Show the "Amplified from sample" as the parent library id and allow

searching on that on the public library index.

Additionally detect if we have an eland_multi or eland extended file
and make the url to download those different files. (and change the
link name slightly to reflect you're getting a different file.)

finally don't bother showing the bed downloader for newer file types
as the bed convertor doesn't work on them.

diff --git a/htsworkflow/frontend/samples/models.py b/htsworkflow/frontend/samples/models.py
index 19190ee3e6444605973eea86008b1d901f7198bd..26d718576d9c45905b9544d733087099d3ec20a3 100644 (file)
--- a/htsworkflow/frontend/samples/models.py
+++ b/htsworkflow/frontend/samples/models.py
@@ -120,8 +120,8 @@ class Library(models.Model):
   library_species = models.ForeignKey(Species)
   # new field 2008 Mar 5, alter table samples_library add column "hidden" NOT NULL default 0;
   hidden = models.BooleanField()
-  cell_line = models.ForeignKey(Cellline)
-  condition = models.ForeignKey(Condition)
+  cell_line = models.ForeignKey(Cellline, null=True)
+  condition = models.ForeignKey(Condition, null=True)
   antibody = models.ForeignKey(Antibody,blank=True,null=True)
   # New field Aug/25/08. SQL: alter table fctracker_library add column "lib_affiliation" varchar(256)  NULL;
   affiliations = models.ManyToManyField(Affiliation,related_name='library_affiliations',null=True)
@@ -149,7 +149,7 @@ class Library(models.Model):
       ('Done', 'Completed'),
     )
   stopping_point = models.CharField(max_length=25, choices=PROTOCOL_END_POINTS, default='Done')
-  amplified_from_sample = models.ForeignKey('self', blank=True, null=True)  
+  amplified_from_sample = models.ForeignKey('self', blank=True, null=True, related_name='amplified_into_sample')  
   
   undiluted_concentration = models.DecimalField("Concentration", 
       max_digits=5, decimal_places=2, blank=True, null=True,

diff --git a/htsworkflow/frontend/samples/results.py b/htsworkflow/frontend/samples/results.py
index d7cb77ea9c62218af744aaec86ed222dca8484b8..c2419cd916d110463297f97d4bf6a5b7449d78dc 100644 (file)
--- a/htsworkflow/frontend/samples/results.py
+++ b/htsworkflow/frontend/samples/results.py
@@ -71,7 +71,7 @@ def get_flowcell_result_dict(flowcell_id):
         
         d[c_dir]['eland_results'] = {}
         
-        result_filepaths = glob.glob(os.path.join(c_dir_path, 's_*_eland_result.txt*'))
+        result_filepaths = glob.glob(os.path.join(c_dir_path, 's_*_eland_*'))
         
         for filepath in result_filepaths:
             

diff --git a/htsworkflow/frontend/samples/views.py b/htsworkflow/frontend/samples/views.py
index b6561a624ed1b54c42a606a305cab1f081d05298..d6647d1dba38311733d9f3d07530df9f77442a6b 100644 (file)
--- a/htsworkflow/frontend/samples/views.py
+++ b/htsworkflow/frontend/samples/views.py
@@ -30,6 +30,10 @@ def create_library_context(cl):
        summary['library_id'] = lib.library_id
        summary['library_name'] = lib.library_name
        summary['species_name' ] = lib.library_species.scientific_name
+       if lib.amplified_from_sample is not None:
+           summary['amplified_from'] = lib.amplified_from_sample.library_id
+       else:
+           summary['amplified_from'] = ''
        lanes_run = 0
        for lane_id in LANE_LIST:
            lane = getattr(lib, 'lane_%d_library' % (lane_id,))
@@ -42,8 +46,8 @@ def create_library_context(cl):
 def library(request):
    # build changelist
     fcl = ChangeList(request, Library,
-        list_filter=['library_species','affiliations'],
-        search_fields=['library_id', 'library_name'],
+        list_filter=['affiliations', 'library_species'],
+        search_fields=['library_id', 'library_name', 'amplified_from_sample__library_id'],
         list_per_page=200,
         queryset=Library.objects.filter(hidden__exact=0)
     )
@@ -318,12 +322,26 @@ def _summary_stats_old(flowcell_id, lane):
     return (dict_list, err_list, summary_list)
     
     
-
+def get_eland_result_type(pathname):
+    """
+    Guess the eland result file type from the filename
+    """
+    path, filename = os.path.split(pathname)
+    if 'extended' in filename:
+        return 'extended'
+    elif 'multi' in filename:
+        return 'multi'
+    elif 'result' in filename:
+        return 'result'
+    else:
+        return 'unknown'
     
 def _files(flowcell_id, lane):
     """
     Sets up available files for download
     """
+    lane = int(lane)
+
     flowcell_id, id = parse_flowcell_id(flowcell_id)
     d = get_flowcell_result_dict(flowcell_id)
     
@@ -340,10 +358,13 @@ def _files(flowcell_id, lane):
                           % (flowcell_id, c_name, c_name))
         
         erd = d[c_name]['eland_results']
-        
-        if int(lane) in erd:
-            output.append('<a href="/results/%s/%s/eland_result/%s">eland_result(%s)</a>' % (flowcell_id, c_name, lane, c_name))
-            output.append('<a href="/results/%s/%s/bedfile/%s">bedfile(%s)</a>' % (flowcell_id, c_name, lane, c_name))
+        if lane in erd:
+            result_type = get_eland_result_type(erd[lane])
+            result_url_pattern = '<a href="/results/%s/%s/eland_result/%s">eland %s(%s)</a>'
+            output.append(result_url_pattern % (flowcell_id, c_name, lane, result_type, c_name))
+            if result_type == 'result':
+                bed_url_pattern = '<a href="/results/%s/%s/bedfile/%s">bedfile(%s)</a>'
+                output.append(bed_url_pattern % (flowcell_id, c_name, lane, c_name))
     
     if len(output) == 0:
         return ''

diff --git a/htsworkflow/frontend/templates/samples/library_index.html b/htsworkflow/frontend/templates/samples/library_index.html
index 4263846c9c3574366c32b722d6072e8077c1f9f0..afae22b85ce1e5806c079ab6d270026f948d5671 100644 (file)
--- a/htsworkflow/frontend/templates/samples/library_index.html
+++ b/htsworkflow/frontend/templates/samples/library_index.html
@@ -29,6 +29,7 @@
 <table>
   <thead>
     <tr>
+    <td>Parent</td>
     <td>Library ID</td>
     <td>Species</td>
     <td>Library Name</td>
@@ -36,8 +37,9 @@
     </tr>
   </thead>
   <tbody>
-    {% for lib in library_list%}
+    {% for lib in library_list %}
     <tr>
+      <td><a href="/library/{{ lib.library_id }}">{{ lib.amplified_from }}</a></td>
       <td><a href="/library/{{ lib.library_id }}">{{ lib.library_id }}</a></td>
       <td><a href="/library/{{ lib.library_id }}">{{ lib.species_name }}</a></td>
       <td><a href="/library/{{ lib.library_id }}">{{ lib.library_name }}</a></td>