4 from htsworkflow.util.rdfhelp import \
16 TYPE_N = rdfNS['type']
17 CREATION_DATE = libraryOntology['date']
19 from encode_find import DBDIR
22 model = get_model('encode', DBDIR)
23 what_have_we_done(model)
25 SUBMISSION_QUERY = """
26 PREFIX xsd:<http://www.w3.org/2001/XMLSchema#>
27 PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
28 PREFIX ucscSubmission:<http://jumpgate.caltech.edu/wiki/UcscSubmissionOntology#>
29 PREFIX libraryOntology:<http://jumpgate.caltech.edu/wiki/LibraryOntology#>
30 PREFIX daf: <http://jumpgate.caltech.edu/wiki/UcscDaf#>
31 PREFIX ddf: <http://encodesubmit.ucsc.edu/pipeline/download_ddf#>
33 SELECT distinct ?library_urn ?library_name ?assembly ?submission ?submission_status ?date
35 ?submission ucscSubmission:library_urn ?library_urn ;
36 ucscSubmission:has_status ?status ;
37 libraryOntology:date ?date .
38 ?status daf:assembly ?assembly ;
39 ucscSubmission:status ?submission_status .
40 OPTIONAL { ?library_urn libraryOntology:name ?library_name . }
41 FILTER(!regex(?submission_status, "revoked", "i"))
42 FILTER(regex(?assembly, "mm9", "i"))
43 #FILTER(!BOUND(?library_name))
45 ORDER BY ?library_urn ?submission
48 SUBMISSION_TEMPLATE = """
51 <style type="text/css">
52 table { border-width: 0 0 1px 1px; border-style: solid; }
53 th,td { border-width: 1px 1px 0 0; border-style: solid; margin: 0;}
60 <td>Library ID</td><td>Submission ID</td><td>Last Updated</td><td>Status</td>
65 {% for record in submissions %}
67 <td><a href="{{record.library_urn}}">{{ record.library_urn | trim_rdf}}</a></td>
68 <td><a href="{{record.submission}}">{{record.submission|trim_rdf}}</a></td>
69 <td>{{ record.date|timestamp_to_date }}</td>
70 <td>{{ record.submission_status }}</td>
71 <td>{{ record.library_name }}</td>
80 def what_have_we_done(model):
81 compiled_query = RDF.SPARQLQuery(SUBMISSION_QUERY)
82 submissions = compiled_query.execute(model)
83 environment = jinja2.Environment()
84 environment.filters['trim_rdf'] = trim_rdf
85 environment.filters['timestamp_to_date'] = timestamp_to_date
86 template = environment.from_string(SUBMISSION_TEMPLATE)
87 print template.render(submissions = submissions)
95 split_value = value.split('/')
96 if len(split_value) == 0:
98 return split_value[-1]
100 def timestamp_to_date(value):
101 datestamp, timestamp = str(value).split('T')
104 if __name__ == "__main__":