Commit 052806cd authored by Lukas Jelonek's avatar Lukas Jelonek
Browse files

Register kegg provider, set default parameters, replace print statements with logging

parent 08c2504f
......@@ -119,9 +119,9 @@
text: ["http://rest.kegg.jp/get/%i"]
check_existence: "http://rest.kegg.jsdjkaap/get/%i"
# not implemented yet
# retriever:
# type: 'internal'
# location: 'dbxref.retrieve.kegg'
retriever:
type: 'internal'
location: 'dbxref.retrieve.kegg'
- name: HTTP
prefixes: ["http", "https"]
resources:
......
......@@ -48,7 +48,7 @@ def main():
print(json.dumps(documents))
def retrieve(dbxrefs, basics, pathway, brite, dbxrefs_links, genes, reference, orthology, motif, formula, reaction):
def retrieve(dbxrefs, basics = True, pathway = True, brite = True, dbxrefs_links = True, genes = True, reference = True, orthology = True, motif = True, formula = True, reaction = True):
"""Parse kegg text file and return a list "documents" including the extracted information of the given entries. """
resolved = dbxref.resolver.resolve(dbxrefs, check_existence=False)
......@@ -79,52 +79,52 @@ def retrieve(dbxrefs, basics, pathway, brite, dbxrefs_links, genes, reference, o
if "ORGANISM" in kegg_information:
output.update({"organism": read_information(kegg_information["ORGANISM"])[0]})
else:
print("Entry: " + NO_INFO)
logger.warn("No Entry")
if pathway:
if "PATHWAY" in kegg_information:
output.update({"pathways": read_information(kegg_information["PATHWAY"])})
else:
print("Pathway: " + NO_INFO)
logger.warn("No Pathway")
if genes:
if "GENES" in kegg_information:
output.update({"genes": read_information(kegg_information["GENES"])})
else:
print("Genes: " + NO_INFO)
logger.warn("No Genes")
if orthology:
if "ORTHOLOGY" in kegg_information:
output.update({"ortholog genes": read_information(kegg_information["ORTHOLOGY"])})
else:
print("Orthology: " + NO_INFO)
logger.warn("No orthology")
if motif:
if "MOTIF" in kegg_information:
output.update({"motif": read_information(kegg_information["MOTIF"])})
else:
print("Motif: " + NO_INFO)
logger.warn("No motif")
if formula:
if "FORMULA" in kegg_information:
output.update({"chemical formula": read_information(kegg_information["FORMULA"][0])})
else:
print("Formula: " + NO_INFO)
logger.warn("No formula")
if reaction:
if "REACTION" in kegg_information:
output.update({"reaction partners": read_information(kegg_information["REACTION"])})
else:
print("Reaction: " + NO_INFO)
logger.warn("No reaction")
if brite:
if "BRITE" in kegg_information:
output.update({"brite": read_brite(kegg_information["BRITE"])})
else:
print("Brite: " + NO_INFO)
logger.warn("No brite")
if reference:
if "REFERENCE" in kegg_information:
output.update({"reference": read_reference(kegg_information["REFERENCE"])})
else:
print("Reference: " + NO_INFO)
logger.warn("No reference")
if dbxrefs_links:
if "DBLINKS" in kegg_information:
output.update({"dbxref_links": read_dbxrefs(kegg_information["DBLINKS"])})
else:
print("dbxref_links: " + NO_INFO)
logger.warn("No dbxref_links")
documents.append(output)
return documents
......
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