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EVA-3402 - release assemblies which contains only deprecated RS #438

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Apr 11, 2024
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EVA-3402 - release assemblies which contains only deprecated RS #438

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27 changes: 20 additions & 7 deletions eva-accession-release-automation/run_release_in_embassy/create_release_tracking_table.py
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Original file line number Diff line number Diff line change
Expand Up @@ -152,23 +152,25 @@ def fill_should_be_released_for_taxonomy(self, tax, asm_sources):
self.fill_should_be_released_for_taxonomy_and_assembly(tax, asm_acc, asm_sources[asm_acc])

def fill_should_be_released_for_taxonomy_and_assembly(self, tax, asm, src):
"""Fills should_be_released for a taxonomy/assembly pair based on whether there are current RS IDs,
and updates the sources column as well.
TODO Also check for deprecated (https://www.ebi.ac.uk/panda/jira/browse/EVA-3402)"""
"""Fills should_be_released for a taxonomy/assembly pair based on whether there are current RS IDs or
deprecated RS IDs and updates the sources column as well."""
should_be_released_eva = should_be_released_dbsnp = False
if asm != 'Unmapped':
ss_query = {'tax': tax, 'seq': asm, 'rs': {'$exists': True}}
rs_query = {'tax': tax, 'asm': asm}
rs_opt_query = {'inactiveObjects.tax': tax, 'inactiveObjects.asm': asm, 'eventType': 'DEPRECATED'}
Comment on lines 160 to +161
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I don't think this will have any effect but the queries on tax should be done on SubmittedVariantEntity and SubmittedVariantOperationEntity. Not on their ClusteredVariants equivalent.

if 'EVA' in src:
eva_ss_coll = 'submittedVariantEntity'
eva_rs_coll = 'clusteredVariantEntity'
eva_rs_opt_coll = "clusteredVariantOperationEntity"
should_be_released_eva = self._determine_should_be_released_for_collection(
tax, asm, eva_ss_coll, eva_rs_coll, ss_query, rs_query)
tax, asm, eva_ss_coll, eva_rs_coll, eva_rs_opt_coll, ss_query, rs_query, rs_opt_query)
if 'DBSNP' in src:
dbsnp_ss_coll = 'dbsnpSubmittedVariantEntity'
dbsnp_rs_coll = 'dbsnpClusteredVariantEntity'
dbsnp_rs_opt_coll = "dbsnpClusteredVariantOperationEntity"
should_be_released_dbsnp = self._determine_should_be_released_for_collection(
tax, asm, dbsnp_ss_coll, dbsnp_rs_coll, ss_query, rs_query)
tax, asm, dbsnp_ss_coll, dbsnp_rs_coll, dbsnp_rs_opt_coll, ss_query, rs_query, rs_opt_query)
should_be_released = should_be_released_eva or should_be_released_dbsnp
else:
should_be_released = False
Expand Down Expand Up @@ -202,7 +204,8 @@ def fill_should_be_released_for_taxonomy_and_assembly(self, tax, asm, src):
and release_version={self.release_version}"""
execute_query(self.metadata_conn, update_sources_query)

def _determine_should_be_released_for_collection(self, tax, asm, ss_coll, rs_coll, ss_query, rs_query):
def _determine_should_be_released_for_collection(self, tax, asm, ss_coll, rs_coll, rs_opt_coll, ss_query, rs_query,
rs_opt_query):
self.info(f"Looking for SS with RS for Taxonomy {tax} and Assembly {asm} in collection {ss_coll}")
collection = self.mongo_conn.mongo_handle[self.mongo_conn.db_name][ss_coll]
ss_with_rs = collection.find_one(ss_query)
Expand All @@ -224,7 +227,17 @@ def _determine_should_be_released_for_collection(self, tax, asm, ss_coll, rs_col
self.info(f'Found RS with Taxonomy {tax} and Assembly {asm} in collection {rs_coll}, RS: {rs_with_tax_asm}')
return True
else:
self.warning(f'No RS found for Taxonomy {tax} and Assembly {asm} in collection {ss_coll}')
self.warning(f'No RS found for Taxonomy {tax} and Assembly {asm} in collection {rs_coll}')

# Looking for Deprecated RS for a tax and asm for cases where an assembly only contains deprecated RS
self.info(f"Looking for Deprecated RS with Taxonomy {tax} and Assembly {asm} in collection {rs_opt_coll}")
collection = self.mongo_conn.mongo_handle[self.mongo_conn.db_name][rs_opt_coll]
deprecated_rs_with_tax_asm = collection.find_one(rs_opt_query)
if deprecated_rs_with_tax_asm:
self.info(f'Found Deprecated RS with Taxonomy {tax} and Assembly {asm} in collection {rs_opt_coll}, RS: {deprecated_rs_with_tax_asm}')
return True
else:
self.warning(f'No Deprecated RS found for Taxonomy {tax} and Assembly {asm} in collection {rs_opt_coll}')
return False

def get_taxonomy_list_for_release(self):
Expand Down
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