Update test to work with species -> species_name rename.

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

diff --git a/htsworkflow/submission/trackhub.py b/htsworkflow/submission/trackhub.py
deleted file mode 100644 (file)
index 8b7b424..0000000
--- a/htsworkflow/submission/trackhub.py
+++ /dev/null
@@ -1,78 +0,0 @@
-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