Fix commands and CLI

Author: josenavas

qiita_db/commands.py

@@ -153,27 +153,24 @@ 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, raw_data_id, study_id,
+def load_prep_template_from_cmd(prep_temp_path, study_id,
                                 data_type):
     r"""Adds a prep template to the database
 
     Parameters
     ----------
     prep_temp_path : str
         Path to the prep template file
-    raw_data_id : int
-        The raw data id to which the prep template belongs
     study_id : int
         The study id to which the prep template belongs
     data_type : str
         The data type of the prep template
     """
     prep_temp = load_template_to_dataframe(prep_temp_path)
-    return PrepTemplate.create(prep_temp, RawData(raw_data_id),
-                               Study(study_id), data_type)
+    return PrepTemplate.create(prep_temp, Study(study_id), data_type)
 
 
-def load_raw_data_cmd(filepaths, filepath_types, filetype, study_ids):
+def load_raw_data_cmd(filepaths, filepath_types, filetype, prep_template_ids):
     """Add new raw data by populating the relevant tables
 
     Parameters
@@ -184,8 +181,8 @@ def load_raw_data_cmd(filepaths, filepath_types, filetype, study_ids):
         Describes the contents of the files.
     filetype : str
         The type of file being loaded
-    study_ids : iterable of int
-        The IDs of the studies with which to associate this raw data
+    prep_template_ids : iterable of int
+        The IDs of the prep templates with which to associate this raw data
 
     Returns
     -------
@@ -202,9 +199,9 @@ def load_raw_data_cmd(filepaths, filepath_types, filetype, study_ids):
     filepath_types_dict = get_filepath_types()
     filepath_types = [filepath_types_dict[x] for x in filepath_types]
 
-    studies = [Study(x) for x in study_ids]
+    prep_templates = [PrepTemplate(x) for x in prep_template_ids]
 
-    return RawData.create(filetype_id, studies,
+    return RawData.create(filetype_id, prep_templates,
                           filepaths=list(zip(filepaths, filepath_types)))
 
 

qiita_db/test/test_commands.py

@@ -15,6 +15,8 @@
 from future import standard_library
 from functools import partial
 
+import pandas as pd
+
 from qiita_db.commands import (load_study_from_cmd, load_raw_data_cmd,
                                load_sample_template_from_cmd,
                                load_prep_template_from_cmd,
@@ -28,6 +30,7 @@
 from qiita_db.data import RawData, PreprocessedData
 from qiita_db.util import (get_count, check_count, get_db_files_base_dir,
                            get_mountpoint)
+from qiita_db.metadata_template import PrepTemplate
 from qiita_core.util import qiita_test_checker
 from qiita_ware.processing_pipeline import generate_demux_file
 
@@ -154,36 +157,12 @@ def test_load_sample_template_from_cmd(self):
 @qiita_test_checker()
 class TestLoadPrepTemplateFromCmd(TestCase):
     def setUp(self):
-        # Create a sample template file
-        fd, seqs_fp = mkstemp(suffix='_seqs.fastq')
-        close(fd)
-        fd, barcodes_fp = mkstemp(suffix='_barcodes.fastq')
-        close(fd)
-
-        with open(seqs_fp, "w") as f:
-            f.write("\n")
-        with open(barcodes_fp, "w") as f:
-            f.write("\n")
-
         self.pt_contents = PREP_TEMPLATE
 
-        self.raw_data = RawData.create(
-            2, [Study(1)], filepaths=[(seqs_fp, 1), (barcodes_fp, 2)])
-
-        join_f = partial(join, join(get_db_files_base_dir(), 'raw_data'))
-        self.files_to_remove = [
-            join_f("%s_%s" % (self.raw_data.id, basename(seqs_fp))),
-            join_f("%s_%s" % (self.raw_data.id, basename(barcodes_fp)))]
-
-    def tearDown(self):
-        for fp in self.files_to_remove:
-            if exists(fp):
-                remove(fp)
-
     def test_load_prep_template_from_cmd(self):
         """Correctly adds a prep template to the DB"""
         fh = StringIO(self.pt_contents)
-        st = load_prep_template_from_cmd(fh, self.raw_data.id, 1, '18S')
+        st = load_prep_template_from_cmd(fh, 1, '18S')
         self.assertEqual(st.id, 2)
 
 
@@ -222,14 +201,24 @@ def test_load_data_from_cmd(self):
                           'raw_barcodes']
 
         filetype = 'FASTQ'
-        study_ids = [1]
+        metadata_dict = {
+            'SKB8.640193': {'center_name': 'ANL',
+                            'primer': 'GTGCCAGCMGCCGCGGTAA',
+                            'barcode': 'GTCCGCAAGTTA',
+                            'run_prefix': "s_G1_L001_sequences",
+                            'platform': 'ILLUMINA',
+                            'library_construction_protocol': 'AAAA',
+                            'experiment_design_description': 'BBBB'}}
+        metadata = pd.DataFrame.from_dict(metadata_dict, orient='index')
+        pt1 = PrepTemplate.create(metadata, Study(1), "16S")
+        prep_templates = [pt1.id]
 
         initial_raw_count = get_count('qiita.raw_data')
         initial_fp_count = get_count('qiita.filepath')
         initial_raw_fp_count = get_count('qiita.raw_filepath')
 
         new = load_raw_data_cmd(filepaths, filepath_types, filetype,
-                                study_ids)
+                                prep_templates)
         raw_data_id = new.id
         self.files_to_remove.append(
             join(self.db_test_raw_dir,
@@ -246,14 +235,12 @@ def test_load_data_from_cmd(self):
                                     initial_fp_count + 3))
         self.assertTrue(check_count('qiita.raw_filepath',
                                     initial_raw_fp_count + 3))
-        self.assertTrue(check_count('qiita.study_raw_data',
-                                    initial_raw_count + 1))
 
         # Ensure that the ValueError is raised when a filepath_type is not
         # provided for each and every filepath
         with self.assertRaises(ValueError):
             load_raw_data_cmd(filepaths, filepath_types[:-1], filetype,
-                              study_ids)
+                              prep_templates)
 
 
 @qiita_test_checker()

scripts/qiita

@@ -109,13 +109,13 @@ def load_study(owner, title, info):
 @click.option('--filetype', required=True,
               type=click.Choice(get_filetypes().keys()),
               help='The type of data')
-@click.option('--study', multiple=True, help='Associate the data with this '
-              'study. This option can be used multiple times if the data '
-              'should be associated with multiple studies', type=int,
-              required=True)
-def load_raw(fp, fp_type, filetype, study):
+@click.option('--prep_template', multiple=True, help='Associate the data with '
+              'this prep template. This option can be used multiple times if '
+              'the data should be associated with multiple prep templates',
+              type=int, required=True)
+def load_raw(fp, fp_type, filetype, prep_template):
     """Loads a raw data to the database"""
-    raw_data = load_raw_data_cmd(fp, fp_type, filetype, study)
+    raw_data = load_raw_data_cmd(fp, fp_type, filetype, prep_template)
     click.echo("Raw data successfully added to the database with id %s"
                % raw_data.id)
 
@@ -202,16 +202,14 @@ def load_sample_template(fp, study):
 @db.command()
 @click.argument('fp', required=True,
                 type=click.Path(resolve_path=True, readable=True, exists=True))
-@click.option('--raw_data', required=True, type=int,
-              help='Associate the prep template with this raw data')
 @click.option('--study', required=True, type=int,
               help='Associate the prep template with this study')
 @click.option('--data_type', required=True,
               type=click.Choice(get_data_types()),
               help="The data type of data")
-def load_prep_template(fp, raw_data, study, data_type):
+def load_prep_template(fp, study, data_type):
     """Loads a sample template to the database"""
-    prep_template = load_prep_template_from_cmd(fp, raw_data, study, data_type)
+    prep_template = load_prep_template_from_cmd(fp, study, data_type)
     click.echo("Prep template successfully added to the database with id %s"
                % prep_template.id)