Adding check for missing QIIME mapping columns plus specially handle ReverseLinkerPrimer

Author: josenavas

qiita_pet/handlers/study_handlers/description_handlers.py

@@ -179,6 +179,8 @@ def process_sample_template(self, study, user, callback):
             raise HTTPError(404, "This file doesn't exist: %s" % fp_rsp)
 
         # Define here the message and message level in case of success
+        msg = "The sample template '%s' has been added" % sample_template
+        msg_level = "success"
         is_mapping_file = looks_like_qiime_mapping_file(fp_rsp)
 
         try:

qiita_ware/metadata_pipeline.py

@@ -15,6 +15,7 @@
                                         CONTROLLED_COLS,
                                         TARGET_GENE_DATA_TYPES)
 from qiita_db.util import convert_from_id
+from qiita_ware.exceptions import QiitaWareError
 
 
 def create_templates_from_qiime_mapping_file(fp, study, data_type):
@@ -41,9 +42,18 @@ def create_templates_from_qiime_mapping_file(fp, study, data_type):
     rename_cols = {
         'BarcodeSequence': 'barcode',
         'LinkerPrimerSequence': 'primer',
-        'ReverseLinkerPrimer': 'reverselinkerprimer',
         'Description': 'description',
     }
+
+    if 'ReverseLinkerPrimer' in qiime_map:
+        rename_cols['ReverseLinkerPrimer'] = 'reverselinkerprimer'
+
+    missing = set(rename_cols).difference(qiime_map.columns)
+    if missing:
+        raise QiitaWareError(
+            "Error generating the templates from the QIIME mapping file. "
+            "Missing QIIME mapping file columns: %s" % ', '.join(missing))
+
     qiime_map.rename(columns=rename_cols, inplace=True)
 
     # Fix the casing in the columns that we control
@@ -64,6 +74,7 @@ def _col_iterator(restriction_set):
     if data_type_str in TARGET_GENE_DATA_TYPES:
         pt_cols.update(
             col for col in _col_iterator(PREP_TEMPLATE_COLUMNS_TARGET_GENE))
+        pt_cols.add('reverselinkerprimer')
 
     qiime_cols = set(qiime_map.columns)
     pt_cols = qiime_cols.intersection(pt_cols)

qiita_ware/test/test_metadata_pipeline.py

@@ -12,6 +12,7 @@
 from os.path import exists
 
 from qiita_core.util import qiita_test_checker
+from qiita_ware.exceptions import QiitaWareError
 from qiita_db.study import Study, StudyPerson
 from qiita_db.user import User
 from qiita_db.util import get_count
@@ -72,6 +73,37 @@ def test_create_templates_from_qiime_mapping_file(self):
                "experiment_design_description"}
         self.assertEqual(set(obs_pt.categories()), exp)
 
+    def test_create_templates_from_qiime_mapping_file_reverse_linker(self):
+        new_pt_id = get_count('qiita.prep_template') + 1
+        obs_st, obs_pt = create_templates_from_qiime_mapping_file(
+            StringIO(QIIME_MAP_WITH_REVERSE_LINKER_PRIMER),
+            self.new_study, "16S")
+
+        # Be green: clean the environment
+        for template in [obs_st, obs_pt]:
+            for _, fp in template.get_filepaths():
+                self._clean_up_files.append(fp)
+
+        self.assertEqual(obs_st.id, self.new_study.id)
+        self.assertEqual(obs_pt.id, new_pt_id)
+
+        # Check that each template has the correct columns
+        exp = {"physical_specimen_location", "physical_specimen_remaining",
+               "dna_extracted", "sample_type", "host_subject_id", "latitude",
+               "longitude", "taxon_id", "scientific_name",
+               "collection_timestamp", "description"}
+        self.assertEqual(set(obs_st.categories()), exp)
+
+        exp = {"barcode", "primer", "center_name", "run_prefix", "platform",
+               "library_construction_protocol",
+               "experiment_design_description", "reverselinkerprimer"}
+        self.assertEqual(set(obs_pt.categories()), exp)
+
+    def test_create_templates_from_qiime_mapping_file_error(self):
+        with self.assertRaises(QiitaWareError):
+            create_templates_from_qiime_mapping_file(
+                StringIO(QIIME_MAP_ERROR), self.new_study, "16S")
+
 
 QIIME_MAP = (
     "#SampleID\tBarcodeSequence\tLinkerPrimerSequence\t"
@@ -90,6 +122,39 @@ def test_create_templates_from_qiime_mapping_file(self):
     "NotIdentified\t4.3\t4.3\t9606\thomo sapiens\tANL\trp_2\tILLUMINA\t"
     "protocol_1\tedd_1\t05/28/15 11:00\tDescription S3\n")
 
+QIIME_MAP_WITH_REVERSE_LINKER_PRIMER = (
+    "#SampleID\tBarcodeSequence\tLinkerPrimerSequence\tReverseLinkerPrimer\t"
+    "physical_specimen_location\tphysical_specimen_remaining\tdna_extracted\t"
+    "sample_type\thost_subject_id\tlatitude\tlongitude\ttaxon_id\t"
+    "scientific_name\tcenter_name\trun_prefix\tplatform\t"
+    "library_construction_protocol\texperiment_design_description\t"
+    "collection_timestamp\tDescription\n"
+    "Sample1\tGTCCGCAAGTTA\tGTGCCAGCMGCCGCGGTAA\tGTGCCAGCMGCCGCGGTAA\tUCSD\t"
+    "TRUE\tTRUE\ttype1\tNotIdentified\t4.1\t4.1\t9606\thomo sapiens\tANL\t"
+    "rp_1\tILLUMINA\tprotocol_1\tedd_1\t05/28/15 11:00\tDescription S1\n"
+    "Sample2\tCGTAGAGCTCTC\tGTGCCAGCMGCCGCGGTAA\tGTGCCAGCMGCCGCGGTAA\tUCSD\t"
+    "TRUE\tTRUE\ttype2\tNotIdentified\t4.2\t4.2\t9606\thomo sapiens\tANL\t"
+    "rp_1\tILLUMINA\tprotocol_1\tedd_1\t05/28/15 11:00\tDescription S2\n"
+    "Sample3\tCCTCTGAGAGCT\tGTGCCAGCMGCCGCGGTAA\tGTGCCAGCMGCCGCGGTAA\tUCSD\t"
+    "TRUE\tTRUE\ttype3\tNotIdentified\t4.3\t4.3\t9606\thomo sapiens\tANL\t"
+    "rp_2\tILLUMINA\tprotocol_1\tedd_1\t05/28/15 11:00\tDescription S3\n")
+
+QIIME_MAP_ERROR = (
+    "#SampleID\tBarcodeSequence\tphysical_specimen_location\t"
+    "physical_specimen_remaining\tdna_extracted\tsample_type\t"
+    "host_subject_id\tlatitude\tlongitude\ttaxon_id\tscientific_name\t"
+    "center_name\trun_prefix\tplatform\tlibrary_construction_protocol\t"
+    "experiment_design_description\tcollection_timestamp\tDescription\n"
+    "Sample1\tGTCCGCAAGTTA\tUCSD\tTRUE\tTRUE\ttype1\tNotIdentified\t4.1\t4.1\t"
+    "9606\thomo sapiens\tANL\trp_1\tILLUMINA\tprotocol_1\tedd_1\t"
+    "05/28/15 11:00\tDescription S1\n"
+    "Sample2\tCGTAGAGCTCTC\tUCSD\tTRUE\tTRUE\ttype2\tNotIdentified\t4.2\t4.2\t"
+    "9606\thomo sapiens\tANL\trp_1\tILLUMINA\tprotocol_1\tedd_1\t"
+    "05/28/15 11:00\tDescription S2\n"
+    "Sample3\tCCTCTGAGAGCT\tUCSD\tTRUE\tTRUE\ttype3\tNotIdentified\t4.3\t4.3\t"
+    "9606\thomo sapiens\tANL\trp_2\tILLUMINA\tprotocol_1\tedd_1\t"
+    "05/28/15 11:00\tDescription S3\n")
+
 
 if __name__ == "__main__":
     main()