Fix 1746

qiita_pet/handlers/api_proxy/artifact.py

@@ -15,7 +15,8 @@
 from qiita_core.qiita_settings import qiita_config
 from qiita_pet.handlers.api_proxy.util import check_access, check_fp
 from qiita_ware.context import safe_submit
-from qiita_ware.dispatchable import delete_artifact
+from qiita_ware.dispatchable import (create_raw_data, copy_raw_data,
+                                     delete_artifact)
 from qiita_db.artifact import Artifact
 from qiita_db.user import User
 from qiita_db.metadata_template.prep_template import PrepTemplate
@@ -293,16 +294,7 @@ def artifact_post_req(user_id, filepaths, artifact_type, name,
 
     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)}
-
+        job_id = safe_submit(user_id, copy_raw_data, prep, artifact_id)
     else:
         uploads_path = get_mountpoint('uploads')[0][1]
         path_builder = partial(join, uploads_path, str(study_id))
@@ -330,20 +322,13 @@ def artifact_post_req(user_id, filepaths, artifact_type, name,
             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)}
+        job_id = safe_submit(user_id, create_raw_data, artifact_type, prep,
+                             cleaned_filepaths, name=name)
+
+    r_client.set(PREP_TEMPLATE_KEY_FORMAT % prep.id, job_id)
 
     return {'status': 'success',
-            'message': '',
-            'artifact': artifact.id}
+            'message': ''}
 
 
 def artifact_patch_request(user_id, req_op, req_path, req_value=None,

qiita_pet/handlers/api_proxy/prep_template.py

@@ -106,6 +106,22 @@ def prep_template_ajax_get_req(user_id, prep_id):
     # Currently there is no name attribute, but it will be soon
     name = "Prep information %d" % prep_id
     pt = PrepTemplate(prep_id)
+
+    job_id = r_client.get(PREP_TEMPLATE_KEY_FORMAT % prep_id)
+    if job_id:
+        redis_info = loads(r_client.get(job_id))
+        processing = redis_info['status_msg'] == 'Running'
+        if processing:
+            alert_type = 'info'
+            alert_msg = 'This prep template is currently being updated'
+        else:
+            alert_type = redis_info['return']['status']
+            alert_msg = redis_info['return']['message'].replace('\n', '</br>')
+    else:
+        processing = False
+        alert_type = ''
+        alert_msg = ''
+
     artifact_attached = pt.artifact is not None
     study_id = pt.study_id
     files = [f for _, f in get_files_from_uploads_folders(study_id)
@@ -130,21 +146,6 @@ def prep_template_ajax_get_req(user_id, prep_id):
 
     ontology = _get_ENA_ontology()
 
-    job_id = r_client.get(PREP_TEMPLATE_KEY_FORMAT % prep_id)
-    if job_id:
-        redis_info = loads(r_client.get(job_id))
-        processing = redis_info['status_msg'] == 'Running'
-        if processing:
-            alert_type = 'info'
-            alert_msg = 'This prep template is currently being updated'
-        else:
-            alert_type = redis_info['return']['status']
-            alert_msg = redis_info['return']['message'].replace('\n', '</br>')
-    else:
-        processing = False
-        alert_type = ''
-        alert_msg = ''
-
     editable = Study(study_id).can_edit(User(user_id)) and not processing
 
     return {'status': 'success',

qiita_pet/handlers/api_proxy/tests/test_artifact.py

@@ -357,9 +357,16 @@ def test_artifact_post_req(self):
         obs = artifact_post_req(
             'test@foo.bar', filepaths, 'FASTQ', 'New Test Artifact', pt.id)
         exp = {'status': 'success',
-               'message': '',
-               'artifact': new_artifact_id}
+               'message': ''}
         self.assertEqual(obs, exp)
+
+        obs = r_client.get('prep_template_%d' % pt.id)
+        self.assertIsNotNone(obs)
+        redis_info = loads(r_client.get(obs))
+        while redis_info['status_msg'] == 'Running':
+            sleep(0.05)
+            redis_info = loads(r_client.get(obs))
+
         # Instantiate the artifact to make sure it was made and
         # to clean the environment
         a = Artifact(new_artifact_id)
@@ -377,12 +384,18 @@ def test_artifact_post_req(self):
             'test@foo.bar', {}, 'FASTQ', 'New Test Artifact 2', pt.id,
             new_artifact_id)
         exp = {'status': 'success',
-               'message': '',
-               'artifact': new_artifact_id_2}
+               'message': ''}
         self.assertEqual(obs, exp)
+
+        obs = r_client.get('prep_template_%d' % pt.id)
+        self.assertIsNotNone(obs)
+        redis_info = loads(r_client.get(obs))
+        while redis_info['status_msg'] == 'Running':
+            sleep(0.05)
+            redis_info = loads(r_client.get(obs))
         # Instantiate the artifact to make sure it was made and
         # to clean the environment
-        a = Artifact(new_artifact_id)
+        a = Artifact(new_artifact_id_2)
         self._files_to_remove.extend([fp for _, fp, _ in a.filepaths])
 
     def test_artifact_post_req_error(self):
@@ -420,20 +433,6 @@ def test_artifact_post_req_error(self):
                'message': "Can't create artifact, no files provided."}
         self.assertEqual(obs, exp)
 
-        # Exception
-        obs = artifact_post_req(user_id, filepaths, artifact_type, name, 1)
-        exp = {'status': 'error',
-               'message': "Error creating artifact: Prep template 1 already "
-                          "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',

qiita_pet/templates/study_ajax/prep_summary.html

@@ -286,9 +286,11 @@
     if ("{{artifact_attached}}" == "True") {
       load_template_graph();
     }
+    {% if editable %}
     else {
       load_new_artifact();
     }
+    {% end %}
     // If the file-selector select changes, check if we need to show the update button
     $("#file-selector").change(function ( event ) {
       if ( $("#file-selector").val() === "" ) {

qiita_ware/dispatchable.py

@@ -8,7 +8,6 @@
 from .analysis_pipeline import RunAnalysis
 from qiita_ware.commands import submit_EBI, submit_VAMPS
 from qiita_db.analysis import Analysis
-from qiita_db.artifact import Artifact
 
 
 def submit_to_ebi(preprocessed_data_id, submission_type):
@@ -31,17 +30,76 @@ def run_analysis(analysis_id, commands, comm_opts=None,
               merge_duplicated_sample_ids)
 
 
-def create_raw_data(filetype, prep_template, filepaths):
+def create_raw_data(artifact_type, prep_template, filepaths, name=None):
     """Creates a new raw data
 
     Needs to be dispachable because it moves large files
+
+    Parameters
+    ----------
+    artifact_type: str
+        The artifact type
+    prep_template : qiita_db.metadata_template.prep_template.PrepTemplate
+        The template to attach the artifact
+    filepaths : list of (str, str)
+        The list with filepaths and their filepath types
+    name : str, optional
+        The name of the new artifact
+
+    Returns
+    -------
+    dict of {str: str}
+        A dict of the form {'status': str, 'message': str}
     """
-    Artifact.create(filepaths, filetype, prep_template=prep_template)
+    from qiita_db.artifact import Artifact
+
+    status = 'success'
+    msg = ''
+    try:
+        Artifact.create(filepaths, artifact_type, name=name,
+                        prep_template=prep_template)
+    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': 'danger',
+                'message': "Error creating artifact: %s" % str(e)}
+
+    return {'status': status, 'message': msg}
 
 
 def copy_raw_data(prep_template, artifact_id):
-    """Creates a new raw data by copying from artifact_id"""
-    Artifact.copy(Artifact(artifact_id), prep_template)
+    """Creates a new raw data by copying from artifact_id
+
+    Parameters
+    ----------
+    prep_template : qiita_db.metadata_template.prep_template.PrepTemplate
+        The template to attach the artifact
+    artifact_id : int
+        The id of the artifact to duplicate
+
+    Returns
+    -------
+    dict of {str: str}
+        A dict of the form {'status': str, 'message': str}
+    """
+    from qiita_db.artifact import Artifact
+
+    status = 'success'
+    msg = ''
+
+    try:
+        Artifact.copy(Artifact(artifact_id), prep_template)
+    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': 'danger',
+                'message': "Error creating artifact: %s" % str(e)}
+
+    return {'status': status, 'message': msg}
 
 
 def delete_artifact(artifact_id):

qiita_ware/test/test_dispatchable.py

@@ -14,10 +14,11 @@
 from qiita_core.util import qiita_test_checker
 from qiita_ware.dispatchable import (
     create_sample_template, update_sample_template, delete_sample_template,
-    update_prep_template, delete_artifact)
+    update_prep_template, delete_artifact, copy_raw_data, create_raw_data)
 from qiita_db.study import Study
 from qiita_db.artifact import Artifact
 from qiita_db.exceptions import QiitaDBUnknownIDError
+from qiita_db.metadata_template.prep_template import PrepTemplate
 
 
 @qiita_test_checker()
@@ -36,6 +37,22 @@ def tearDown(self):
             if exists(fp):
                 remove(fp)
 
+    def test_create_raw_data(self):
+        fps = {'raw_barcodes': 'uploaded_file.txt',
+               'raw_forward_seqs': 'update.txt'}
+        obs = create_raw_data("FASTQ", PrepTemplate(1), fps, name="New name")
+        exp = {'status': 'danger',
+               'message': "Error creating artifact: Prep template 1 already "
+                          "has an artifact associated"}
+        self.assertEqual(obs, exp)
+
+    def test_copy_raw_data(self):
+        obs = copy_raw_data(PrepTemplate(1), 1)
+        exp = {'status': 'danger',
+               'message': "Error creating artifact: Prep template 1 already "
+                          "has an artifact associated"}
+        self.assertEqual(obs, exp)
+
     def test_delete_artifact(self):
         obs = delete_artifact(1)
         exp = {'status': 'danger',