Add qiime map func

qiita_db/metadata_template/prep_template.py

@@ -524,3 +524,25 @@ def status(self):
         pd_statuses = conn_handler.execute_fetchall(sql, (self._id,))
 
         return infer_status(pd_statuses)
+
+    @property
+    def qiime_map_fp(self):
+        """The QIIME mapping file path of the prep template
+
+        Returns
+        -------
+        str
+            The filepath of the QIIME mapping file
+        """
+        conn_handler = SQLConnectionHandler()
+
+        sql = """SELECT filepath_id, filepath
+                 FROM qiita.filepath
+                    JOIN qiita.{0} USING (filepath_id)
+                    JOIN qiita.filepath_type USING (filepath_type_id)
+                 WHERE {1} = %s AND filepath_type = 'qiime_map'
+                 ORDER BY filepath_id DESC""".format(self._filepath_table,
+                                                     self._id_column)
+        fn = conn_handler.execute_fetchall(sql, (self._id,))[0][1]
+        base_dir = get_mountpoint('templates')[0][1]
+        return join(base_dir, fn)

qiita_db/metadata_template/test/test_prep_template.py

@@ -1293,6 +1293,12 @@ def test_update_category(self):
         self.assertEqual(self.tester['1.SKB8.640193']['center_name'], 'FOO')
         self.assertEqual(self.tester['1.SKD8.640184']['center_name'], 'BAR')
 
+    def test_qiime_map_fp(self):
+        pt = PrepTemplate(1)
+        exp = join(get_mountpoint('templates')[0][1],
+                   '1_prep_1_qiime_19700101-000000.txt')
+        self.assertEqual(pt.qiime_map_fp, exp)
+
 
 EXP_PREP_TEMPLATE = (
     'sample_name\tbarcode\tcenter_name\tcenter_project_name\t'

qiita_ware/test/test_processing_pipeline.py

@@ -242,19 +242,20 @@ def test_get_preprocess_fasta_cmd_sff_run_prefix(self):
     def test_get_preprocess_fasta_cmd_sff_run_prefix_match(self):
         # Test that the run prefixes in the prep_template and the file names
         # actually match and raise an error if not
+        new_fp_id = get_count('qiita.filepath') + 1
         conn_handler = SQLConnectionHandler()
         sql = ("""
             INSERT INTO qiita.filepath (filepath_id, filepath,
                 filepath_type_id, checksum, checksum_algorithm_id,
-                data_directory_id) VALUES (19, '1_new.sff', 17, 852952723, 1,
+                data_directory_id) VALUES (%s, '1_new.sff', 17, 852952723, 1,
                 5);
             INSERT INTO qiita.raw_filepath (raw_data_id , filepath_id) VALUES
-                (3, 19);
+                (3, %s);
             UPDATE qiita.prep_1 SET run_prefix='preprocess_test';
             UPDATE qiita.prep_1 SET run_prefix='new' WHERE
                 sample_id = '1.SKB8.640193';
         """)
-        conn_handler.execute(sql)
+        conn_handler.execute(sql, (new_fp_id, new_fp_id))
 
         raw_data = RawData(3)
         params = Preprocessed454Params(1)
@@ -287,25 +288,27 @@ 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
+        fp_count = get_count('qiita.filepath')
         conn_handler = SQLConnectionHandler()
         sql = ("""
             INSERT INTO qiita.filepath (filepath_id, filepath,
                 filepath_type_id, checksum, checksum_algorithm_id,
-                data_directory_id) VALUES (19, '1_new.sff', 17, 852952723, 1,
+                data_directory_id) VALUES (%s, '1_new.sff', 17, 852952723, 1,
                 5);
             INSERT INTO qiita.raw_filepath (raw_data_id , filepath_id) VALUES
-                (3, 19);
+                (3, %s);
             INSERT INTO qiita.filepath (filepath_id, filepath,
                 filepath_type_id, checksum, checksum_algorithm_id,
-                data_directory_id) VALUES (20, '1_error.sff', 17, 852952723,
+                data_directory_id) VALUES (%s, '1_error.sff', 17, 852952723,
                 1, 5);
             INSERT INTO qiita.raw_filepath (raw_data_id , filepath_id) VALUES
-                (3, 20);
+                (3, %s);
             UPDATE qiita.prep_1 SET run_prefix='preprocess_test';
             UPDATE qiita.prep_1 SET run_prefix='new' WHERE
                 sample_id = '1.SKB8.640193';
         """)
-        conn_handler.execute(sql)
+        conn_handler.execute(
+            sql, (fp_count + 1, fp_count + 1, fp_count + 2, fp_count + 2))
 
         raw_data = RawData(3)
         params = Preprocessed454Params(1)

qiita_ware/test/test_util.py

@@ -277,6 +277,7 @@ def test_hdf5IO_open(self):
                               ('Diesel Rhizo', 3),
                               ('Diesel Root', 3),
                               ('Diesel bulk', 3)],
+    'dna_extracted': [('True', 27)],
     'ebi_study_accession': [('None', 27)],
     'ebi_submission_accession': [('None', 27)],
     'elevation': [('114.0', 27)],
@@ -288,8 +289,6 @@ def test_hdf5IO_open(self):
     'experiment_design_description': [('micro biome of soil and rhizosphere '
                                        'of cannabis plants from CA', 27)],
     'experiment_title': [('Cannabis Soil Microbiome', 27)],
-    'has_extracted_data': [('True', 27)],
-    'has_physical_specimen': [('True', 27)],
     'host_subject_id': [('1001:B1', 1),
                         ('1001:B2', 1),
                         ('1001:B3', 1),
@@ -397,7 +396,8 @@ def test_hdf5IO_open(self):
         ('96.0693176066', 1)],
     'pcr_primers': [('FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT', 27)],
     'ph': [('6.8', 9), ('6.82', 10), ('6.94', 8)],
-    'physical_location': [('ANL', 27)],
+    'physical_specimen_location': [('ANL', 27)],
+    'physical_specimen_remaining': [('True', 27)],
     'platform': [('Illumina', 27)],
     'required_sample_info_status': [('completed', 27)],
     'run_center': [('ANL', 27)],