--- /dev/null
+import argparse
+import RDF
+import jinja2
+from pprint import pprint
+
+from htsworkflow.util.rdfhelp import \
+ dafTermOntology, \
+ dublinCoreNS, \
+ get_model, \
+ get_serializer, \
+ sparql_query, \
+ submissionOntology, \
+ libraryOntology, \
+ load_into_model, \
+ rdfNS, \
+ rdfsNS, \
+ xsdNS
+TYPE_N = rdfNS['type']
+CREATION_DATE = libraryOntology['date']
+
+from encode_find import DBDIR
+
+DEFAULT_GENOME='hg19'
+DEFAULT_OUTPUT='/tmp/submission_report.html'
+
+def main(cmdline=None):
+ parser = make_parser()
+ args = parser.parse_args(cmdline)
+ model = get_model('encode', DBDIR)
+ report = what_have_we_done(model, genome=args.genome)
+ with open(DEFAULT_OUTPUT,'w') as stream:
+ stream.write(report)
+
+def make_parser():
+ parser = argparse.ArgumentParser()
+ parser.add_argument('--genome', default=DEFAULT_GENOME,
+ help='limit to one genome')
+ parser.add_argument('--output', default='/tmp/submission_report.html',
+ help="specify where to write to write report")
+ return parser
+
+SUBMISSION_QUERY = """
+PREFIX xsd:<http://www.w3.org/2001/XMLSchema#>
+PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
+PREFIX ucscSubmission:<http://jumpgate.caltech.edu/wiki/UcscSubmissionOntology#>
+PREFIX libraryOntology:<http://jumpgate.caltech.edu/wiki/LibraryOntology#>
+PREFIX daf: <http://jumpgate.caltech.edu/wiki/UcscDaf#>
+PREFIX ddf: <http://encodesubmit.ucsc.edu/pipeline/download_ddf#>
+
+SELECT distinct ?assembly ?experiment ?library_urn ?library_name ?submission ?submission_status ?submission_name ?date
+WHERE {{
+ ?submission ucscSubmission:library_urn ?library_urn ;
+ ucscSubmission:has_status ?status ;
+ ucscSubmission:name ?submission_name ;
+ libraryOntology:date ?date .
+ ?status daf:assembly ?assembly ;
+ ucscSubmission:status ?submission_status .
+ OPTIONAL {{ ?library_urn libraryOntology:name ?library_name . }}
+ OPTIONAL {{ ?library_urn libraryOntology:experiment_type ?experiment . }}
+ FILTER(!regex(?submission_status, "revoked", "i"))
+ {assembly_filter}
+}}
+ORDER BY ?assembly ?experiment ?library_urn ?submission
+"""
+
+SUBMISSION_TEMPLATE = '''
+<html>
+<head>
+<style type="text/css">
+table { border-width: 0 0 1px 1px; border-style: solid; }
+th,td { border-width: 1px 1px 0 0; border-style: solid; margin: 0;}
+.library { font-size: 18pt; background-color: #EEF; }
+.submission { font-size: 12pt; background-color: #EFE;}
+</style>
+ <title>Submission report for {{ genome }}</title>
+</head>
+<body>
+<h1>Genome: {{ genome }}</h1>
+{% for experiment in libraries %}
+ <h2>{{ experiment }}</h2>
+ <table>
+ <thead>
+ <tr class="library">
+ <td>Library ID</td>
+ <td colspan="3">Library Name</td>
+ </tr>
+ <tr class="submission">
+ <td>Submission ID</td>
+ <td>Last Updated</td>
+ <td>Status</td>
+ <td>Submission name</td>
+ </tr>
+ </thead>
+ <tbody>
+ {% for liburn, records in libraries[experiment]|dictsort %}
+ <!-- {{ liburn }} -->
+ <tr class="library">
+ <td>
+ <a href="{{libraries[experiment][liburn].0.library_urn}}">
+ {{ libraries[experiment][liburn].0.library_urn | trim_rdf}}
+ </a>
+ </td>
+ <td colspan="3">{{ libraries[experiment][liburn].0.library_name }}</td>
+ </tr>
+ {% for record in records|sort %}
+ <tr class="submission">
+ <td><a href="{{record.submission}}">{{record.submission|trim_rdf}}</a></td>
+ <td>{{ record.date|timestamp_to_date }}</td>
+ <td>{{ record.submission_status }}</td>
+ <td>{{ record.submission_name }}</td>
+ </tr>
+ {% endfor %}
+ {% endfor %}
+ </tbody>
+ </table>
+{% endfor %}
+ </body>
+</html>
+'''
+
+def what_have_we_done(model, genome):
+ assembly_filter = ''
+ assembly_filter = 'FILTER(regex(?assembly, "{0}", "i"))'.format(genome)
+
+ query = SUBMISSION_QUERY.format(
+ assembly_filter=assembly_filter
+ )
+ compiled_query = RDF.SPARQLQuery(query)
+ submissions = compiled_query.execute(model)
+ libraries = group_by_library(submissions)
+ environment = jinja2.Environment()
+ environment.filters['trim_rdf'] = trim_rdf
+ environment.filters['timestamp_to_date'] = timestamp_to_date
+ template = environment.from_string(SUBMISSION_TEMPLATE)
+ return template.render(libraries=libraries,
+ genome=genome)
+
+def group_by_library(submissions):
+ libraries = {}
+ for record in submissions:
+ urn = str(record['library_urn'].uri)
+ experiment = str(record['experiment'])
+ libraries.setdefault(experiment, {}).setdefault(urn, []).append(record)
+ return libraries
+
+def trim_rdf(value):
+ if value is None:
+ return
+ value = str(value)
+ if len(value) == 0:
+ return value
+ if value[-1] == '/':
+ value = value[:-1]
+ split_value = value.split('/')
+ if len(split_value) == 0:
+ return value
+ return split_value[-1]
+
+def timestamp_to_date(value):
+ datestamp, timestamp = str(value).split('T')
+ return datestamp
+
+if __name__ == "__main__":
+ main()
projects / htsworkflow.git / blobdiff