* Added option to use default return type by adding /ucsc/ at the end

   of the bedfile url (good for debugging, and possibly for displaying
   on ucsc genome browser, but may have been another bug that was
   preventing the default return method from working with UCSC).
 * Used Diane's auto open feature for reading the bz2 eland_result files.

diff --git a/gaworkflow/frontend/fctracker/views.py b/gaworkflow/frontend/fctracker/views.py
index ad3937c9e68e0bda32a21c864f516cbd3cbb1b9d..b653d4e2c5f32e94ec1f5028a585dbbebbe735ab 100644 (file)
--- a/gaworkflow/frontend/fctracker/views.py
+++ b/gaworkflow/frontend/fctracker/views.py
@@ -86,7 +86,14 @@ def result_fc_cnm_eland_lane(request, fc_id, cnm, lane):
     return HttpResponse(f, mimetype="application/x-elandresult")
 
 
-def bedfile_fc_cnm_eland_lane(request, fc_id, cnm, lane):
+def bedfile_fc_cnm_eland_lane_ucsc(request, fc_id, cnm, lane):
+    """
+    returns a bed file for a given flowcell, CN-M (i.e. C1-33), and lane (ucsc compatible)
+    """
+    return bedfile_fc_cnm_eland_lane(request, fc_id, cnm, lane, ucsc_compatible=True)
+
+
+def bedfile_fc_cnm_eland_lane(request, fc_id, cnm, lane, ucsc_compatible=False):
     """
     returns a bed file for a given flowcell, CN-M (i.e. C1-33), and lane
     """
@@ -108,7 +115,7 @@ def bedfile_fc_cnm_eland_lane(request, fc_id, cnm, lane):
     filepath = erd[lane]
     
     # Eland result file
-    fi = open(filepath, 'r')
+    fi = opener.autoopen(filepath, 'r')
     # output memory file
     
     
@@ -118,7 +125,10 @@ def bedfile_fc_cnm_eland_lane(request, fc_id, cnm, lane):
     
     bedgen = makebed.make_bed_from_eland_stream_generator(fi, name, description)
     
-    return HttpResponse(bedgen, mimetype="application/x-bedfile")
+    if ucsc_compatible:
+        return HttpResponse(bedgen)
+    else:
+        return HttpResponse(bedgen, mimetype="application/x-bedfile")
 
     
 def _files(flowcell_id, lane):

diff --git a/gaworkflow/frontend/urls.py b/gaworkflow/frontend/urls.py
index add92790f2e24a31759f0de514077451ffcfb7cb..37bf0d119d88b7b75bfa774bdf4b1e3f4e719b67 100644 (file)
--- a/gaworkflow/frontend/urls.py
+++ b/gaworkflow/frontend/urls.py
@@ -16,5 +16,6 @@ urlpatterns = patterns('',
      (r'^library/$', 'gaworkflow.frontend.fctracker.views.library'),
      (r'^library/(?P<lib_id>\w+)/$', 'gaworkflow.frontend.fctracker.views.library_to_flowcells'),
      (r'^results/(?P<fc_id>\w+)/(?P<cnm>C[1-9]-[0-9]+)/eland_result/(?P<lane>[1-8])','gaworkflow.frontend.fctracker.views.result_fc_cnm_eland_lane'),
+     (r'^results/(?P<fc_id>\w+)/(?P<cnm>C[1-9]-[0-9]+)/bedfile/(?P<lane>[1-8])/ucsc','gaworkflow.frontend.fctracker.views.bedfile_fc_cnm_eland_lane_ucsc'),
      (r'^results/(?P<fc_id>\w+)/(?P<cnm>C[1-9]-[0-9]+)/bedfile/(?P<lane>[1-8])','gaworkflow.frontend.fctracker.views.bedfile_fc_cnm_eland_lane'),
 )