generalizing this functionality

Author: antgonza

qiita_pet/handlers/api_proxy/studies.py

@@ -248,34 +248,28 @@ def study_files_get_req(user_id, study_id, prep_template_id, artifact_type):
     if any(ftypes_if) and 'run_prefix' in pt.columns:
         prep_prefixes = tuple(set(pt['run_prefix']))
         num_prefixes = len(prep_prefixes)
-        # special case for per_sample_FASTQ
-        if artifact_type == 'per_sample_FASTQ':
-            # sorting prefixes by length to avoid collisions like: 100 1002
-            # 10003
-            prep_prefixes = sorted(prep_prefixes, key=len, reverse=True)
-            # group files by prefix
-            sfiles = {p: [f for _, f in uploaded if f.startswith(p)]
-                      for p in prep_prefixes}
-            for k, v in viewitems(sfiles):
-                len_files = len(v)
-                if len_files != 1 and len_files != 2:
-                    remaining.extend(v)
-                else:
-                    v.sort()
-                    selected.append(v)
-        else:
-            len_files = 1
-            for _, filename in uploaded:
-                if filename.startswith(prep_prefixes):
-                    selected.append(filename)
-                else:
-                    remaining.append(filename)
+        # sorting prefixes by length to avoid collisions like: 100 1002
+        # 10003
+        prep_prefixes = sorted(prep_prefixes, key=len, reverse=True)
+        # group files by prefix
+        sfiles = {p: [f for _, f in uploaded if f.startswith(p)]
+                  for p in prep_prefixes}
+        inuse = [y for x in sfiles.values() for y in x]
+        remaining.extend([f for _, f in uploaded if f not in inuse])
+
+        for k, v in viewitems(sfiles):
+            len_files = len(v)
+            if len_files != 1 and len_files != 2:
+                remaining.extend(v)
+            else:
+                v.sort()
+                selected.append(v)
     else:
         num_prefixes = 0
         remaining = [f for _, f in uploaded]
 
     # get file_types, format: filetype, required, list of files
-    file_types = [(t, req, [x[i] for x in selected if i+1 <= len_files])
+    file_types = [(t, req, [x[i] for x in selected if i+1 <= len(x)])
                   for i, (t, req) in enumerate(supp_file_types)]
 
     # Create a list of artifacts that the user has access to, in case that

qiita_pet/handlers/api_proxy/tests/test_studies.py

@@ -238,6 +238,8 @@ def test_study_prep_get_req(self):
         for i in range(4, 0, -1):
             qdb.artifact.Artifact(i).visibility = "private"
 
+        qdb.metadata_template.prep_template.PrepTemplate.delete(pt.id)
+
     def test_study_prep_get_req_failed_EBI(self):
         temp_dir = mkdtemp()
         self._clean_up_files.append(temp_dir)
@@ -337,6 +339,8 @@ def test_study_prep_get_req_failed_EBI(self):
             'status': 'success'}
         self.assertEqual(obs, exp)
 
+        qdb.metadata_template.prep_template.PrepTemplate.delete(pt.id)
+
     def test_study_prep_get_req_no_access(self):
         obs = study_prep_get_req(1, 'demo@microbio.me')
         exp = {'status': 'error',
@@ -463,7 +467,7 @@ def test_study_files_get_req_per_sample_FASTQ(self):
             'shared@foo.bar', 1, pt.id, 'per_sample_FASTQ')
         exp = {
             'status': 'success', 'num_prefixes': 2, 'artifacts': [],
-            'remaining': [], 'message': '',
+            'remaining': ['uploaded_file.txt'], 'message': '',
             'file_types': [
                 ('raw_forward_seqs', True,
                  ['test_2.R1.fastq.gz', 'test_1.R1.fastq.gz']),
@@ -479,7 +483,7 @@ def test_study_files_get_req_per_sample_FASTQ(self):
         obs = study_files_get_req(
             'shared@foo.bar', 1, pt.id, 'per_sample_FASTQ')
         exp = {'status': 'success', 'num_prefixes': 2, 'artifacts': [],
-               'remaining': [], 'message': '',
+               'remaining': ['uploaded_file.txt'], 'message': '',
                'file_types': [('raw_forward_seqs', True,
                                ['test_2.R1.fastq.gz', 'test_1.R1.fastq.gz']),
                               ('raw_reverse_seqs', False,
@@ -496,7 +500,7 @@ def test_study_files_get_req_per_sample_FASTQ(self):
             'shared@foo.bar', 1, pt.id, 'per_sample_FASTQ')
         exp = {'status': 'success', 'num_prefixes': 2, 'artifacts': [],
                'remaining': ['test_1.R1.fastq.gz', 'test_1.R2.fastq.gz',
-                             'test_1.R3.fastq.gz'],
+                             'test_1.R3.fastq.gz', 'uploaded_file.txt'],
                'message': '',
                'file_types': [('raw_forward_seqs', True,
                                ['test_2.R1.fastq.gz']),

qiita_pet/templates/study_ajax/add_artifact.html

@@ -90,9 +90,6 @@ <h4><i>No files attached to this preparation</i></h4>
 
 <form action="{% raw qiita_config.portal_dir %}/study/new_artifact/" method="POST" id="create-artifact-form">
   <div class="row">
-    <div class="col-md-12">
-      <b>Name:</b> <input type="text" id="name" name="name" maxlength="35" required>
-    </div>
     <div class="col-md-12">
       <b>Select type:</b>
       <select name="artifact-type" id="artifact-type">
@@ -102,6 +99,9 @@ <h4><i>No files attached to this preparation</i></h4>
         {% end %}
       </select>
     </div>
+    <div class="col-md-12">
+      <b>Add a name for the file:</b> <input type="text" id="name" name="name" maxlength="35" required>
+    </div>
   </div>
   <div id="files-selector" hidden>
   </div>

qiita_pet/templates/study_ajax/artifact_file_selector.html

@@ -183,7 +183,7 @@
 </style>
 <div class="row">
   <div class="col-md-12">
-    <b>Import files from other studies:</b>
+    <b>Now, you can import files from other studies</b>
     <select id="import-artifact" name="import-artifact">
       <option value="">Choose an artfact to import...</option>
       {% for a_id, label in artifacts %}
@@ -195,7 +195,12 @@
 </div>
 <div id="drag-files-div" class="row">
   <div class="col-md-12">
-    <b>Or click and drag your uploaded files to the correct file type:</b><br/>
+    <b>or click and drag your uploaded files to the correct file type</b><br/>
+      <div class="blinking-message">
+        Note: the system will try to auto select the files based on run_prefix, if that doesn't work, either the type you selected doesn't support
+        it or the run_prefix is wrong
+      </div>
+
   </div>
   <div class="col-md-3" id="files-div">
     <p style="text-align: center;"><i>Available Files</i></p>