Update test to work with species -> species_name rename.

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

diff --git a/htsworkflow/submission/trackhub_submission.py b/htsworkflow/submission/trackhub_submission.py
new file mode 100644 (file)
index 0000000..8b7b424
--- /dev/null
+++ b/htsworkflow/submission/trackhub_submission.py
@@ -0,0 +1,78 @@
+import logging
+import os
+
+import RDF
+
+from htsworkflow.submission.submission import Submission
+
+from htsworkflow.util.rdfhelp import \
+     fromTypedNode, \
+     geoSoftNS, \
+     stripNamespace, \
+     submissionOntology
+
+from django.conf import settings
+from django.template import Context, loader
+
+LOGGER = logging.getLogger(__name__)
+
+class TrackHubSubmission(Submission):
+    def __init__(self, name, model, host):
+        super(TrackHubSubmission, self).__init__(name, model, host)
+
+    def make_hub(self, result_map):
+        samples = []
+        for lib_id, result_dir in result_map.items():
+            an_analysis = self.get_submission_node(result_dir)
+            metadata = self.get_sample_metadata(an_analysis)
+            if len(metadata) == 0:
+                errmsg = 'No metadata found for {0}'
+                LOGGER.error(errmsg.format(str(an_analysis),))
+                continue
+            elif len(metadata) > 1:
+                errmsg = 'Confused there are more than one sample for %s'
+                LOGGER.debug(errmsg % (str(an_analysis),))
+            metadata = metadata[0]
+            samples.append(metadata)
+
+        template = loader.get_template('trackDb.txt')
+        context = Context({
+            'samples': samples,
+        })
+        return str(template.render(context))
+
+    def make_manifest(self, result_map):
+        files = []
+        for lib_id, result_dir in result_map.items():
+            an_analysis = self.get_submission_node(result_dir)
+            metadata = self.get_manifest_metadata(an_analysis)
+            files.extend(metadata)
+
+        template = loader.get_template('manifest.txt')
+        context = Context({
+            'files': files
+        })
+        return str(template.render(context))
+        
+    def get_sample_metadata(self, analysis_node):
+        """Gather information for filling out sample section of a SOFT file
+        """
+        query_template = loader.get_template('trackhub_samples.sparql')
+
+        context = Context({
+            'submission': str(analysis_node.uri),
+            'submissionSet': str(self.submissionSetNS[''].uri),
+            })
+
+        results = self.execute_query(query_template, context)
+        return results
+
+    def get_manifest_metadata(self, analysis_node):
+        query_template = loader.get_template('trackhub_manifest.sparql')
+
+        context = Context({
+            'submission': str(analysis_node.uri),
+            'submissionSet': str(self.submissionSetNS[''].uri),
+            })
+        results = self.execute_query(query_template, context)
+        return results