Merge branch 'fix-1084' of https://github.com/biocore/qiita into 1084-qiita-pet

Author: josenavas

qiita_db/commands.py

@@ -153,8 +153,7 @@ def load_sample_template_from_cmd(sample_temp_path, study_id):
     return SampleTemplate.create(sample_temp, Study(study_id))
 
 
-def load_prep_template_from_cmd(prep_temp_path, study_id,
-                                data_type):
+def load_prep_template_from_cmd(prep_temp_path, study_id, data_type):
     r"""Adds a prep template to the database
 
     Parameters

qiita_db/data.py

@@ -307,11 +307,11 @@ def create(cls, filetype, prep_templates, filepaths):
 
         Raises
         ------
-        IncompetentQiitaDeveloperError
+        QiitaDBError
             If any of the passed prep templates already have a raw data id
         """
         conn_handler = SQLConnectionHandler()
-        # We first need to check if the passed prep templates doesn't have
+        # We first need to check if the passed prep templates don't have
         # a raw data already attached to them
         sql = """SELECT EXISTS(
                     SELECT *
@@ -322,7 +322,7 @@ def create(cls, filetype, prep_templates, filepaths):
         exists = conn_handler.execute_fetchone(
             sql, [pt.id for pt in prep_templates])[0]
         if exists:
-            raise IncompetentQiitaDeveloperError(
+            raise QiitaDBError(
                 "Cannot create raw data because the passed prep templates "
                 "already have a raw data associated with it. "
                 "Prep templates: %s"

qiita_db/metadata_template/prep_template.py

@@ -108,7 +108,7 @@ def create(cls, md_template, study, data_type, investigation_type=None):
 
         # Get a connection handler
         conn_handler = SQLConnectionHandler()
-        queue_name = "CREATE_PREP_TEMPLATE_%d" % study.id
+        queue_name = "CREATE_PREP_TEMPLATE_%d_%d" % (study.id, id(md_template))
         conn_handler.create_queue(queue_name)
 
         # Check if the data_type is the id or the string

qiita_db/metadata_template/test/test_prep_template.py

@@ -1341,7 +1341,7 @@ def test_raw_data_setter(self):
                                  self.data_type_id)
         self.assertEqual(pt.raw_data, None)
         pt.raw_data = rd
-        self.assertEqual(pt.raw_data, 1)
+        self.assertEqual(pt.raw_data, rd.id)
 
 
 EXP_PREP_TEMPLATE = (

qiita_db/support_files/patches/python_patches/25.py

@@ -1,6 +1,6 @@
 # May 19, 2015
 # We attach the prep template directly to the study. The raw data is no longer
-# attached to the study directly, the prep template point to them. This will
+# attached to the study directly, the prep template points to them. This will
 # make the RawData to be effectively just a container for the raw files,
 # which is how it was acting previously.
 
@@ -47,7 +47,7 @@
 
     conn_handler.add_to_queue(queue, sql_delete, (rd_id,))
 
-# We can now perform all changes in the DB. Although this changes can be
+# We can now perform all changes in the DB. Although these changes can be
 # done in an SQL patch, they are done here because we need to execute the
 # previous clean up in the database before we can actually execute the SQL
 # patch.

qiita_db/test/test_data.py

@@ -128,7 +128,7 @@ def test_create(self):
         self.assertEqual(obs, [[exp_id, top_id - 1], [exp_id, top_id]])
 
     def test_create_error(self):
-        with self.assertRaises(IncompetentQiitaDeveloperError):
+        with self.assertRaises(QiitaDBError):
             RawData.create(self.filetype, [PrepTemplate(1)], self.filepaths)
 
     def test_get_filepaths(self):

qiita_ware/test/test_processing_pipeline.py

@@ -71,14 +71,15 @@ def setUp(self):
         self.sff_prep_template = PrepTemplate.create(md, study, "16S")
 
         tmp_dir = mkdtemp()
-        path_builder = partial(join, tmp_dir)
-        fp1 = path_builder('preprocess_test1.sff')
+        self.path_builder = partial(join, tmp_dir)
+        fp1 = self.path_builder('preprocess_test1.sff')
         with open(fp1, 'w') as f:
             f.write('\n')
-        fp2 = path_builder('preprocess_test2.sff')
+        fp2 = self.path_builder('preprocess_test2.sff')
         with open(fp2, 'w') as f:
             f.write('\n')
-        fps = [(fp1, 17), (fp2, 17)]
+        self.raw_sff_id = convert_to_id('raw_sff', 'filepath_type')
+        fps = [(fp1, self.raw_sff_id), (fp2, self.raw_sff_id)]
 
         # Magic number 1: is the filetype id
         self.raw_data = RawData.create(1, [self.sff_prep_template], fps)
@@ -89,14 +90,13 @@ def setUp(self):
         md_rp = pd.DataFrame.from_dict(md_dict, orient='index')
         self.sff_prep_template_rp = PrepTemplate.create(md_rp, study, "16S")
 
-        path_builder = partial(join, tmp_dir)
-        rp_fp1 = path_builder('preprocess_test1.sff')
+        rp_fp1 = self.path_builder('preprocess_test1.sff')
         with open(rp_fp1, 'w') as f:
             f.write('\n')
-        rp_fp2 = path_builder('preprocess_test2.sff')
+        rp_fp2 = self.path_builder('preprocess_test2.sff')
         with open(rp_fp2, 'w') as f:
             f.write('\n')
-        fps = [(rp_fp1, 17), (rp_fp2, 17)]
+        fps = [(rp_fp1, self.raw_sff_id), (rp_fp2, self.raw_sff_id)]
 
         # Magic number 1: is the filetype id
         self.raw_data_rp = RawData.create(1, [self.sff_prep_template_rp], fps)
@@ -355,7 +355,7 @@ def test_get_preprocess_fasta_cmd_sff_run_prefix_match(self):
             f.write('\n')
         self.files_to_remove.append(fp)
         self.dirs_to_remove.append(tmp_dir)
-        self.raw_data_rp.add_filepaths([(fp, 17)])
+        self.raw_data_rp.add_filepaths([(fp, self.raw_sff_id)])
         params = Preprocessed454Params(1)
 
         obs_cmd, obs_output_dir = _get_preprocess_fasta_cmd(
@@ -385,17 +385,16 @@ def test_get_preprocess_fasta_cmd_sff_run_prefix_match(self):
     def test_get_preprocess_fasta_cmd_sff_run_prefix_match_error_1(self):
         # Test that the run prefixes in the prep_template and the file names
         # actually match and raise an error if not
-        tmp_dir = mkdtemp()
-        fp = join(tmp_dir, 'new.sff')
+        fp = self.path_builder('new.sff')
         with open(fp, 'w') as f:
             f.write('\n')
         self.files_to_remove.append(fp)
-        fp_error = join(tmp_dir, 'error.sff')
+        fp_error = self.path_builder('error.sff')
         with open(fp_error, 'w') as f:
             f.write('\n')
         self.files_to_remove.append(fp_error)
-        self.dirs_to_remove.append(tmp_dir)
-        self.raw_data_rp.add_filepaths([(fp, 17), (fp_error, 17)])
+        self.raw_data_rp.add_filepaths(
+            [(fp, self.raw_sff_id), (fp_error, self.raw_sff_id)])
         params = Preprocessed454Params(1)
         with self.assertRaises(ValueError):
             _get_preprocess_fasta_cmd(