A Database-based knowledge back-end built on and for INDRA. The INDRA Database is a service that can be set up by any user with their own content and knowledge access. Our implementation of the database is the back-end to many of our projects, providing a vast and detailed knowledge base derived from many resources.
EMMAA is trying to import this and can't because there's a missing mid-level import
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Input In [8], in <module>
----> 1 gene_prior.make_config()
File ~/dev/emmaa/emmaa/priors/gene_list_prior.py:69, in GeneListPrior.make_config(self)
67 self.make_search_terms()
68 if not self.stmts:
---> 69 self.make_gene_statements()
70 config = dict()
71 config['name'] = self.name
File ~/dev/emmaa/emmaa/priors/gene_list_prior.py:59, in GeneListPrior.make_gene_statements(self)
56 """Generate Statements from the gene list."""
57 drug_names = [st.name for st in self.search_terms if
58 st.type == 'drug']
---> 59 indra_stmts = get_stmts_for_gene_list(self.gene_list, drug_names)
60 estmts = [EmmaaStatement(stmt, datetime.datetime.now(), [])
61 for stmt in indra_stmts]
62 self.stmts = estmts
File ~/dev/emmaa/emmaa/priors/prior_stmts.py:45, in get_stmts_for_gene_list(gene_list, other_entities)
43 for gene in gene_list:
44 logger.info(f'Querying {gene}')
---> 45 st = get_stmts_for_gene(gene)
46 logger.info(f'Got {len(st)} statements for {gene}')
47 stmts += st
File ~/dev/emmaa/emmaa/priors/prior_stmts.py:22, in get_stmts_for_gene(gene)
9 def get_stmts_for_gene(gene):
10 """Return all existing Statements for a given gene from the DB.
11
12 Parameters
(...)
20 A list of INDRA Statements in which the given gene is involved.
21 """
---> 22 return client.get_statements_by_gene_role_type(gene, preassembled=False,
23 count=100000)
AttributeError: module 'indra_db.client' has no attribute 'get_statements_by_gene_role_type'
This PR fixes it since the get_statements_by_gene_role_type is inside indra_db.client.statements. This PR also puts some more stuff into the .gitignore so any packaging artifacts don't accidentally get committed.
EMMAA is trying to import this and can't because there's a missing mid-level import
This PR fixes it since the
get_statements_by_gene_role_type
is insideindra_db.client.statements
. This PR also puts some more stuff into the .gitignore so any packaging artifacts don't accidentally get committed.