--- /dev/null
+import RDF
+import jinja2
+
+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
+
+def main():
+ model = get_model('encode', DBDIR)
+ what_have_we_done(model)
+
+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 ?library_urn ?library_name ?assembly ?submission ?submission_status ?date
+WHERE {
+ ?submission ucscSubmission:library_urn ?library_urn ;
+ ucscSubmission:has_status ?status ;
+ libraryOntology:date ?date .
+ ?status daf:assembly ?assembly ;
+ ucscSubmission:status ?submission_status .
+ OPTIONAL { ?library_urn libraryOntology:name ?library_name . }
+ FILTER(!regex(?submission_status, "revoked", "i"))
+ FILTER(regex(?assembly, "mm9", "i"))
+ #FILTER(!BOUND(?library_name))
+}
+ORDER BY ?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;}
+</style>
+</head>
+<body>
+<table>
+<thead>
+ <tr>
+ <td>Library ID</td><td>Submission ID</td><td>Last Updated</td><td>Status</td>
+ <td>Library Name</td>
+ </tr>
+</thead>
+<tbody>
+{% for record in submissions %}
+ <tr>
+ <td><a href="{{record.library_urn}}">{{ record.library_urn | trim_rdf}}</a></td>
+ <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.library_name }}</td>
+ </tr>
+{% endfor %}
+</tbody>
+</table>
+</body>
+</html>
+"""
+
+def what_have_we_done(model):
+ compiled_query = RDF.SPARQLQuery(SUBMISSION_QUERY)
+ submissions = compiled_query.execute(model)
+ environment = jinja2.Environment()
+ environment.filters['trim_rdf'] = trim_rdf
+ environment.filters['timestamp_to_date'] = timestamp_to_date
+ template = environment.from_string(SUBMISSION_TEMPLATE)
+ print template.render(submissions = submissions)
+
+def trim_rdf(value):
+ if value is None:
+ return
+ value = str(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 / commitdiff