j_commit_size()
batch_size = self.data_type_config.get_generator_batch_size()
generators = self.get_generators(filepath,
sub_type.get_data_provider(),
sub_types, batch_size)
query_template_list = []
for mod_sub_type in sub_types:
if mod_sub_type != sub_type.get_data_provider():
query_template_list.append([
self.main_query_template, "100000", "orthology_data_" +
sub_type.get_data_provider() + "_" + mod_sub_type + ".csv"
])
query_template_list.append([
self.matched_algorithm_query_template, commit_size,
"orthology_matched_algorithm_data_{}.csv".format(
sub_type.get_data_provider())
])
query_template_list.append([
self.not_matched_algorithm_query_template, commit_size,
"orthology_not_matched_algorithm_data_" +
sub_type.get_data_provider() + ".csv"
])
query_template_list.append([
self.not_called_algorithm_query_template, commit_size,
"orthology_not_called_algorithm_data_" +
sub_type.get_data_provider() + ".csv"
])
query_and_file_list = self.process_query_params(query_template_list)
CSVTransactor.save_file_static(generators, query_and_file_list)
for item in query_and_file_list:
query_tracking_list.append(item)
self.error_messages("Ortho-{}: ".format(sub_type.get_data_provider()))
self.logger.info("Finished Loading Orthology Data: %s",
sub_type.get_data_provider())
def _process_sub_type(self, sub_type):
filepath = sub_type.get_single_filepath()
commit_size = self.data_type_config.get_neo4j_commit_size()
batch_size = self.data_type_config.get_generator_batch_size()
generators = self.get_generators(filepath, batch_size)
query_template_list = [
[self.query_template, commit_size, "stub_data.csv"],
]
query_and_file_list = self.process_query_params(query_template_list)
CSVTransactor.save_file_static(generators, query_and_file_list)
Neo4jTransactor.execute_query_batch(query_and_file_list)
def _process_sub_type(self, sub_type):
self.logger.info("Loading Variation Data: %s",
sub_type.get_data_provider())
filepath = sub_type.get_filepath()
data = JSONFile().get_data(filepath)
self.logger.info("Finished Loading Variation Data: %s",
sub_type.get_data_provider())
if data is None:
self.logger.warning("No Data found for %s skipping",
sub_type.get_data_provider())
return
# This order is the same as the lists yielded from the get_generators function.
# A list of tuples.
commit_size = self.data_type_config.get_neo4j_commit_size()
batch_size = self.data_type_config.get_generator_batch_size()
# This needs to be in this format (template, param1, params2) others will be ignored
query_template_list = [
[
self.variation_query_template, commit_size,
"variation_data_" + sub_type.get_data_provider() + ".csv"
],
[
self.genomic_locations_query_template, commit_size,
"variant_genomiclocations_" + sub_type.get_data_provider() +
".csv"
],
[
self.so_terms_query_template, commit_size,
"variant_so_terms_" + sub_type.get_data_provider() + ".csv"
],
[
self.xrefs_query_template, commit_size,
"variant_xrefs_" + sub_type.get_data_provider() + ".csv"
]
]
generators = self.get_generators(data, batch_size)
query_and_file_list = self.process_query_params(query_template_list)
CSVTransactor.save_file_static(generators, query_and_file_list)
Neo4jTransactor.execute_query_batch(query_and_file_list)
self.error_messages("Var-{}: ".format(sub_type.get_data_provider()))
def _process_sub_type(self, sub_type):
self.logger.info("Loading VEP Data: %s", sub_type.get_data_provider())
commit_size = self.data_type_config.get_neo4j_commit_size()
filepath = sub_type.get_filepath()
# This needs to be in this format (template, param1, params2) others will be ignored
query_template_list = [[
self.vep_transcript_query_template, commit_size,
"vep_transcript_data_" + sub_type.get_data_provider() + ".csv"
]]
# Obtain the generator
generators = self.get_generators(filepath)
query_and_file_list = self.process_query_params(query_template_list)
CSVTransactor.save_file_static(generators, query_and_file_list)
Neo4jTransactor.execute_query_batch(query_and_file_list)
def _process_sub_type(self, subtype):
self.logger.info("Starting Gene Disease Ortho Data: %s", subtype)
query_template_list = [
[self.insert_gene_disease_ortho_query_template, "10000",
"gene_disease_by_orthology.csv"]
]
self.logger.info("gene disease ortho pub created")
generators = self.retrieve_gene_disease_ortho()
query_and_file_list = self.process_query_params(query_template_list)
CSVTransactor.save_file_static(generators, query_and_file_list)
Neo4jTransactor.execute_query_batch(query_and_file_list)
self.logger.info("Finished Gene Disease Ortho Data")
def _process_sub_type(self, sub_type):
self.logger.info("Loading Disease Data: %s", sub_type.get_data_provider())
filepath = sub_type.get_filepath()
data = JSONFile().get_data(filepath)
self.logger.info("Finished Loading Disease Data: %s", sub_type.get_data_provider())
if data is None:
self.logger.warning("No Data found for %s skipping", sub_type.get_data_provider())
return
commit_size = self.data_type_config.get_neo4j_commit_size()
batch_size = self.data_type_config.get_generator_batch_size()
# This needs to be in this format (template, param1, params2) others will be ignored
query_template_list = [
[self.execute_allele_query_template, commit_size,
"disease_allele_data_" + sub_type.get_data_provider() + ".csv"],
[self.execute_gene_query_template, commit_size,
"disease_gene_data_" + sub_type.get_data_provider() + ".csv"],
[self.execute_agms_query_template, commit_size,
"disease_agms_data_" + sub_type.get_data_provider() + ".csv"],
[self.execute_pges_gene_query_template, commit_size,
"disease_pges_gene_data_" + sub_type.get_data_provider() + ".csv"],
[self.execute_pges_allele_query_template, commit_size,
"disease_pges_allele_data_" + sub_type.get_data_provider() + ".csv"],
[self.execute_pges_agm_query_template, commit_size,
"disease_pges_agms_data_" + sub_type.get_data_provider() + ".csv"],
[self.execute_withs_query_template, commit_size,
"disease_withs_data_" + sub_type.get_data_provider() + ".csv"],
[self.execute_ecode_query_template, commit_size,
"disease_evidence_code_data_" + sub_type.get_data_provider() + ".csv"],
[self.execute_annotation_xrefs_query_template, commit_size,
"disease_annotation_xrefs_data_" + sub_type.get_data_provider() + ".csv"]
]
# Obtain the generator
generators = self.get_generators(data, batch_size, sub_type.get_data_provider())
query_and_file_list = self.process_query_params(query_template_list)
CSVTransactor.save_file_static(generators, query_and_file_list)
Neo4jTransactor.execute_query_batch(query_and_file_list)
self.error_messages("Disease-{}: ".format(sub_type.get_data_provider()))
self.logger.info("Finished Loading Disease Data: %s", sub_type.get_data_provider())
def _load_and_process_data(self):
filepath = self.data_type_config.get_single_filepath()
commit_size = self.data_type_config.get_neo4j_commit_size()
batch_size = self.data_type_config.get_generator_batch_size()
generators = self.get_generators(filepath, batch_size)
query_template_list = [
[self.main_query_template, commit_size, "go_term_data.csv"],
[self.goterm_isas_query_template, commit_size, "go_isas_data.csv"],
[
self.goterm_partofs_query_template, commit_size,
"go_partofs_data.csv"
],
[
self.goterm_synonyms_query_template, commit_size,
"go_synonym_data.csv"
],
[
self.goterm_regulates_query_template, commit_size,
"go_regulates_data.csv"
],
[
self.goterm_negatively_regulates_query_template, commit_size,
"go_negatively_regulates_data.csv"
],
[
self.goterm_positively_regulates_query_template, commit_size,
"go_positively_regulates_data.csv"
],
[
self.goterm_secondary_query_template, commit_size,
"goterm_secondary_data.csv"
]
]
query_and_file_list = self.process_query_params(query_template_list)
CSVTransactor.save_file_static(generators, query_and_file_list)
Neo4jTransactor.execute_query_batch(query_and_file_list)
self.error_messages()
def _load_and_process_data(self):
# filepath = self.data_type_config.get_single_filepath()
# Temporary fix for 3.0 release.
filepath = 'tmp/alliance_molecular_interactions.tsv'
commit_size = self.data_type_config.get_neo4j_commit_size()
batch_size = self.data_type_config.get_generator_batch_size()
generators = self.get_generators(filepath, batch_size)
query_template_list = [
[self.main_query_template, commit_size, "mol_int_data.csv"],
[self.xref_query_template, commit_size, "mol_int_xref.csv"],
[self.mod_xref_query_template, commit_size, "mol_int_mod_xref.csv"]
]
query_and_file_list = self.process_query_params(query_template_list)
CSVTransactor.save_file_static(generators, query_and_file_list)
Neo4jTransactor.execute_query_batch(query_and_file_list)
def _process_sub_type(self, sub_type, ensg_to_gene_primary_id_map):
data_provider = sub_type.get_data_provider()
expression_atlas_gene_pages = self._get_expression_atlas_gene_pages(
sub_type, data_provider, ensg_to_gene_primary_id_map)
commit_size = self.data_type_config.get_neo4j_commit_size()
batch_size = self.data_type_config.get_generator_batch_size()
generators = self.get_generators(expression_atlas_gene_pages,
data_provider, batch_size)
query_template_list = [
[
self.add_expression_atlas_crossreferences_query_template,
commit_size, "expression_atlas_" + data_provider + "_data.csv"
],
]
query_and_file_list = self.process_query_params(query_template_list)
CSVTransactor.save_file_static(generators, query_and_file_list)
Neo4jTransactor.execute_query_batch(query_and_file_list)
self.error_messages("ExpAtlas-{}: ".format(
sub_type.get_data_provider()))
def _process_sub_type(self, sub_type):
logger.info("Loading Allele Data: %s" % sub_type.get_data_provider())
filepath = sub_type.get_filepath()
logger.info(filepath)
data = JSONFile().get_data(filepath)
if data is None:
logger.warn("No Data found for %s skipping" %
sub_type.get_data_provider())
return
# This order is the same as the lists yielded from the get_generators function.
# A list of tuples.
commit_size = self.data_type_config.get_neo4j_commit_size()
batch_size = self.data_type_config.get_generator_batch_size()
# This needs to be in this format (template, param1, params2) others will be ignored
query_list = [
[
AlleleETL.allele_gene_no_construct_query_template, commit_size,
"allele_gene_no_construct_data_" +
sub_type.get_data_provider() + ".csv"
],
[
AlleleETL.allele_construct_gene_query_template, commit_size,
"allele_construct_gene_data_" + sub_type.get_data_provider() +
".csv"
],
[
AlleleETL.allele_construct_no_gene_query_template, commit_size,
"allele_construct_no_gene_data_" +
sub_type.get_data_provider() + ".csv"
],
[
AlleleETL.allele_no_gene_no_construct_query_template,
commit_size, "allele_no_gene_no_construct_data_" +
sub_type.get_data_provider() + ".csv"
],
[
AlleleETL.allele_secondaryids_template, commit_size,
"allele_secondaryids_" + sub_type.get_data_provider() + ".csv"
],
[
AlleleETL.allele_synonyms_template, commit_size,
"allele_synonyms_" + sub_type.get_data_provider() + ".csv"
],
[
AlleleETL.allele_xrefs_template, commit_size,
"allele_xrefs_" + sub_type.get_data_provider() + ".csv"
],
]
# Obtain the generator
generators = self.get_generators(data, batch_size)
query_and_file_list = self.process_query_params(query_list)
CSVTransactor.save_file_static(generators, query_and_file_list)
Neo4jTransactor.execute_query_batch(query_and_file_list)
self.error_messages("Allele-{}: ".format(sub_type.get_data_provider()))
logger.info("Finished Loading Allele Data: %s" %
sub_type.get_data_provider())
def _process_sub_type(self, sub_type):
logger.info("Loading HTP metadata sample data: %s" %
sub_type.get_data_provider())
filepath = sub_type.get_filepath()
logger.info(filepath)
data = JSONFile().get_data(filepath)
logger.info("Finished Loading HTP metadata sample data: %s" %
sub_type.get_data_provider())
if data is None:
logger.warn("No Data found for %s skipping" %
sub_type.get_data_provider())
return
# This order is the same as the lists yielded from the get_generators function.
# A list of tuples.
commit_size = self.data_type_config.get_neo4j_commit_size()
batch_size = self.data_type_config.get_generator_batch_size()
# This needs to be in this format (template, param1, params2) others will be ignored
query_list = [
[
HTPMetaDatasetSampleETL.htp_dataset_sample_query_template,
commit_size, "htp_metadataset_sample_samples_" +
sub_type.get_data_provider() + ".csv"
],
[
HTPMetaDatasetSampleETL.
htp_bio_entity_expression_query_template, commit_size,
"htp_metadataset_sample_bioentities_" +
sub_type.get_data_provider() + ".csv"
],
[
HTPMetaDatasetSampleETL.htp_secondaryIds_query_template,
commit_size, "htp_metadataset_sample_secondaryIds_" +
sub_type.get_data_provider() + ".csv"
],
[
HTPMetaDatasetSampleETL.htp_dataset_join_query_template,
commit_size, "htp_metadataset_sample_datasets_" +
sub_type.get_data_provider() + ".csv"
],
[
HTPMetaDatasetSampleETL.htp_stages_query_template, commit_size,
"htp_metadataset_sample_stages_" +
sub_type.get_data_provider() + ".csv"
],
[
HTPMetaDatasetSampleETL.ao_terms_query_template, commit_size,
"htp_metadataset_sample_aoterms_" +
sub_type.get_data_provider() + ".csv"
],
[
HTPMetaDatasetSampleETL.ao_substructures_query_template,
commit_size, "htp_metadataset_sample_ao_substructures_" +
sub_type.get_data_provider() + ".csv"
],
[
HTPMetaDatasetSampleETL.ao_qualifiers_query_template,
commit_size, "htp_metadataset_sample_ao_qualifiers_" +
sub_type.get_data_provider() + ".csv"
],
[
HTPMetaDatasetSampleETL.ao_ss_qualifiers_query_template,
commit_size, "htp_metadataset_sample_ao_ss_qualifiers_" +
sub_type.get_data_provider() + ".csv"
],
[
HTPMetaDatasetSampleETL.cc_term_query_template, commit_size,
"htp_metadataset_sample_ccterms" +
sub_type.get_data_provider() + ".csv"
],
[
HTPMetaDatasetSampleETL.ccq_expression_query_template,
commit_size, "htp_metadataset_sample_ccqterms_" +
sub_type.get_data_provider() + ".csv"
],
[
HTPMetaDatasetSampleETL.uberon_ao_query_template, commit_size,
"htp_metadataset_sample_uberon_ao_" +
sub_type.get_data_provider() + ".csv"
],
[
HTPMetaDatasetSampleETL.uberon_ao_other_query_template,
commit_size, "htp_metadataset_sample_uberon_ao_other_" +
sub_type.get_data_provider() + ".csv"
],
[
HTPMetaDatasetSampleETL.htp_dataset_sample_agm_query_template,
commit_size, "htp_metadataset_sample_agms_" +
sub_type.get_data_provider() + ".csv"
],
[
HTPMetaDatasetSampleETL.
htp_dataset_sample_agmtext_query_template, commit_size,
"htp_metadataset_sample_agmstext_" +
sub_type.get_data_provider() + ".csv"
],
[
HTPMetaDatasetSampleETL.
htp_dataset_sample_assemblies_query_template, commit_size,
"htp_metadataset_sample_assemblies_" +
sub_type.get_data_provider() + ".csv"
]
]
# Obtain the generator
generators = self.get_generators(data, batch_size)
query_and_file_list = self.process_query_params(query_list)
CSVTransactor.save_file_static(generators, query_and_file_list)
Neo4jTransactor.execute_query_batch(query_and_file_list)
def _load_and_process_data(self):
# create gene descriptions data manager and load common data
context_info = ContextInfo()
data_manager = DataFileManager(context_info.config_file_location)
#go_onto_config = data_manager.get_config('GO')
go_annot_config = data_manager.get_config('GAF')
#do_onto_config = data_manager.get_config('DOID')
go_annot_sub_dict = {sub.get_data_provider(): sub for sub in go_annot_config.get_sub_type_objects()}
this_dir = os.path.split(__file__)[0]
gd_config = GenedescConfigParser(os.path.join(this_dir,
os.pardir,
os.pardir,
"gene_descriptions.yml"))
gd_data_manager = DataManager(do_relations=None, go_relations=["subClassOf", "BFO:0000050"])
gd_data_manager.set_ontology(ontology_type=DataType.GO,
ontology=self.get_ontology(data_type=DataType.GO),
config=gd_config)
gd_data_manager.set_ontology(ontology_type=DataType.DO,
ontology=self.get_ontology(data_type=DataType.DO),
config=gd_config)
# generate descriptions for each MOD
for prvdr in [sub_type.get_data_provider().upper() \
for sub_type in self.data_type_config.get_sub_type_objects()]:
gd_config_mod_specific = copy.deepcopy(gd_config)
if prvdr == "WB":
gd_config_mod_specific.config["expression_sentences_options"][
"remove_children_if_parent_is_present"] = True
self.logger.info("Generating gene descriptions for %s", prvdr)
data_provider = prvdr if prvdr != "HUMAN" else "RGD"
json_desc_writer = DescriptionsWriter()
go_annot_path = "file://" + os.path.join(os.getcwd(),
"tmp",
go_annot_sub_dict[prvdr].file_to_download)
gd_data_manager.load_associations_from_file(
associations_type=DataType.GO, associations_url=go_annot_path,
associations_cache_path=os.path.join(os.getcwd(),
"tmp",
"gd_cache",
"go_annot_" + prvdr + ".gaf"),
config=gd_config_mod_specific)
gd_data_manager.set_associations(associations_type=DataType.DO,
associations=self.get_disease_annotations_from_db(
data_provider=data_provider,
gd_data_manager=gd_data_manager,
logger=self.logger),
config=gd_config_mod_specific)
if prvdr in EXPRESSION_PRVD_SUBTYPE_MAP:
gd_data_manager.set_ontology(ontology_type=DataType.EXPR,
ontology=self.get_ontology(data_type=DataType.EXPR,
provider=prvdr),
config=gd_config_mod_specific)
gd_data_manager.set_associations(
associations_type=DataType.EXPR,
associations=self.get_expression_annotations_from_db(data_provider=data_provider,
gd_data_manager=gd_data_manager,
logger=self.logger),
config=gd_config_mod_specific)
commit_size = self.data_type_config.get_neo4j_commit_size()
generators = self.get_generators(prvdr,
gd_data_manager,
gd_config_mod_specific,
json_desc_writer)
query_template_list = [
[self.gene_descriptions_query_template, commit_size,
"genedescriptions_data_" + prvdr + ".csv"]
]
query_and_file_list = self.process_query_params(query_template_list)
CSVTransactor.save_file_static(generators, query_and_file_list)
Neo4jTransactor.execute_query_batch(query_and_file_list)
self.save_descriptions_report_files(data_provider=prvdr,
json_desc_writer=json_desc_writer,
context_info=context_info,
gd_data_manager=gd_data_manager)
def _process_sub_type(self, sub_type, query_tracking_list):
self.logger.info("Loading BGI Data: %s", sub_type.get_data_provider())
filepath = sub_type.get_filepath()
if filepath is None:
self.logger.error("Can't find input file for %s", sub_type)
sys.exit()
data = JSONFile().get_data(filepath)
# This order is the same as the lists yielded from the get_generators function.
# A list of tuples.
commit_size = self.data_type_config.get_neo4j_commit_size()
batch_size = self.data_type_config.get_generator_batch_size()
# gene_metadata, gene_dataset, secondary_ids, genomic_locations, cross_references, synonyms
# This needs to be in this format (template, param1, params2) others will be ignored
query_template_list = [
[
self.gene_metadata_query_template, commit_size,
"gene_metadata_" + sub_type.get_data_provider() + ".csv"
],
[
self.gene_query_template, commit_size,
"gene_data_" + sub_type.get_data_provider() + ".csv"
],
[
self.basic_gene_load_relations_query_template, commit_size,
"gene_data_load_" + sub_type.get_data_provider() + ".csv"
],
[
self.basic_gene_species_relations_query_template, commit_size,
"gene_data_species_" + sub_type.get_data_provider() + ".csv"
],
[
self.so_terms_query_template, commit_size,
"gene_so_terms_" + sub_type.get_data_provider() + ".csv"
],
[
self.chromosomes_query_template, commit_size,
"gene_chromosomes_" + sub_type.get_data_provider() + ".csv"
],
[
self.gene_secondary_ids_query_template, commit_size,
"gene_secondary_ids_" + sub_type.get_data_provider() + ".csv"
],
[
self.genomic_locations_query_template, commit_size,
"gene_genomic_locations_" + sub_type.get_data_provider() +
".csv"
],
[
self.xrefs_query_template, commit_size,
"gene_cross_references_" + sub_type.get_data_provider() +
".csv"
],
[
self.xrefs_relationships_query_template, commit_size,
"gene_cross_references_relationships_" +
sub_type.get_data_provider() + ".csv"
],
[
self.gene_synonyms_query_template, 600000,
"gene_synonyms_" + sub_type.get_data_provider() + ".csv"
]
]
# Obtain the generator
generators = self.get_generators(data, sub_type.get_data_provider(),
batch_size)
query_and_file_list = self.process_query_params(query_template_list)
CSVTransactor.save_file_static(generators, query_and_file_list)
for item in query_and_file_list:
query_tracking_list.append(item)
self.error_messages("BGI-{}: ".format(sub_type.get_data_provider()))
self.logger.info("Finished Loading BGI Data: %s",
sub_type.get_data_provider())
def _process_sub_type(self, sub_type, query_tracking_list):
self.logger.info("Loading Expression Data: %s",
sub_type.get_data_provider())
data_file = sub_type.get_filepath()
data_provider = sub_type.get_data_provider()
if data_file is None:
self.logger.warning("No Data found for %s skipping",
sub_type.get_data_provider())
return
commit_size = self.data_type_config.get_neo4j_commit_size()
batch_size = self.data_type_config.get_generator_batch_size()
# This needs to be in this format (template, param1, params2) others will be ignored
query_template_list = [
[
self.bio_entity_expression_query_template, commit_size,
"expression_entities_" + sub_type.get_data_provider() + ".csv"
],
[
self.bio_entity_gene_ao_query_template, commit_size,
"expression_gene_ao_" + sub_type.get_data_provider() + ".csv"
],
[
self.bio_entity_gene_expression_join_query_template,
commit_size, "expression_entity_joins_" +
sub_type.get_data_provider() + ".csv"
],
[
self.ao_expression_query_template, commit_size,
"expression_ao_expression_" + sub_type.get_data_provider() +
".csv"
]
]
if data_provider == 'SGD':
query_template_list += [[
self.sgd_cc_expression_query_template, commit_size,
"expression_SGD_cc_expression_" +
sub_type.get_data_provider() + ".csv"
]]
else:
query_template_list += [[
self.cc_expression_query_template, commit_size,
"expression_cc_expression_" + sub_type.get_data_provider() +
".csv"
]]
query_template_list += [
[
self.ao_cc_expression_query_template, commit_size,
"expression_ao_cc_expression_" + sub_type.get_data_provider() +
".csv"
],
[
self.eas_qualified_query_template, commit_size,
"expression_eas_qualified_" + sub_type.get_data_provider() +
".csv"
],
[
self.eas_substructure_query_template, commit_size,
"expression_eas_substructure_" + sub_type.get_data_provider() +
".csv"
],
[
self.eass_qualified_query_template, commit_size,
"expression_eass_qualified_" + sub_type.get_data_provider() +
".csv"
],
[
self.ccq_expression_query_template, commit_size,
"expression_ccq_expression_" + sub_type.get_data_provider() +
".csv"
],
[
self.stage_expression_query_template, commit_size,
"expression_stage_expression_" + sub_type.get_data_provider() +
".csv"
],
[
self.uberon_stage_query_template, commit_size,
"expression_uberon_stage_" + sub_type.get_data_provider() +
".csv"
],
[
self.uberon_ao_query_template, commit_size,
"expression_uberon_ao_" + sub_type.get_data_provider() + ".csv"
],
[
self.uberon_ao_other_query_template, commit_size,
"expression_uberon_ao_other_" + sub_type.get_data_provider() +
".csv"
],
[
self.uberon_stage_other_query_template, commit_size,
"expression_uberon_stage_other_" +
sub_type.get_data_provider() + ".csv"
],
[
self.xrefs_query_template, commit_size,
"expression_cross_references_" + sub_type.get_data_provider() +
".csv"
],
[
self.add_pubs_query_template, commit_size,
"expression_add_pubs_" + sub_type.get_data_provider() + ".csv"
]
]
# Obtain the generator
generators = self.get_generators(data_file, batch_size)
query_and_file_list = self.process_query_params(query_template_list)
CSVTransactor.save_file_static(generators, query_and_file_list)
for item in query_and_file_list:
query_tracking_list.append(item)
self.logger.info("Finished Loading Expression Data: %s",
sub_type.get_data_provider())
def _process_sub_type(self, sub_type):
self.logger.info("Loading Construct Data: %s",
sub_type.get_data_provider())
filepath = sub_type.get_filepath()
data = JSONFile().get_data(filepath)
self.logger.info("Finished Loading Construct Data: %s",
sub_type.get_data_provider())
if data is None:
self.logger.warning("No Data found for %s skipping",
sub_type.get_data_provider())
return
# This order is the same as the lists yielded from the get_generators function.
# A list of tuples.
commit_size = self.data_type_config.get_neo4j_commit_size()
batch_size = self.data_type_config.get_generator_batch_size()
# This needs to be in this format (template, param1, params2) others will be ignored
query_template_list = [
[
ConstructETL.construct_query_template, commit_size,
"Construct_data_" + sub_type.get_data_provider() + ".csv"
],
[
ConstructETL.construct_secondary_ids_query_template,
commit_size, "Construct_secondary_ids_" +
sub_type.get_data_provider() + ".csv"
],
[
ConstructETL.construct_synonyms_query_template, commit_size,
"Construct_synonyms_" + sub_type.get_data_provider() + ".csv"
],
[
ConstructETL.construct_xrefs_query_template, commit_size,
"Construct_xrefs_" + sub_type.get_data_provider() + ".csv"
],
[
ConstructETL.non_bgi_component_query_template, commit_size,
"Construct_non_bgi_component_" + sub_type.get_data_provider() +
".csv"
],
[
ConstructETL.construct_gene_component_query_template,
commit_size, "Construct_components_gene" +
sub_type.get_data_provider() + ".csv"
],
[
ConstructETL.construct_no_gene_component_query_template,
commit_size, "Construct_components_no_gene" +
sub_type.get_data_provider() + ".csv"
]
]
# Obtain the generator
generators = self.get_generators(data, sub_type.get_data_provider(),
batch_size)
query_and_file_list = self.process_query_params(query_template_list)
CSVTransactor.save_file_static(generators, query_and_file_list)
Neo4jTransactor.execute_query_batch(query_and_file_list)