Start developing GEO SOFT submission tool.

[htsworkflow.git] / htsworkflow / submission / geo.py

diff --git a/htsworkflow/submission/geo.py b/htsworkflow/submission/geo.py
new file mode 100644 (file)
index 0000000..737b1bb
--- /dev/null
+++ b/htsworkflow/submission/geo.py
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+import logging
+
+import RDF
+
+from htsworkflow.submission.submission import Submission
+
+from htsworkflow.util.rdfhelp import \
+     fromTypedNode, \
+     submissionOntology
+
+from django.conf import settings
+from django.template import Context, loader
+
+LOGGER = logging.getLogger(__name__)
+
+class GEOSubmission(Submission):
+    def __init__(self, name, model):
+        super(GEOSubmission, self).__init__(name, model)
+
+    def make_soft(self, result_map):
+        samples = []
+        for lib_id, result_dir in result_map.items():
+            an_analysis = self.get_submission_node(result_dir)
+            samples.append(self.get_sample_metadata(an_analysis))
+
+        soft_template = loader.get_template('geo_submission.soft')
+        context = Context({
+            'samples': samples
+        })
+        print str(soft_template.render(context))
+
+    def check_for_name(self, analysis_node):
+        name = fromTypedNode(
+            self.model.get_target(analysis_node,
+                                  submissionOntology['name']))
+        if name is None:
+            logger.error("Need name for %s" % (str(analysis_node)))
+            return False
+        else:
+            return True
+
+    def get_sample_metadata(self, analysis_node):
+        """Gather information for filling out sample section of a SOFT file
+        """
+        query_template = loader.get_template('geo_submission.sparql')
+
+        context = Context({
+            'submission': str(analysis_node.uri),
+            })
+
+        formatted_query = query_template.render(context)
+        query = RDF.SPARQLQuery(str(formatted_query))
+        rdfstream = query.execute(self.model)
+        results = []
+        for r in rdfstream:
+            results.append(r)
+        return results