Merge pull request #2088 from antgonza/adding-tags

Adding tags

Author: wasade

qiita_db/study.py

@@ -475,11 +475,23 @@ def get_tags(cls):
             accessed as a list of dictionaries, keyed on column name.
         """
         with qdb.sql_connection.TRN:
-            sql = """SELECT study_tag_id, study_tag
-                     FROM qiita.study_tags"""
+            sql = """SELECT qiita.user_level.name AS user_level,
+                        array_agg(study_tag)
+                    FROM qiita.study_tags
+                    LEFT JOIN qiita.qiita_user USING (email)
+                    LEFT JOIN qiita.user_level USING (user_level_id)
+                    GROUP BY qiita.user_level.name"""
 
             qdb.sql_connection.TRN.add(sql)
-            return qdb.sql_connection.TRN.execute_fetchindex()
+            results = dict(qdb.sql_connection.TRN.execute_fetchindex())
+            # when the system is empty,
+            # it's possible to get an empty dict, fixing
+            if 'admin' not in results:
+                results['admin'] = []
+            if 'user' not in results:
+                results['user'] = []
+
+            return results
 
     @classmethod
     def insert_tags(cls, user, tags):
@@ -493,14 +505,15 @@ def insert_tags(cls, user, tags):
             The list of tags to add
         """
         with qdb.sql_connection.TRN:
+            email = user.email
             sql = """INSERT INTO qiita.study_tags (email, study_tag)
-                     VALUES (%s, %s)"""
-            sql_args = [[user.email, tag] for tag in tags]
+                     SELECT %s, %s WHERE NOT EXISTS (
+                        SELECT 1 FROM qiita.study_tags WHERE study_tag = %s)"""
+            sql_args = [[email, tag, tag] for tag in tags]
 
             qdb.sql_connection.TRN.add(sql, sql_args, many=True)
             qdb.sql_connection.TRN.execute()
 
-
 # --- Attributes ---
     @property
     def title(self):
@@ -967,40 +980,12 @@ def tags(self):
             The study tags
         """
         with qdb.sql_connection.TRN:
-            sql = """SELECT study_tag_id, study_tag
+            sql = """SELECT study_tag
                         FROM qiita.study_tags
-                        LEFT JOIN qiita.per_study_tags USING (study_tag_id)
+                        LEFT JOIN qiita.per_study_tags USING (study_tag)
                         WHERE study_id = {0}""".format(self._id)
             qdb.sql_connection.TRN.add(sql)
-            return qdb.sql_connection.TRN.execute_fetchindex()
-
-    @tags.setter
-    def tags(self, tag_ids):
-        """Sets the tags of the study
-
-        Parameters
-        ----------
-        tag_ids : list of int
-            The tag ids of the study
-        """
-        with qdb.sql_connection.TRN:
-            sql = """DELETE FROM qiita.per_study_tags WHERE study_id = %s"""
-            qdb.sql_connection.TRN.add(sql, [self._id])
-
-            if tag_ids:
-                sql = """INSERT INTO qiita.per_study_tags
-                            (study_tag_id, study_id)
-                         SELECT %s, %s
-                            WHERE
-                                NOT EXISTS (
-                                    SELECT study_tag_id, study_id
-                                    FROM qiita.per_study_tags
-                                    WHERE study_tag_id = %s AND study_id = %s
-                                )"""
-                sql_args = [[tid, self._id, tid, self._id] for tid in tag_ids]
-                qdb.sql_connection.TRN.add(sql, sql_args, many=True)
-
-            qdb.sql_connection.TRN.execute()
+            return [t[0] for t in qdb.sql_connection.TRN.execute_fetchindex()]
 
 # --- methods ---
     def artifacts(self, dtype=None, artifact_type=None):
@@ -1152,6 +1137,75 @@ def unshare(self, user):
             qdb.sql_connection.TRN.add(sql, [self._id, user.id])
             qdb.sql_connection.TRN.execute()
 
+    def update_tags(self, user, tags):
+        """Sets the tags of the study
+
+        Parameters
+        ----------
+        user: User object
+            The user reqesting the study tags update
+        tags : list of str
+            The tags to update within the study
+
+        Returns
+        -------
+        str
+            Warnings during insertion
+        """
+        message = ''
+        # converting to set just to facilitate operations
+        system_tags_admin = set(self.get_tags()['admin'])
+        user_level = user.level
+        current_tags = set(self.tags)
+        to_delete = current_tags - set(tags)
+        to_add = set(tags) - current_tags
+
+        if to_delete or to_add:
+            with qdb.sql_connection.TRN:
+                if to_delete:
+                    if user_level != 'admin':
+                        admin_tags = to_delete & system_tags_admin
+                        if admin_tags:
+                            message += 'You cannot remove: %s' % ', '.join(
+                                admin_tags)
+                        to_delete = to_delete - admin_tags
+
+                    if to_delete:
+                        sql = """DELETE FROM qiita.per_study_tags
+                                     WHERE study_id = %s AND study_tag IN %s"""
+                        qdb.sql_connection.TRN.add(
+                            sql, [self._id, tuple(to_delete)])
+
+                if to_add:
+                    if user_level != 'admin':
+                        admin_tags = to_add & system_tags_admin
+                        if admin_tags:
+                            message += ('Only admins can assign: '
+                                        '%s' % ', '.join(admin_tags))
+                        to_add = to_add - admin_tags
+
+                    if to_add:
+                        self.insert_tags(user, to_add)
+
+                        sql = """INSERT INTO qiita.per_study_tags
+                                    (study_tag, study_id)
+                                 SELECT %s, %s
+                                    WHERE
+                                        NOT EXISTS (
+                                            SELECT study_tag, study_id
+                                            FROM qiita.per_study_tags
+                                            WHERE study_tag = %s
+                                                AND study_id = %s
+                                        )"""
+                        sql_args = [[t, self._id, t, self._id] for t in to_add]
+                        qdb.sql_connection.TRN.add(sql, sql_args, many=True)
+
+                qdb.sql_connection.TRN.execute()
+        else:
+            message = 'No changes in the tags.'
+
+        return message
+
 
 class StudyPerson(qdb.base.QiitaObject):
     r"""Object handling information pertaining to people involved in a study

qiita_db/support_files/patches/52.sql

@@ -0,0 +1,30 @@
+-- Mar 16, 2017
+-- Changing tagging system structure, now study_tag will be the index
+
+-- dropping all not required constrints, indexes and columns
+ALTER TABLE qiita.study_tags DROP CONSTRAINT fk_study_tags;
+DROP INDEX qiita.idx_study_tag_id;
+ALTER TABLE qiita.study_tags DROP CONSTRAINT pk_study_tag;
+ALTER TABLE qiita.study_tags DROP CONSTRAINT pk_study_tag_id;
+ALTER TABLE qiita.study_tags DROP COLUMN study_tag_id;
+ALTER TABLE qiita.per_study_tags ADD COLUMN study_tag varchar NOT NULL;
+ALTER TABLE qiita.per_study_tags DROP CONSTRAINT pk_per_study_tags;
+ALTER TABLE qiita.per_study_tags DROP COLUMN study_tag_id;
+
+-- adding new restrictions
+ALTER TABLE qiita.study_tags ADD CONSTRAINT pk_study_tags PRIMARY KEY ( study_tag );
+ALTER TABLE qiita.study_tags ADD CONSTRAINT fk_email FOREIGN KEY ( email ) REFERENCES qiita.qiita_user( email );
+ALTER TABLE qiita.per_study_tags ADD CONSTRAINT fk_study_tags FOREIGN KEY ( study_tag ) REFERENCES qiita.study_tags( study_tag );
+ALTER TABLE qiita.per_study_tags ADD CONSTRAINT fk_study_id FOREIGN KEY ( study_id ) REFERENCES qiita.study( study_id );
+ALTER TABLE qiita.per_study_tags ADD CONSTRAINT pk_per_study_tags PRIMARY KEY ( study_tag, study_id);
+
+-- New structure:
+-- CREATE TABLE qiita.study_tags (
+--   email varchar NOT NULL,
+--   study_tag varchar NOT NULL,
+-- ) ;
+--
+-- CREATE TABLE qiita.per_study_tags (
+--   study_tag varchar NOT NULL,
+--   study_id bigint NOT NULL,
+-- ) ;

qiita_db/test/test_study.py

@@ -833,31 +833,43 @@ def test_environmental_packages_sandboxed(self):
             self.study.environmental_packages = ['air']
 
     def test_study_tags(self):
+        # testing empty tags
+        obs = qdb.study.Study.get_tags()
+        self.assertEqual(obs, {'admin': [], 'user': []})
+
         # inserting new tags
         user = qdb.user.User('test@foo.bar')
-        tags = ['this is my tag', 'I want GOLD!!']
+        tags = ['this is my tag', 'I want GOLD!!', 'this is my tag']
         qdb.study.Study.insert_tags(user, tags)
+        # now as admin
+        admin = qdb.user.User('admin@foo.bar')
+        admin_tags = ['actual GOLD!', 'this is my tag']
+        qdb.study.Study.insert_tags(admin, admin_tags)
 
         # testing that insertion went fine
         obs = qdb.study.Study.get_tags()
-        exp = [[i + 1, tag] for i, tag in enumerate(tags)]
+        exp = {'user': ['this is my tag', 'I want GOLD!!'],
+               'admin': ['actual GOLD!']}
         self.assertEqual(obs, exp)
 
-        # assigning the tags to study
+        # assigning the tags to study as user
         study = qdb.study.Study(1)
-        self.assertEqual(study.tags, [])
-        study.tags = [tig for tig, tag in obs]
-        # and checking that everything went fine
-        self.assertEqual(obs, study.tags)
-
-        # making sure that everything is overwritten
-        obs.pop()
-        study.tags = [tig for tig, tag in obs]
-        self.assertEqual(obs, study.tags)
+        tags = ['this is my tag', 'actual GOLD!']
+        message = study.update_tags(user, tags)
+        self.assertItemsEqual(study.tags, tags[:1])
+        self.assertEqual(message, 'Only admins can assign: actual GOLD!')
+        # now like admin
+        message = study.update_tags(admin, tags)
+        self.assertItemsEqual(study.tags, tags)
+        self.assertEqual(message, '')
 
         # cleaning tags
-        study.tags = []
+        message = study.update_tags(user, [])
+        self.assertEqual(study.tags, ['actual GOLD!'])
+        self.assertEqual(message, 'You cannot remove: actual GOLD!')
+        message = study.update_tags(admin, [])
         self.assertEqual(study.tags, [])
+        self.assertEqual(message, '')
 
 
 if __name__ == "__main__":

qiita_pet/handlers/api_proxy/__init__.py

@@ -26,7 +26,8 @@
     prep_template_patch_req)
 from .studies import (
     data_types_get_req, study_get_req, study_prep_get_req, study_delete_req,
-    study_files_get_req)
+    study_files_get_req, study_tags_patch_request, study_get_tags_request,
+    study_tags_request)
 from .artifact import (artifact_graph_get_req, artifact_types_get_req,
                        artifact_post_req, artifact_get_req,
                        artifact_status_put_req, artifact_delete_req,
@@ -58,6 +59,8 @@
            'sample_template_samples_get_req', 'prep_template_samples_get_req',
            'sample_template_category_get_req', 'new_prep_template_get_req',
            'study_files_get_req', 'prep_template_ajax_get_req',
+           'study_tags_request', 'study_tags_patch_request',
+           'study_get_tags_request',
            'prep_template_patch_req', 'ontology_patch_handler',
            'artifact_summary_get_request', 'artifact_summary_post_request',
            'list_commands_handler_get_req', 'process_artifact_handler_get_req',

qiita_pet/handlers/api_proxy/studies.py

@@ -296,3 +296,103 @@ def study_files_get_req(user_id, study_id, prep_template_id, artifact_type):
             'file_types': file_types,
             'num_prefixes': num_prefixes,
             'artifacts': artifact_options}
+
+
+def study_tags_request():
+    """Retrieve available study tags
+
+    Returns
+    -------
+    dict of {str, str}
+        A dictionary with the following keys:
+        - status: str, whether if the request is successful or not
+        - message: str, if the request is unsuccessful, a human readable error
+        - tags: {level: value, ..., ...}
+    """
+    return {'status': 'success',
+            'message': '',
+            'tags': Study.get_tags()}
+
+
+def study_get_tags_request(user_id, study_id):
+    """Retrieve available study tags for study_id
+
+    Parameters
+    ----------
+    user_id : int
+        The id of the user performing the operation
+    study_id : int
+        The id of the study on which we will be performing the operation
+
+    Returns
+    -------
+    dict of {str, str}
+        A dictionary with the following keys:
+        - status: str, whether if the request is successful or not
+        - message: str, if the request is unsuccessful, a human readable error
+        - tags: [value, ..., ...]
+    """
+
+    access_error = check_access(study_id, user_id)
+    if access_error:
+        return access_error
+    study = Study(study_id)
+
+    return {'status': 'success',
+            'message': '',
+            'tags': study.tags}
+
+
+def study_tags_patch_request(user_id, study_id,
+                             req_op, req_path, req_value=None, req_from=None):
+    """Modifies an attribute of the artifact
+
+    Parameters
+    ----------
+    user_id : int
+        The id of the user performing the patch operation
+    study_id : int
+        The id of the study on which we will be performing the patch operation
+    req_op : str
+        The operation to perform on the study
+    req_path : str
+        The attribute to patch
+    req_value : str, optional
+        The value that needs to be modified
+    req_from : str, optional
+        The original path of the element
+
+    Returns
+    -------
+    dict of {str, str}
+        A dictionary with the following keys:
+        - status: str, whether if the request is successful or not
+        - message: str, if the request is unsuccessful, a human readable error
+    """
+    if req_op == 'replace':
+        req_path = [v for v in req_path.split('/') if v]
+        if len(req_path) != 1:
+            return {'status': 'error',
+                    'message': 'Incorrect path parameter'}
+
+        attribute = req_path[0]
+
+        # Check if the user actually has access to the study
+        access_error = check_access(study_id, user_id)
+        if access_error:
+            return access_error
+        study = Study(study_id)
+
+        if attribute == 'tags':
+            message = study.update_tags(User(user_id), req_value)
+            return {'status': 'success',
+                    'message': message}
+        else:
+            # We don't understand the attribute so return an error
+            return {'status': 'error',
+                    'message': 'Attribute "%s" not found. '
+                               'Please, check the path parameter' % attribute}
+    else:
+        return {'status': 'error',
+                'message': 'Operation "%s" not supported. '
+                           'Current supported operations: replace' % req_op}