Sync-ing with master (again) (#2073)

josenavas · antgonza · commit 1377640e0272 · 2017-02-08T20:46:38.000+04:00
* fix #1505 * improving some GUI stuff * improving some GUI stuff - missing lines * addressing all comments * ready for review * fix #1987 * initial commit * requested changes * fix filter job list * Fixing server cert (#2051) * fix get_studies * flake8 * fix #503 * fix #2010 * fix #1913 * fix errors * addressing @josenavas comment * flake8 * fix #1010 * fix #1066 (#2058) * addressing @josenavas comments * fix #1961 * fix #1837 * Automatic jobs & new stats (#2057) * fix #814, fix #1636 * fixing error in test-env * fixing stats.html call * adding img * addressing @josenavas comments * rm for loops * addresssing @ElDeveloper comments * generalizing this functionality * fix #1816 * fix #1959 * addressing @josenavas comments * addressing @josenavas comments * fixing error * fixed? * addressing @josenavas comments * addressing @wasade comments * fix flake8 * generate biom and metadata release (#2066) * initial commit * adding portal * addressing @josenavas comments * pid -> qiita_artifact_id * addressing @josenavas comments * addressing @ElDeveloper comments * rm 50.sql * database changes to fix 969 * adding delete * addressing @josenavas comments * addressing @ElDeveloper comments * duh! * fix generate_biom_and_metadata_release (#2072) * fix generate_biom_and_metadata_release * addressing @ElDeveloper comment
diff --git a/qiita_db/artifact.py b/qiita_db/artifact.py
@@ -429,6 +429,7 @@ def _associate_with_analysis(instance, analysis_id):
                     instance.visibility = 'private'
                 else:
                     instance.visibility = 'public'
+
             elif prep_template:
                 # This artifact is uploaded by the user in the
                 # processing pipeline
diff --git a/qiita_db/test/test_meta_util.py b/qiita_db/test/test_meta_util.py
@@ -47,6 +47,7 @@ def test_validate_filepath_access_by_user(self):
         for i in [1, 2, 3, 4, 5, 9, 12, 17, 18, 19, 20, 21]:
             self.assertFalse(qdb.meta_util.validate_filepath_access_by_user(
                 user, i))
+
         for i in [15, 16]:
             self.assertTrue(qdb.meta_util.validate_filepath_access_by_user(
                 user, i))
diff --git a/qiita_db/test/test_util.py b/qiita_db/test/test_util.py
@@ -777,6 +777,62 @@ def test_generate_biom_and_metadata_release(self):
             'FASTQ\n']
         self.assertEqual(txt_obs, txt_exp)
 
+        # whatever the configuration was, we will change to settings so we can
+        # test the other option when dealing with the end '/'
+        with qdb.sql_connection.TRN:
+            qdb.sql_connection.TRN.add(
+                "SELECT base_data_dir FROM settings")
+            obdr = qdb.sql_connection.TRN.execute_fetchlast()
+            if obdr[-1] == '/':
+                bdr = obdr[:-1]
+            else:
+                bdr = obdr + '/'
+
+            qdb.sql_connection.TRN.add(
+                "UPDATE settings SET base_data_dir = '%s'" % bdr)
+            bdr = qdb.sql_connection.TRN.execute()
+
+        tgz, txt = qdb.util.generate_biom_and_metadata_release('private')
+        self.files_to_remove.extend([tgz, txt])
+
+        tmp = topen(tgz, "r:gz")
+        tgz_obs = [ti.name for ti in tmp]
+        tmp.close()
+        tgz_exp = [
+            'processed_data/1_study_1001_closed_reference_otu_table.biom',
+            'templates/1_19700101-000000.txt',
+            'templates/1_prep_1_19700101-000000.txt',
+            'processed_data/1_study_1001_closed_reference_otu_table.biom',
+            'templates/1_19700101-000000.txt',
+            'templates/1_prep_1_19700101-000000.txt',
+            'processed_data/1_study_1001_closed_reference_otu_table_'
+            'Silva.biom', 'templates/1_19700101-000000.txt',
+            'templates/1_prep_1_19700101-000000.txt']
+        self.assertEqual(tgz_obs, tgz_exp)
+
+        tmp = open(txt)
+        txt_obs = tmp.readlines()
+        tmp.close()
+        txt_exp = [
+            'biom_fp\tsample_fp\tprep_fp\tqiita_artifact_id\tcommand\n',
+            'processed_data/1_study_1001_closed_reference_otu_table.biom\ttem'
+            'plates/1_19700101-000000.txt\ttemplates/1_prep_1_19700101-000000'
+            '.txt\t4\tPick closed-reference OTUs, Split libraries FASTQ\n',
+            'processed_data/1_study_1001_closed_reference_otu_table.biom\ttem'
+            'plates/1_19700101-000000.txt\ttemplates/1_prep_1_19700101-000000'
+            '.txt\t5\tPick closed-reference OTUs, Split libraries FASTQ\n',
+            'processed_data/1_study_1001_closed_reference_otu_table_Silva.bio'
+            'm\ttemplates/1_19700101-000000.txt\ttemplates/1_prep_1_19700101-'
+            '000000.txt\t6\tPick closed-reference OTUs, Split libraries '
+            'FASTQ\n']
+        self.assertEqual(txt_obs, txt_exp)
+
+        # returning configuration
+        with qdb.sql_connection.TRN:
+                    qdb.sql_connection.TRN.add(
+                        "UPDATE settings SET base_data_dir = '%s'" % obdr)
+                    bdr = qdb.sql_connection.TRN.execute()
+
 
 @qiita_test_checker()
 class UtilTests(TestCase):
diff --git a/qiita_db/util.py b/qiita_db/util.py
@@ -1531,14 +1531,11 @@ def generate_biom_and_metadata_release(study_status='public'):
     working_dir = qiita_config.working_dir
     portal = qiita_config.portal
     bdir = qdb.util.get_db_files_base_dir()
-    bdir_len = len(bdir) + 1
 
     data = []
     for s in studies:
         # [0] latest is first, [1] only getting the filepath
-        sample_fp = s.sample_template.get_filepaths()[0][1]
-        if sample_fp.startswith(bdir):
-            sample_fp = sample_fp[bdir_len:]
+        sample_fp = relpath(s.sample_template.get_filepaths()[0][1], bdir)
 
         for a in s.artifacts(artifact_type='BIOM'):
             if a.processing_parameters is None:
@@ -1562,16 +1559,14 @@ def generate_biom_and_metadata_release(study_status='public'):
             for _, fp, fp_type in a.filepaths:
                 if fp_type != 'biom' or 'only-16s' in fp:
                     continue
-                if fp.startswith(bdir):
-                    fp = fp[bdir_len:]
+                fp = relpath(fp, bdir)
                 # format: (biom_fp, sample_fp, prep_fp, qiita_artifact_id,
                 #          human readable name)
                 for pt in a.prep_templates:
                     for _, prep_fp in pt.get_filepaths():
                         if 'qiime' not in prep_fp:
                             break
-                    if prep_fp.startswith(bdir):
-                        prep_fp = prep_fp[bdir_len:]
+                    prep_fp = relpath(prep_fp, bdir)
                     data.append((fp, sample_fp, prep_fp, a.id, human_cmd))
 
     # writing text and tgz file
