Merge a674a8d into 28ad6d8

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
@@ -8,6 +17,7 @@
 
 from qiita_db.study import Study, StudyPerson
 from qiita_db.user import User
+from qiita_db.metadata_template import SampleTemplate
 
 
 def make_study_from_cmd(owner, title, info):
@@ -55,3 +65,18 @@ def make_study_from_cmd(owner, title, info):
     efo_ids = [x.strip() for x in efo_ids.split(',')]
 
     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))

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

@@ -1,3 +1,11 @@
+# -----------------------------------------------------------------------------
+# 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 unittest import TestCase, main
 from future.utils.six import StringIO
 try:
@@ -7,10 +15,10 @@
     # Python 3
     from configparser import NoOptionError
 
-from qiita_db.commands import make_study_from_cmd
-from qiita_db.study import StudyPerson
+from qiita_db.study import Study, StudyPerson
 from qiita_db.user import User
 from qiita_core.util import qiita_test_checker
+from qiita_db.commands import make_study_from_cmd, sample_template_adder
 
 
 @qiita_test_checker()
@@ -35,6 +43,38 @@ def test_make_study_from_cmd(self):
         with self.assertRaises(NoOptionError):
             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)
+
+
 CONFIG_1 = """[required]
 timeseries_type_id = 1
 metadata_complete = True
@@ -72,5 +112,18 @@ def test_make_study_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

@@ -18,7 +18,7 @@ from qiita_db.environment_manager import (make_test_environment,
                                           drop_demo_environment,
                                           DFLT_BASE_DATA_FOLDER,
                                           DFLT_BASE_WORK_FOLDER)
-from qiita_db.commands import make_study_from_cmd
+from qiita_db.commands import sample_template_adder, make_study_from_cmd
 
 
 @click.group()
@@ -119,6 +119,13 @@ def drop_demo_env(user, host):
     """Drops the demo database environment."""
     drop_demo_environment(user, None, host)
 
+
+@click.command()
+def add_sample_template():
+    """Adds a sample template to the database"""
+    sample_template_adder()
+
+
 qiita_db.add_command(make_test_env)
 qiita_db.add_command(clean_test_env)
 qiita_db.add_command(drop_test_env)