Merge pull request #1716 from josenavas/artifact-study-pages-import-a…

…rtifact

Import artifact

qiita_db/study.py

@@ -952,33 +952,41 @@ def ebi_submission_status(self, value):
     ebi_submission_status.__doc__.format(', '.join(_VALID_EBI_STATUS))
 
     # --- methods ---
-    def artifacts(self, dtype=None):
+    def artifacts(self, dtype=None, artifact_type=None):
         """Returns the list of artifacts associated with the study
 
         Parameters
         ----------
         dtype : str, optional
             If given, retrieve only artifacts for given data type. Default,
             return all artifacts associated with the study.
+        artifact_type : str, optional
+            If given, retrieve only artifacts of given data type. Default,
+            return all artifacts associated with the study
 
         Returns
         -------
         list of qiita_db.artifact.Artifact
         """
         with qdb.sql_connection.TRN:
+            sql_args = [self._id]
+            sql_where = ""
             if dtype:
-                sql = """SELECT artifact_id
-                         FROM qiita.artifact
-                            JOIN qiita.data_type USING (data_type_id)
-                            JOIN qiita.study_artifact USING (artifact_id)
-                         WHERE study_id = %s AND data_type = %s"""
-                sql_args = [self._id, dtype]
-            else:
-                sql = """SELECT artifact_id
-                         FROM qiita.artifact
-                            JOIN qiita.study_artifact USING (artifact_id)
-                         WHERE study_id = %s"""
-                sql_args = [self._id]
+                sql_args.append(dtype)
+                sql_where = " AND data_type = %s"
+
+            if artifact_type:
+                sql_args.append(artifact_type)
+                sql_where += "AND artifact_type = %s"
+
+            sql = """SELECT artifact_id
+                     FROM qiita.artifact
+                        JOIN qiita.data_type USING (data_type_id)
+                        JOIN qiita.study_artifact USING (artifact_id)
+                        JOIN qiita.artifact_type USING (artifact_type_id)
+                     WHERE study_id = %s{0}
+                     ORDER BY artifact_id""".format(sql_where)
+
             qdb.sql_connection.TRN.add(sql, sql_args)
             return [qdb.artifact.Artifact(aid)
                     for aid in qdb.sql_connection.TRN.execute_fetchflatten()]

qiita_db/test/test_study.py

@@ -712,6 +712,16 @@ def test_retrieve_artifacts(self):
         self.assertEqual(self.study.artifacts(dtype="16S"), [exp[-1]])
         self.assertEqual(self.study.artifacts(dtype="18S"), exp[:-1])
 
+        self.assertEqual(self.study.artifacts(artifact_type="BIOM"),
+                         [qdb.artifact.Artifact(4),
+                          qdb.artifact.Artifact(5),
+                          qdb.artifact.Artifact(6)])
+
+        self.assertEqual(self.study.artifacts(dtype="18S",
+                                              artifact_type="BIOM"),
+                         [qdb.artifact.Artifact(4),
+                          qdb.artifact.Artifact(5)])
+
     def test_retrieve_artifacts_none(self):
         new = qdb.study.Study.create(
             qdb.user.User('test@foo.bar'),

qiita_db/test/test_user.py

@@ -418,5 +418,21 @@ def test_delete_messages(self):
         obs = self.conn_handler.execute_fetchall(sql)
         self.assertItemsEqual(obs, [[1], [3]])
 
+    def test_user_artifacts(self):
+        user = qdb.user.User('test@foo.bar')
+        obs = user.user_artifacts()
+        exp = {qdb.study.Study(1): [qdb.artifact.Artifact(1),
+                                    qdb.artifact.Artifact(2),
+                                    qdb.artifact.Artifact(3),
+                                    qdb.artifact.Artifact(4),
+                                    qdb.artifact.Artifact(5),
+                                    qdb.artifact.Artifact(6)]}
+        self.assertEqual(obs, exp)
+        obs = user.user_artifacts(artifact_type='BIOM')
+        exp = {qdb.study.Study(1): [qdb.artifact.Artifact(4),
+                                    qdb.artifact.Artifact(5),
+                                    qdb.artifact.Artifact(6)]}
+        self.assertEqual(obs, exp)
+
 if __name__ == "__main__":
     main()

qiita_db/user.py

@@ -31,6 +31,8 @@
 from re import sub
 from datetime import datetime
 
+from future.utils import viewitems
+
 from qiita_core.exceptions import (IncorrectEmailError, IncorrectPasswordError,
                                    IncompetentQiitaDeveloperError)
 from qiita_core.qiita_settings import qiita_config
@@ -475,6 +477,46 @@ def unread_messages(self):
             return qdb.sql_connection.TRN.execute_fetchindex()
 
     # ------- methods ---------
+    def user_artifacts(self, artifact_type=None):
+        """Returns the artifacts owned by the user, grouped by study
+
+        Parameters
+        ----------
+        artifact_type : str, optional
+            The artifact type to retrieve. Default: retrieve all artfact types
+
+        Returns
+        -------
+        dict of {qiita_db.study.Study: list of qiita_db.artifact.Artifact}
+            The artifacts owned by the user
+        """
+        with qdb.sql_connection.TRN:
+            sql_args = [self.id, qiita_config.portal]
+            sql_a_type = ""
+            if artifact_type:
+                sql_a_type = " AND artifact_type = %s"
+                sql_args.append(artifact_type)
+
+            sql = """SELECT study_id, array_agg(
+                        artifact_id ORDER BY artifact_id)
+                     FROM qiita.study
+                        JOIN qiita.study_portal USING (study_id)
+                        JOIN qiita.portal_type USING (portal_type_id)
+                        JOIN qiita.study_artifact USING (study_id)
+                        JOIN qiita.artifact USING (artifact_id)
+                        JOIN qiita.artifact_type USING (artifact_type_id)
+                        WHERE email = %s AND portal = %s{0}
+                        GROUP BY study_id
+                        ORDER BY study_id""".format(sql_a_type)
+            qdb.sql_connection.TRN.add(sql, sql_args)
+            db_res = dict(qdb.sql_connection.TRN.execute_fetchindex())
+            res = {}
+            for s_id, artifact_ids in viewitems(db_res):
+                res[qdb.study.Study(s_id)] = [
+                    qdb.artifact.Artifact(a_id) for a_id in artifact_ids]
+
+            return res
+
     def change_password(self, oldpass, newpass):
         """Changes the password from oldpass to newpass
 

qiita_pet/handlers/api_proxy/artifact.py

@@ -234,7 +234,7 @@ def artifact_get_req(user_id, artifact_id):
 
 @execute_as_transaction
 def artifact_post_req(user_id, filepaths, artifact_type, name,
-                      prep_template_id):
+                      prep_template_id, artifact_id=None):
     """Creates the initial artifact for the prep template
 
     Parameters
@@ -250,6 +250,8 @@ def artifact_post_req(user_id, filepaths, artifact_type, name,
         Name to give the artifact
     prep_template_id : int or str castable to int
         Prep template to attach the artifact to
+    artifact_id : int or str castable to int, optional
+        The id of the imported artifact
 
     Returns
     -------
@@ -267,41 +269,55 @@ def artifact_post_req(user_id, filepaths, artifact_type, name,
     if access_error:
         return access_error
 
-    uploads_path = get_mountpoint('uploads')[0][1]
-    path_builder = partial(join, uploads_path, str(study_id))
-    cleaned_filepaths = []
-    for ftype, file_list in viewitems(filepaths):
-        # JavaScript sends us this list as a comma-separated list
-        for fp in file_list.split(','):
-            # JavaScript will send this value as an empty string if the
-            # list of files was empty. In such case, the split will generate
-            # a single element containing the empty string. Check for that case
-            # here and, if fp is not the empty string, proceed to check if
-            # the file exists
-            if fp:
-                # Check if filepath being passed exists for study
-                full_fp = path_builder(fp)
-                exists = check_fp(study_id, full_fp)
-                if exists['status'] != 'success':
-                    return {'status': 'error',
-                            'message': 'File does not exist: %s' % fp}
-                cleaned_filepaths.append((full_fp, ftype))
-
-    # This should never happen, but it doesn't hurt to actually have
-    # a explicit check, in case there is something odd with the JS
-    if not cleaned_filepaths:
-        return {'status': 'error',
-                'message': "Can't create artifact, no files provided."}
+    if artifact_id:
+        # if the artifact id has been provided, import the artifact
+        try:
+            artifact = Artifact.copy(Artifact(artifact_id), prep)
+        except Exception as e:
+            # We should hit this exception rarely (that's why it is an
+            # exception)  since at this point we have done multiple checks.
+            # However, it can occur in weird cases, so better let the GUI know
+            # that this failed
+            return {'status': 'error',
+                    'message': "Error creating artifact: %s" % str(e)}
 
-    try:
-        artifact = Artifact.create(cleaned_filepaths, artifact_type, name=name,
-                                   prep_template=prep)
-    except Exception as e:
-        # We should hit this exception rarely (that's why it is an exception)
-        # since at this point we have done multiple checks. However, it can
-        # occur in weird cases, so better let the GUI know that this failed
-        return {'status': 'error',
-                'message': "Error creating artifact: %s" % str(e)}
+    else:
+        uploads_path = get_mountpoint('uploads')[0][1]
+        path_builder = partial(join, uploads_path, str(study_id))
+        cleaned_filepaths = []
+        for ftype, file_list in viewitems(filepaths):
+            # JavaScript sends us this list as a comma-separated list
+            for fp in file_list.split(','):
+                # JavaScript will send this value as an empty string if the
+                # list of files was empty. In such case, the split will
+                # generate a single element containing the empty string. Check
+                # for that case here and, if fp is not the empty string,
+                # proceed to check if the file exists
+                if fp:
+                    # Check if filepath being passed exists for study
+                    full_fp = path_builder(fp)
+                    exists = check_fp(study_id, full_fp)
+                    if exists['status'] != 'success':
+                        return {'status': 'error',
+                                'message': 'File does not exist: %s' % fp}
+                    cleaned_filepaths.append((full_fp, ftype))
+
+        # This should never happen, but it doesn't hurt to actually have
+        # a explicit check, in case there is something odd with the JS
+        if not cleaned_filepaths:
+            return {'status': 'error',
+                    'message': "Can't create artifact, no files provided."}
+
+        try:
+            artifact = Artifact.create(cleaned_filepaths, artifact_type,
+                                       name=name, prep_template=prep)
+        except Exception as e:
+            # We should hit this exception rarely (that's why it is an
+            # exception)  since at this point we have done multiple checks.
+            # However, it can occur in weird cases, so better let the GUI know
+            # that this failed
+            return {'status': 'error',
+                    'message': "Error creating artifact: %s" % str(e)}
 
     return {'status': 'success',
             'message': '',

qiita_pet/handlers/api_proxy/studies.py

@@ -8,6 +8,8 @@
 from __future__ import division
 from collections import defaultdict
 
+from future.utils import viewitems
+
 from qiita_db.user import User
 from qiita_db.study import Study
 from qiita_db.metadata_template.prep_template import PrepTemplate
@@ -180,7 +182,7 @@ def study_prep_get_req(study_id, user_id):
             'info': prep_info}
 
 
-def study_files_get_req(study_id, prep_template_id, artifact_type):
+def study_files_get_req(user_id, study_id, prep_template_id, artifact_type):
     """Returns the uploaded files for the study id categorized by artifact_type
 
     It retrieves the files uploaded for the given study and tries to do a
@@ -189,6 +191,8 @@ def study_files_get_req(study_id, prep_template_id, artifact_type):
 
     Parameters
     ----------
+    user_id : str
+        The id of the user making the request
     study_id : int
         The study id
     prep_template_id : int
@@ -242,8 +246,23 @@ def study_files_get_req(study_id, prep_template_id, artifact_type):
     # because selected is initialized to the empty list
     file_types.insert(0, (first[0], first[1], selected))
 
+    # Create a list of artifacts that the user has access to, in case that
+    # he wants to import the files from another artifact
+    user = User(user_id)
+    artifact_options = []
+    user_artifacts = user.user_artifacts(artifact_type=artifact_type)
+    study = Study(study_id)
+    if study not in user_artifacts:
+        user_artifacts[study] = study.artifacts(artifact_type=artifact_type)
+    for study, artifacts in viewitems(user_artifacts):
+        study_label = "%s (%d)" % (study.title, study.id)
+        for a in artifacts:
+            artifact_options.append(
+                (a.id, "%s - %s (%d)" % (study_label, a.name, a.id)))
+
     return {'status': 'success',
             'message': '',
             'remaining': remaining,
             'file_types': file_types,
-            'num_prefixes': num_prefixes}
+            'num_prefixes': num_prefixes,
+            'artifacts': artifact_options}

qiita_pet/handlers/api_proxy/tests/test_artifact.py

@@ -326,6 +326,26 @@ def test_artifact_post_req(self):
         a = Artifact(new_artifact_id)
         self._files_to_remove.extend([fp for _, fp, _ in a.filepaths])
 
+        # Test importing an artifact
+        # Create new prep template to attach artifact to
+        pt = npt.assert_warns(
+            QiitaDBWarning, PrepTemplate.create,
+            pd.DataFrame({'new_col': {'1.SKD6.640190': 1}}), Study(1), '16S')
+        self._files_to_remove.extend([fp for _, fp in pt.get_filepaths()])
+
+        new_artifact_id_2 = get_count('qiita.artifact') + 1
+        obs = artifact_post_req(
+            'test@foo.bar', {}, 'FASTQ', 'New Test Artifact 2', pt.id,
+            new_artifact_id)
+        exp = {'status': 'success',
+               'message': '',
+               'artifact': new_artifact_id_2}
+        self.assertEqual(obs, exp)
+        # Instantiate the artifact to make sure it was made and
+        # to clean the environment
+        a = Artifact(new_artifact_id)
+        self._files_to_remove.extend([fp for _, fp, _ in a.filepaths])
+
     def test_artifact_post_req_error(self):
         # Create a new prep template to attach the artifact to
         pt = npt.assert_warns(
@@ -368,6 +388,13 @@ def test_artifact_post_req_error(self):
                           "has an artifact associated"}
         self.assertEqual(obs, exp)
 
+        # Exception
+        obs = artifact_post_req(user_id, {}, artifact_type, name, 1, 1)
+        exp = {'status': 'error',
+               'message': "Error creating artifact: Prep template 1 already "
+                          "has an artifact associated"}
+        self.assertEqual(obs, exp)
+
     def test_artifact_status_put_req(self):
         obs = artifact_status_put_req(1, 'test@foo.bar', 'sandbox')
         exp = {'status': 'success',