Merge pull request qiita-spots#2199 from antgonza/fix-494

fix qiita-spots#494

Author: ElDeveloper

qiita_db/commands.py

@@ -49,20 +49,14 @@ def get_optional(name):
     required_fields = ['timeseries_type_id', 'mixs_compliant',
                        'reprocess', 'study_alias',
                        'study_description', 'study_abstract',
-                       'metadata_complete', 'efo_ids',
-                       'principal_investigator']
+                       'metadata_complete', 'principal_investigator']
     optional_fields = ['funding', 'most_recent_contact', 'spatial_series',
                        'number_samples_collected', 'number_samples_promised',
                        'vamps_id', 'study_id']
     infodict = {}
     for value in required_fields:
         infodict[value] = get_required(value)
 
-    # this will eventually change to using the Experimental Factory Ontolgoy
-    # names
-    efo_ids = infodict.pop('efo_ids')
-    efo_ids = [x.strip() for x in efo_ids.split(',')]
-
     for value in optional_fields:
         optvalue = get_optional(value)
         if optvalue is not None:
@@ -86,8 +80,7 @@ def get_optional(name):
         infodict['principal_investigator_id'] = qdb.study.StudyPerson.create(
             pi_name.strip(), pi_email.strip(), pi_affiliation.strip())
 
-        return qdb.study.Study.create(
-            qdb.user.User(owner), title, efo_ids, infodict)
+        return qdb.study.Study.create(qdb.user.User(owner), title, infodict)
 
 
 def load_artifact_from_cmd(filepaths, filepath_types, artifact_type,

qiita_db/metadata_template/test/test_sample_template.py

@@ -253,8 +253,7 @@ def setUp(self):
         }
         self.new_study = qdb.study.Study.create(
             qdb.user.User('test@foo.bar'),
-            "Fried Chicken Microbiome %s" % time(), [1],
-            info)
+            "Fried Chicken Microbiome %s" % time(), info)
 
         self.metadata_dict = {
             'Sample1': {'physical_specimen_location': 'location1',

qiita_db/study.py

@@ -113,7 +113,6 @@ class Study(qdb.base.QiitaObject):
     Attributes
     ----------
     data_types
-    efo
     info
     investigation
     name
@@ -302,7 +301,7 @@ def exists(cls, study_title):
             return qdb.sql_connection.TRN.execute_fetchlast()
 
     @classmethod
-    def create(cls, owner, title, efo, info, investigation=None):
+    def create(cls, owner, title, info, investigation=None):
         """Creates a new study on the database
 
         Parameters
@@ -311,8 +310,6 @@ def create(cls, owner, title, efo, info, investigation=None):
             the study's owner
         title : str
             Title of the study
-        efo : list
-            Experimental Factor Ontology id(s) for the study
         info : dict
             the information attached to the study. All "*_id" keys must pass
             the objects associated with them.
@@ -326,24 +323,19 @@ def create(cls, owner, title, efo, info, investigation=None):
             All required keys not passed
         IncompetentQiitaDeveloperError
             email, study_id, study_status_id, or study_title passed as a key
-            empty efo list passed
         QiitaDBDuplicateError
             If a study with the given title already exists
 
         Notes
         -----
-        All keys in info, except the efo, must be equal to columns in
-        qiita.study table in the database.
+        All keys in info, must be equal to columns in qiita.study table in the
+        database.
         """
         # make sure not passing non-info columns in the info dict
         if cls._non_info.intersection(info):
             raise qdb.exceptions.QiitaDBColumnError(
                 "non info keys passed: %s" % cls._non_info.intersection(info))
 
-        # make sure efo info passed
-        if not efo:
-            raise IncompetentQiitaDeveloperError("Need EFO information!")
-
         with qdb.sql_connection.TRN:
             if cls.exists(title):
                 raise qdb.exceptions.QiitaDBDuplicateError(
@@ -383,13 +375,6 @@ def create(cls, owner, title, efo, info, investigation=None):
             qdb.sql_connection.TRN.add(sql, data)
             study_id = qdb.sql_connection.TRN.execute_fetchlast()
 
-            # insert efo information into database
-            sql = """INSERT INTO qiita.{0}_experimental_factor
-                        (study_id, efo_id)
-                     VALUES (%s, %s)""".format(cls._table)
-            qdb.sql_connection.TRN.add(
-                sql, [[study_id, e] for e in efo], many=True)
-
             # Add to both QIITA and given portal (if not QIITA)
             portal_id = qdb.util.convert_to_id(
                 qiita_config.portal, 'portal_type', 'portal')
@@ -442,10 +427,6 @@ def delete(cls, id_):
             sql = "DELETE FROM qiita.study_portal WHERE study_id = %s"
             qdb.sql_connection.TRN.add(sql, args)
 
-            sql = """DELETE FROM qiita.study_experimental_factor
-                     WHERE study_id = %s"""
-            qdb.sql_connection.TRN.add(sql, args)
-
             sql = "DELETE FROM qiita.study_publication WHERE study_id = %s"
             qdb.sql_connection.TRN.add(sql, args)
 
@@ -631,44 +612,6 @@ def info(self, info):
             qdb.sql_connection.TRN.add(sql, data)
             qdb.sql_connection.TRN.execute()
 
-    @property
-    def efo(self):
-        with qdb.sql_connection.TRN:
-            sql = """SELECT efo_id FROM qiita.{0}_experimental_factor
-                     WHERE study_id = %s""".format(self._table)
-            qdb.sql_connection.TRN.add(sql, [self._id])
-            return qdb.sql_connection.TRN.execute_fetchflatten()
-
-    @efo.setter
-    def efo(self, efo_vals):
-        """Sets the efo for the study
-
-        Parameters
-        ----------
-        efo_vals : list
-            Id(s) for the new efo values
-
-        Raises
-        ------
-        IncompetentQiitaDeveloperError
-            Empty efo list passed
-        """
-        if not efo_vals:
-            raise IncompetentQiitaDeveloperError("Need EFO information!")
-        with qdb.sql_connection.TRN:
-            self._lock_non_sandbox()
-            # wipe out any EFOs currently attached to study
-            sql = """DELETE FROM qiita.{0}_experimental_factor
-                     WHERE study_id = %s""".format(self._table)
-            qdb.sql_connection.TRN.add(sql, [self._id])
-            # insert new EFO information into database
-            sql = """INSERT INTO qiita.{0}_experimental_factor
-                        (study_id, efo_id)
-                     VALUES (%s, %s)""".format(self._table)
-            qdb.sql_connection.TRN.add(
-                sql, [[self._id, efo] for efo in efo_vals], many=True)
-            qdb.sql_connection.TRN.execute()
-
     @property
     def shared_with(self):
         """list of users the study is shared with

qiita_db/support_files/patches/56.sql

@@ -0,0 +1,4 @@
+-- Aug 4, 2017
+-- DROP qiita.study_experimental_factor
+
+DROP TABLE IF EXISTS qiita.study_experimental_factor;

qiita_db/support_files/populate_test_db.sql

@@ -62,9 +62,6 @@ INSERT INTO qiita.investigation (investigation_name, investigation_description,
 -- Insert investigation_study (link study 1 with investigation 1)
 INSERT INTO qiita.investigation_study (investigation_id, study_id) VALUES (1, 1);
 
--- Insert the study experimental factor for study 1
-INSERT INTO qiita.study_experimental_factor (study_id, efo_id) VALUES (1, 1);
-
 -- Add the study_sample for study 1
 INSERT INTO qiita.study_sample (study_id, sample_id, ebi_sample_accession, biosample_accession) VALUES
     (1, '1.SKB8.640193', 'ERS000000', 'SAMEA0000000'),