fixes #2245 (#2350)

* fixes #2245

* Addressing @antgonza's comments

* Fixing test

Author: josenavas

qiita_db/analysis.py

@@ -429,15 +429,17 @@ def mapping_file(self):
 
         Returns
         -------
-        str or None
-            full filepath to the mapping file or None if not generated
+        int or None
+            The filepath id of the analysis mapping file or None
+            if not generated
         """
-        fp = [fp for _, fp, fp_type in qdb.util.retrieve_filepaths(
-            "analysis_filepath", "analysis_id", self._id)
-            if fp_type == 'plain_text']
+        fp = [fp_id
+              for fp_id, _, fp_type in qdb.util.retrieve_filepaths(
+                "analysis_filepath", "analysis_id", self._id)
+              if fp_type == 'plain_text']
 
         if fp:
-            # returning the actual path vs. an array
+            # returning the actual filepath id vs. an array
             return fp[0]
         else:
             return None

qiita_db/handlers/analysis.py

@@ -59,7 +59,8 @@ def get(self, analysis_id):
         """
         with qdb.sql_connection.TRN:
             a = _get_analysis(analysis_id)
-            mf_fp = a.mapping_file
+            mf_fp = qdb.util.get_filepath_information(
+                a.mapping_file)['fullpath']
             response = None
             if mf_fp is not None:
                 df = qdb.metadata_template.util.load_template_to_dataframe(

qiita_db/test/test_analysis.py

@@ -290,7 +290,9 @@ def test_set_pmid(self):
     def test_retrieve_mapping_file(self):
         exp = join(self.fp, "1_analysis_mapping.txt")
         obs = self.analysis.mapping_file
-        self.assertEqual(obs, exp)
+        self.assertIsNotNone(obs)
+        self.assertEqual(
+            qdb.util.get_filepath_information(obs)['fullpath'], exp)
         self.assertTrue(exists(exp))
 
     def test_retrieve_tgz(self):
@@ -370,7 +372,8 @@ def test_build_mapping_file(self):
 
         npt.assert_warns(qdb.exceptions.QiitaDBWarning,
                          analysis._build_mapping_file, samples)
-        obs = analysis.mapping_file
+        obs = qdb.util.get_filepath_information(
+            analysis.mapping_file)['fullpath']
 
         exp = self.get_fp("%s_analysis_mapping.txt" % analysis.id)
         self.assertEqual(obs, exp)
@@ -388,8 +391,10 @@ def test_build_mapping_file_duplicated_samples_no_merge(self):
         npt.assert_warns(qdb.exceptions.QiitaDBWarning,
                          analysis._build_mapping_file, samples, True)
 
+        mapping_fp = qdb.util.get_filepath_information(
+            analysis.mapping_file)['fullpath']
         obs = qdb.metadata_template.util.load_template_to_dataframe(
-            analysis.mapping_file, index='#SampleID')
+            mapping_fp, index='#SampleID')
         exp = qdb.metadata_template.util.load_template_to_dataframe(
             self.duplicated_samples_not_merged, index='#SampleID')
 
@@ -405,8 +410,10 @@ def test_build_mapping_file_duplicated_samples_merge(self):
                    3: ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196']}
         npt.assert_warns(qdb.exceptions.QiitaDBWarning,
                          analysis._build_mapping_file, samples)
+        mapping_fp = qdb.util.get_filepath_information(
+            analysis.mapping_file)['fullpath']
         obs = qdb.metadata_template.util.load_template_to_dataframe(
-            analysis.mapping_file, index='#SampleID')
+            mapping_fp, index='#SampleID')
         exp = qdb.metadata_template.util.load_template_to_dataframe(
             self.map_exp_fp, index='#SampleID')
         assert_frame_equal(obs, exp)
@@ -460,8 +467,10 @@ def test_build_files(self):
         # testing that the generated files have the same sample ids
         biom_fp = biom_tables[0][1]
         biom_ids = load_table(biom_fp).ids(axis='sample')
+        mapping_fp = qdb.util.get_filepath_information(
+            analysis.mapping_file)['fullpath']
         mf_ids = qdb.metadata_template.util.load_template_to_dataframe(
-            analysis.mapping_file, index='#SampleID').index
+            mapping_fp, index='#SampleID').index
 
         self.assertItemsEqual(biom_ids, mf_ids)
 
@@ -493,8 +502,11 @@ def test_build_files_merge_duplicated_sample_ids(self):
         biom_ids = []
         for _, fp in biom_tables:
             biom_ids.extend(load_table(fp).ids(axis='sample'))
+
+        mapping_fp = qdb.util.get_filepath_information(
+            new.mapping_file)['fullpath']
         mf_ids = qdb.metadata_template.util.load_template_to_dataframe(
-            new.mapping_file, index='#SampleID').index
+            mapping_fp, index='#SampleID').index
 
         self.assertItemsEqual(biom_ids, mf_ids)
 

qiita_pet/handlers/analysis_handlers/base_handlers.py

@@ -64,6 +64,7 @@ def analysis_description_handler_get_request(analysis_id, user):
     return {'analysis_name': analysis.name,
             'analysis_id': analysis.id,
             'analysis_description': analysis.description,
+            'analysis_mapping_id': analysis.mapping_file,
             'alert_type': alert_type,
             'alert_msg': alert_msg}
 

qiita_pet/handlers/analysis_handlers/tests/test_base_handlers.py

@@ -32,6 +32,7 @@ def test_analysis_description_handler_get_request(self):
         exp = {'analysis_name': 'SomeAnalysis',
                'analysis_id': 1,
                'analysis_description': 'A test analysis',
+               'analysis_mapping_id': 16,
                'alert_type': 'info',
                'alert_msg': ''}
         self.assertEqual(obs, exp)
@@ -42,6 +43,7 @@ def test_analysis_description_handler_get_request(self):
         exp = {'analysis_name': 'SomeAnalysis',
                'analysis_id': 1,
                'analysis_description': 'A test analysis',
+               'analysis_mapping_id': 16,
                'alert_type': 'info',
                'alert_msg': 'An artifact is being deleted from this analysis'}
         self.assertEqual(obs, exp)
@@ -54,6 +56,7 @@ def test_analysis_description_handler_get_request(self):
         exp = {'analysis_name': 'SomeAnalysis',
                'analysis_id': 1,
                'analysis_description': 'A test analysis',
+               'analysis_mapping_id': 16,
                'alert_type': 'danger',
                'alert_msg': 'Error deleting artifact'}
         self.assertEqual(obs, exp)

qiita_pet/templates/analysis_description.html

@@ -242,7 +242,10 @@
   <div class="col">
     <h2>
         {{analysis_name}} - ID {{analysis_id}}
-        <a class="btn btn-info glyphicon glyphicon-share" data-toggle="modal" data-target="#share-analysis-modal-view" onclick="modify_sharing({{analysis_id}});"></a>
+        <a class="btn btn-info" data-toggle="modal" data-target="#share-analysis-modal-view" onclick="modify_sharing({{analysis_id}});"><span class=" glyphicon glyphicon-share"></span></a>
+        {% if analysis_mapping_id is not None %}
+          <a class="btn btn-default" href="{% raw qiita_config.portal_dir %}/download/{{analysis_mapping_id}}"><span class="glyphicon glyphicon-download-alt"></span> Mapping file</a>
+        {% end %}
     </h2>
     <h3>{{analysis_description}}</h3>
     Shared with: <span id="shared_html_{{analysis_id}}"></span>