From 7009e5d733d449e6eddd3e754de22ad8a4f0ce51 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Thu, 30 Jun 2011 15:47:40 -0700 Subject: [PATCH] The proper DDF variable name for files to be submitted is files Also the older librdf resource formatting used [] instead of <> so can't be directly placed into a sparql query --- extra/ucsc_encode_submission/ucsc_gather.py | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/extra/ucsc_encode_submission/ucsc_gather.py b/extra/ucsc_encode_submission/ucsc_gather.py index d52b11b..37169c0 100755 --- a/extra/ucsc_encode_submission/ucsc_gather.py +++ b/extra/ucsc_encode_submission/ucsc_gather.py @@ -210,15 +210,15 @@ def make_ddf(view_map, submissionNode, daf_name, make_condor=False, outdir=None) PREFIX submissionOntology: PREFIX ucscDaf: -select ?submitView ?filename ?md5sum ?view ?cell ?antibody ?sex ?control ?controlId ?labExpId ?labVersion ?treatment ?protocol +select ?submitView ?files ?md5sum ?view ?cell ?antibody ?sex ?control ?controlId ?labExpId ?labVersion ?treatment ?protocol WHERE { - ?file ucscDaf:filename ?filename ; + ?file ucscDaf:filename ?files ; ucscDaf:md5sum ?md5sum . ?submitView ucscDaf:has_file ?file ; ucscDaf:view ?dafView ; - ucscDaf:submission %(submission)s . + ucscDaf:submission <%(submission)s> . ?dafView ucscDaf:name ?view . - %(submission)s submissionOntology:library ?library . + <%(submission)s> submissionOntology:library ?library . OPTIONAL { ?submitView ucscDaf:antibody ?antibody } OPTIONAL { ?submitView ucscDaf:cell ?cell } @@ -245,12 +245,12 @@ ORDER BY ?submitView""" else: output = sys.stdout - formatted_query = query_template % {'submission': str(submissionNode)} + formatted_query = query_template % {'submission': str(submissionNode.uri)} query = RDF.SPARQLQuery(formatted_query) results = query.execute(view_map.model) - variables = ['filename'] + variables = ['files'] # filename goes first variables.extend(view_map.get_daf_variables()) variables += ['controlId', 'labExpId', 'md5sum'] @@ -264,7 +264,7 @@ ORDER BY ?submitView""" current = all_views.setdefault(viewname, {}) for variable_name in variables: value = str(fromTypedNode(row[variable_name])) - if variable_name in ('filename', 'md5sum'): + if variable_name in ('files', 'md5sum'): current.setdefault(variable_name,[]).append(value) else: current[variable_name] = value @@ -272,13 +272,13 @@ ORDER BY ?submitView""" for view in all_views.keys(): line = [] for variable_name in variables: - if variable_name in ('filename', 'md5sum'): + if variable_name in ('files', 'md5sum'): line.append(','.join(all_views[view][variable_name])) else: line.append(all_views[view][variable_name]) output.write("\t".join(line)) output.write(os.linesep) - all_files.extend(all_views[view]['filename']) + all_files.extend(all_views[view]['files']) logging.info( "Examined {0}, found files: {1}".format( -- 2.30.2