def search(args):
"""
args contains a dict with one or key:values
"""
ident_arg = args["identifier"]
primaryId = tools.getProteinPrimaryIdentifier(ident_arg)
ident = ident_arg
if primaryId and primaryId != '':
ident = primaryId
# get a new query on the class (table) from the model
query = service.new_query("Protein")
# views specify the output columns
query.add_view("primaryIdentifier", "comments.type", "comments.description")
# set the constraint value(s)
query.add_constraint("primaryIdentifier", "=", ident, code = "A")
# loop over rows of data to build the JSON object
# print row["primaryIdentifier"], row["comments.type"], row["comments.description"]
for row in query.rows():
record = {
'class': 'protein_property',
'source_text_description': 'ThaleMine Protein Curated Comments',
'protein_id': row["primaryIdentifier"],
'comment_type': row["comments.type"],
'comment_description': row["comments.description"]
}
print json.dumps(record, indent=2)
print '---'
def search(args):
"""
args contains a dict with one or key:values
"""
ident_arg = args["identifier"]
primaryId = tools.getProteinPrimaryIdentifier(ident_arg)
ident = ident_arg
if primaryId and primaryId != '':
ident = primaryId
# get a new query on the class (table) from the model
query = service.new_query("Protein")
# views specify the output columns
query.add_view(
"publications.firstAuthor", "publications.title", "publications.year",
"publications.journal", "publications.volume", "publications.pages",
"publications.pubMedId", "publications.issue", "primaryIdentifier"
)
# set the constraint value(s)
query.add_constraint("primaryIdentifier", "=", ident, code = "A")
# loop over rows of data to build the JSON object
for row in query.rows():
record = {
'class': 'protein_property',
'source_text_description': 'ThaleMine protein publication',
'protein_id': row["primaryIdentifier"],
'first_author': row["publications.firstAuthor"],
'title': row["publications.title"],
'year': row["publications.year"],
'journal': row["publications.journal"],
'volume': row["publications.volume"],
'pages': row["publications.pages"],
'pubmed_id': row["publications.pubMedId"],
'issue': row["publications.issue"]
}
print json.dumps(record, indent=2)
print '---'
def search(args):
"""
args contains a dict with one or key:values
"""
ident_arg = args["identifier"]
primaryId = tools.getProteinPrimaryIdentifier(ident_arg)
ident = ident_arg
if primaryId and primaryId != '':
ident = primaryId
# get a new query on the class (table) from the model
query = service.new_query("Protein")
# views specify the output columns
query.add_view("primaryIdentifier", "molecularWeight", "length", "isFragment",
"isUniprotCanonical", "name", "dataSets.dataSource.name",
"primaryAccession", "secondaryIdentifier", "uniprotAccession",
"uniprotName", "synonyms.value", "keywords.name"
)
# set the constraint value(s)
query.add_constraint("primaryIdentifier", "=", ident, code = "A")
# outer join on synonyms
query.outerjoin("synonyms")
query.outerjoin("keywords")
# loop over rows of data to build the JSON object
synonyms = {}
keywords = {}
found = False
for row in query.rows():
protein_id = row["primaryIdentifier"]
molecular_weight = row["molecularWeight"]
length = row["length"]
is_fragment = row["isFragment"]
is_uniprot_canonical = row["isUniprotCanonical"]
name = row["name"]
source = row["dataSets.dataSource.name"]
primary_accession = row["primaryAccession"]
secondary_identifier = row["secondaryIdentifier"]
uniprot_accession = row["uniprotAccession"]
uniprot_name = row["uniprotName"]
if row["synonyms.value"]:
if not synonyms.has_key(row["synonyms.value"]):
synonyms[row["synonyms.value"]] = 1
if row["keywords.name"]:
if not keywords.has_key(row["keywords.name"]):
keywords[row["keywords.name"]] = 1
found = True
if found:
record = {
'class': 'protein_property',
'source_text_description': 'ThaleMine Protein Summary',
'protein_id': protein_id,
'molecular_weight': molecular_weight,
'length': length,
'is_fragment': is_fragment,
'is_uniprot_canonical': is_uniprot_canonical,
'name': name,
'source': source,
'primary_accession': primary_accession,
'secondary_identifier': secondary_identifier,
'uniprot_accession': uniprot_accession,
'uniprot_name': uniprot_name,
'synonyms': synonyms.keys(),
'keywords': keywords.keys()
}
print json.dumps(record, indent=2)
print '---'
