htsworkflow/submission/geo.py

   1 import logging
   2
   3 import RDF
   4
   5 from htsworkflow.submission.submission import Submission
   6
   7 from htsworkflow.util.rdfhelp import \
   8      fromTypedNode, \
   9      submissionOntology
  10
  11 from django.conf import settings
  12 from django.template import Context, loader
  13
  14 LOGGER = logging.getLogger(__name__)
  15
  16 class GEOSubmission(Submission):
  17     def __init__(self, name, model):
  18         super(GEOSubmission, self).__init__(name, model)
  19
  20     def make_soft(self, result_map):
  21         samples = []
  22         for lib_id, result_dir in result_map.items():
  23             an_analysis = self.get_submission_node(result_dir)
  24             samples.append(self.get_sample_metadata(an_analysis))
  25
  26         soft_template = loader.get_template('geo_submission.soft')
  27         context = Context({
  28             'samples': samples
  29         })
  30         print str(soft_template.render(context))
  31
  32     def check_for_name(self, analysis_node):
  33         name = fromTypedNode(
  34             self.model.get_target(analysis_node,
  35                                   submissionOntology['name']))
  36         if name is None:
  37             logger.error("Need name for %s" % (str(analysis_node)))
  38             return False
  39         else:
  40             return True
  41
  42     def get_sample_metadata(self, analysis_node):
  43         """Gather information for filling out sample section of a SOFT file
  44         """
  45         query_template = loader.get_template('geo_submission.sparql')
  46
  47         context = Context({
  48             'submission': str(analysis_node.uri),
  49             })
  50
  51         formatted_query = query_template.render(context)
  52         query = RDF.SPARQLQuery(str(formatted_query))
  53         rdfstream = query.execute(self.model)
  54         results = []
  55         for r in rdfstream:
  56             results.append(r)
  57         return results