Merge pull request #116 from josenavas/STadder

Adds the sample template adder command

Author: ElDeveloper

qiita_db/commands.py

@@ -1,3 +1,12 @@
+# -----------------------------------------------------------------------------
+# Copyright (c) 2014--, The Qiita Development Team.
+#
+# Distributed under the terms of the BSD 3-clause License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# -----------------------------------------------------------------------------
+
+import pandas as pd
 from functools import partial
 try:
     # Python 2
@@ -10,6 +19,7 @@
 from .user import User
 from .util import get_filetypes, get_filepath_types
 from .data import RawData
+from .metadata_template import SampleTemplate
 
 
 def make_study_from_cmd(owner, title, info):
@@ -59,6 +69,21 @@ def make_study_from_cmd(owner, title, info):
     Study.create(User(owner), title, efo_ids, infodict)
 
 
+def sample_template_adder(sample_temp_path, study_id):
+    r"""Adds a sample template to the database
+
+    Parameters
+    ----------
+    sample_temp_path : str
+        Path to the sample template file
+    study_id : int
+        The study id to wich the sample template belongs to
+    """
+    sample_temp = pd.DataFrame.from_csv(sample_temp_path, sep='\t',
+                                        infer_datetime_format=True)
+    return SampleTemplate.create(sample_temp, Study(study_id))
+
+
 def load_raw_data_cmd(filepaths, filepath_types, filetype, study_ids):
     """Add new raw data by populating the relevant tables
 

qiita_db/metadata_template.py

@@ -19,6 +19,14 @@
     MetadataTemplate
     SampleTemplate
     PrepTemplate
+
+Methods
+-------
+
+..autosummary::
+    :toctree: generated/
+
+    sample_template_adder
 """
 
 # -----------------------------------------------------------------------------

qiita_db/test/test_commands.py

@@ -1,5 +1,13 @@
+# -----------------------------------------------------------------------------
+# Copyright (c) 2014--, The Qiita Development Team.
+#
+# Distributed under the terms of the BSD 3-clause License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# -----------------------------------------------------------------------------
+
 from os import remove, close
-from os.path import exists, abspath, join, basename
+from os.path import exists, join, basename
 from tempfile import mkstemp
 from unittest import TestCase, main
 from future.utils.six import StringIO
@@ -10,8 +18,9 @@
     # Python 3
     from configparser import NoOptionError
 
-from qiita_db.commands import make_study_from_cmd, load_raw_data_cmd
-from qiita_db.study import StudyPerson
+from qiita_db.commands import (make_study_from_cmd, load_raw_data_cmd,
+                               sample_template_adder)
+from qiita_db.study import Study, StudyPerson
 from qiita_db.user import User
 from qiita_db.util import get_count, check_count, get_db_files_base_dir
 from qiita_core.util import qiita_test_checker
@@ -40,6 +49,37 @@ def test_make_study_from_cmd(self):
             make_study_from_cmd('test@test.com', 'newstudy2', fh2)
 
 
+@qiita_test_checker()
+class SampleTemplateAdderTests(TestCase):
+    def setUp(self):
+        # Create a sample template file
+        self.st_contents = SAMPLE_TEMPLATE
+
+        # create a new study to attach the sample template
+        info = {
+            "timeseries_type_id": 1,
+            "metadata_complete": True,
+            "mixs_compliant": True,
+            "number_samples_collected": 4,
+            "number_samples_promised": 4,
+            "portal_type_id": 3,
+            "study_alias": "TestStudy",
+            "study_description": "Description of a test study",
+            "study_abstract": "No abstract right now...",
+            "emp_person_id": StudyPerson(2),
+            "principal_investigator_id": StudyPerson(3),
+            "lab_person_id": StudyPerson(1)
+        }
+        self.study = Study.create(User('test@foo.bar'),
+                                  "Test study", [1], info)
+
+    def test_sample_template_adder(self):
+        """Correctly adds a sample template to the DB"""
+        fh = StringIO(self.st_contents)
+        st = sample_template_adder(fh, self.study.id)
+        self.assertEqual(st.id, self.study.id)
+
+
 @qiita_test_checker()
 class TestLoadRawDataFromCmd(TestCase):
     def setUp(self):
@@ -79,7 +119,6 @@ def test_load_data_from_cmd(self):
         initial_raw_count = get_count('qiita.raw_data')
         initial_fp_count = get_count('qiita.filepath')
         initial_raw_fp_count = get_count('qiita.raw_filepath')
-        initial_study_raw_data_count = get_count('qiita.study_raw_data')
 
         new = load_raw_data_cmd(filepaths, filepath_types, filetype,
                                 study_ids)
@@ -146,5 +185,18 @@ def test_load_data_from_cmd(self):
 vamps_id = vamps_id
 """
 
+SAMPLE_TEMPLATE = (
+    "#SampleID\trequired_sample_info_status_id\tcollection_timestamp\t"
+    "sample_type\thas_physical_specimen\tphysical_location\thas_extracted_data"
+    "\thost_subject_id\tTreatment\tDOB\tDescription\n"
+    "PC.354\t1\t2014-06-18 16:44\ttype_1\tTrue\tLocation_1\tTrue\tHS_ID_PC.354"
+    "\tControl\t20061218\tControl_mouse_I.D._354\n"
+    "PC.593\t1\t2014-06-18 16:44\ttype_1\tTrue\tLocation_1\tTrue\tHS_ID_PC.593"
+    "\tControl\t20071210\tControl_mouse_I.D._593\n"
+    "PC.607\t1\t2014-06-18 16:44\ttype_1\tTrue\tLocation_1\tTrue\tHS_ID_PC.607"
+    "\tFast\t20071112\tFasting_mouse_I.D._607\n"
+    "PC.636\t1\t2014-06-18 16:44\ttype_1\tTrue\tLocation_1\tTrue\tHS_ID_PC.636"
+    "\tFast\t20080116\tFasting_mouse_I.D._636")
+
 if __name__ == "__main__":
     main()

qiita_db/test/test_data/sample_template.txt

@@ -0,0 +1,5 @@
+#SampleID	required_sample_info_status_id	collection_timestamp	sample_type	has_physical_specimen	physical_location	has_extracted_data	host_subject_id	Treatment	DOB	Description
+PC.354	1	2014-06-18 16:44	type_1	True	Location_1	True	HS_ID_PC.354	Control	20061218	Control_mouse_I.D._354
+PC.593	1	2014-06-18 16:44	type_1	True	Location_1	True	HS_ID_PC.593	Control	20071210	Control_mouse_I.D._593
+PC.607	1	2014-06-18 16:44	type_1	True	Location_1	True	HS_ID_PC.607	Fast	20071112	Fasting_mouse_I.D._607
+PC.636	1	2014-06-18 16:44	type_1	True	Location_1	True	HS_ID_PC.636	Fast	20080116	Fasting_mouse_I.D._636

scripts/qiita_db

@@ -11,7 +11,8 @@
 import click
 
 from qiita_db.util import get_filetypes, get_filepath_types
-from qiita_db.commands import make_study_from_cmd, load_raw_data_cmd
+from qiita_db.commands import (sample_template_adder, make_study_from_cmd,
+                               load_raw_data_cmd)
 
 
 @click.group()
@@ -48,5 +49,17 @@ def insert_study_to_db(owner, title, info):
     make_study_from_cmd(owner, title, info)
 
 
+@qiita_db.command()
+@click.option('--fp', required=True,
+              type=click.Path(resolve_path=True, readable=True, exists=True),
+              help='Path to the tab delimited file holding the sample '
+                   'template information')
+@click.option('--study', required=True, type=int,
+              help='Associate the sample template with this study')
+def add_sample_template(fp, study):
+    """Adds a sample template to the database"""
+    sample_template_adder(fp, study)
+
+
 if __name__ == '__main__':
     qiita_db()