Analysis refactor gui part4 (#2079)

josenavas · antgonza · commit 937b13f8e020 · 2017-04-24T09:27:46.000-06:00
* fix #1505 * improving some GUI stuff * improving some GUI stuff - missing lines * addressing all comments * ready for review * fix #1987 * initial commit * requested changes * fix filter job list * Fixing server cert (#2051) * fix get_studies * flake8 * fix #503 * fix #2010 * fix #1913 * fix errors * addressing @josenavas comment * flake8 * fix #1010 * fix #1066 (#2058) * addressing @josenavas comments * fix #1961 * fix #1837 * Automatic jobs & new stats (#2057) * fix #814, fix #1636 * fixing error in test-env * fixing stats.html call * adding img * addressing @josenavas comments * rm for loops * addresssing @ElDeveloper comments * generalizing this functionality * fix #1816 * fix #1959 * addressing @josenavas comments * addressing @josenavas comments * fixing error * fixed? * addressing @josenavas comments * addressing @wasade comments * fix flake8 * generate biom and metadata release (#2066) * initial commit * adding portal * addressing @josenavas comments * pid -> qiita_artifact_id * addressing @josenavas comments * addressing @ElDeveloper comments * rm 50.sql * database changes to fix 969 * adding delete * addressing @josenavas comments * addressing @ElDeveloper comments * duh! * fix generate_biom_and_metadata_release (#2072) * fix generate_biom_and_metadata_release * addressing @ElDeveloper comment * Removing qiita ware code that will not be used anymore * Organizing the handlers and new analysis description page * Connecting the analysis creation and making interface responsive * Addressing @antgonza's comments * Initial artifact GUI refactor * Removing unused code * Adding can_edit call to the analysis * Fixing artifact rest API since not all artifacts have study * Adding can_be_publicized call to analysis * Adding QiitaHTTPError to handle errors gracefully * Adding safe_execution contextmanager * Fixing typo * Adding qiita test checker * Adapting some artifact handlers * Abstracting the graph reloading and adding some documentation * Fixing typo * Fixing changing artifact visibility * Fixing delete * Fixing artifact deletion
diff --git a/qiita_db/artifact.py b/qiita_db/artifact.py
@@ -571,6 +571,10 @@ def delete(cls, artifact_id):
             sql = "DELETE FROM qiita.study_artifact WHERE artifact_id = %s"
             qdb.sql_connection.TRN.add(sql, [artifact_id])
 
+            # Detach the artifact from the analysis_artifact table
+            sql = "DELETE FROM qiita.analysis_artifact WHERE artifact_id = %s"
+            qdb.sql_connection.TRN.add(sql, [artifact_id])
+
             # Delete the row in the artifact table
             sql = "DELETE FROM qiita.artifact WHERE artifact_id = %s"
             qdb.sql_connection.TRN.add(sql, [artifact_id])
diff --git a/qiita_db/test/test_artifact.py b/qiita_db/test/test_artifact.py
@@ -919,6 +919,21 @@ def test_delete(self):
         with self.assertRaises(qdb.exceptions.QiitaDBUnknownIDError):
             qdb.artifact.Artifact(test.id)
 
+        # Analysis artifact
+        parameters = qdb.software.Parameters.from_default_params(
+            qdb.software.DefaultParameters(1), {'input_data': 1})
+        test = qdb.artifact.Artifact.create(
+            self.filepaths_processed, "Demultiplexed",
+            parents=[qdb.artifact.Artifact(9)],
+            processing_parameters=parameters)
+
+        self._clean_up_files.extend(
+            [join(uploads_fp, basename(fp)) for _, fp, _ in test.filepaths])
+        qdb.artifact.Artifact.delete(test.id)
+
+        with self.assertRaises(qdb.exceptions.QiitaDBUnknownIDError):
+            qdb.artifact.Artifact(test.id)
+
     def test_delete_with_html(self):
         fd, html_fp = mkstemp(suffix=".html")
         close(fd)
diff --git a/qiita_pet/handlers/analysis_handlers/base_handlers.py b/qiita_pet/handlers/analysis_handlers/base_handlers.py
@@ -6,7 +6,10 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
+from json import loads
+
 from tornado.web import authenticated
+from moi import r_client
 
 from qiita_core.util import execute_as_transaction
 from qiita_core.qiita_settings import qiita_config
@@ -29,16 +32,49 @@ def post(self):
                       % (qiita_config.portal_dir, analysis.id))
 
 
+def analysis_description_handler_get_request(analysis_id, user):
+    """Returns the analysis information
+
+    Parameters
+    ----------
+    analysis_id : int
+        The analysis id
+    user : qiita_db.user.User
+        The user performing the request
+    """
+    analysis = Analysis(analysis_id)
+    check_analysis_access(user, analysis)
+
+    job_info = r_client.get("analysis_%s" % analysis.id)
+    alert_type = 'info'
+    alert_msg = ''
+    if job_info:
+        job_info = loads(job_info)
+        job_id = job_info['job_id']
+        if job_id:
+            redis_info = loads(r_client.get(job_id))
+            if redis_info['status_msg'] == 'running':
+                alert_msg = 'An artifact is being deleted from this analysis'
+            elif redis_info['return'] is not None:
+                alert_type = redis_info['return']['status']
+                alert_msg = redis_info['return']['message'].replace(
+                    '\n', '</br>')
+
+    return {'analysis_name': analysis.name,
+            'analysis_id': analysis.id,
+            'analysis_description': analysis.description,
+            'alert_type': alert_type,
+            'alert_msg': alert_msg}
+
+
 class AnalysisDescriptionHandler(BaseHandler):
     @authenticated
     @execute_as_transaction
     def get(self, analysis_id):
-        analysis = Analysis(analysis_id)
-        check_analysis_access(self.current_user, analysis)
+        res = analysis_description_handler_get_request(analysis_id,
+                                                       self.current_user)
 
-        self.render("analysis_description.html", analysis_name=analysis.name,
-                    analysis_id=analysis_id,
-                    analysis_description=analysis.description)
+        self.render("analysis_description.html", **res)
 
 
 def analyisis_graph_handler_get_request(analysis_id, user):
diff --git a/qiita_pet/handlers/analysis_handlers/tests/test_base_handlers.py b/qiita_pet/handlers/analysis_handlers/tests/test_base_handlers.py
@@ -7,20 +7,56 @@
 # -----------------------------------------------------------------------------
 
 from unittest import TestCase, main
-from json import loads
+from json import loads, dumps
 
 from tornado.web import HTTPError
+from moi import r_client
 
 from qiita_core.util import qiita_test_checker
 from qiita_db.user import User
 from qiita_db.analysis import Analysis
 from qiita_pet.test.tornado_test_base import TestHandlerBase
 from qiita_pet.handlers.analysis_handlers.base_handlers import (
-    analyisis_graph_handler_get_request)
+    analyisis_graph_handler_get_request,
+    analysis_description_handler_get_request)
 
 
 @qiita_test_checker()
 class TestBaseHandlersUtils(TestCase):
+    def tearDown(self):
+        r_client.flushdb()
+
+    def test_analysis_description_handler_get_request(self):
+        obs = analysis_description_handler_get_request(1, User('test@foo.bar'))
+        exp = {'analysis_name': 'SomeAnalysis',
+               'analysis_id': 1,
+               'analysis_description': 'A test analysis',
+               'alert_type': 'info',
+               'alert_msg': ''}
+        self.assertEqual(obs, exp)
+
+        r_client.set('analysis_1', dumps({'job_id': 'job_id'}))
+        r_client.set('job_id', dumps({'status_msg': 'running'}))
+        obs = analysis_description_handler_get_request(1, User('test@foo.bar'))
+        exp = {'analysis_name': 'SomeAnalysis',
+               'analysis_id': 1,
+               'analysis_description': 'A test analysis',
+               'alert_type': 'info',
+               'alert_msg': 'An artifact is being deleted from this analysis'}
+        self.assertEqual(obs, exp)
+
+        r_client.set('job_id', dumps(
+            {'status_msg': 'Success',
+             'return': {'status': 'danger',
+                        'message': 'Error deleting artifact'}}))
+        obs = analysis_description_handler_get_request(1, User('test@foo.bar'))
+        exp = {'analysis_name': 'SomeAnalysis',
+               'analysis_id': 1,
+               'analysis_description': 'A test analysis',
+               'alert_type': 'danger',
+               'alert_msg': 'Error deleting artifact'}
+        self.assertEqual(obs, exp)
+
     def test_analyisis_graph_handler_get_request(self):
         obs = analyisis_graph_handler_get_request(1, User('test@foo.bar'))
         # The job id is randomly generated in the test environment. Gather
diff --git a/qiita_pet/handlers/artifact_handlers/base_handlers.py b/qiita_pet/handlers/artifact_handlers/base_handlers.py
@@ -7,16 +7,24 @@
 # -----------------------------------------------------------------------------
 
 from os.path import basename
+from json import dumps
 
 from tornado.web import authenticated
+from moi import r_client
 
 from qiita_core.qiita_settings import qiita_config
 from qiita_pet.handlers.base_handlers import BaseHandler
 from qiita_pet.handlers.util import safe_execution
 from qiita_pet.exceptions import QiitaHTTPError
+from qiita_ware.context import safe_submit
+from qiita_ware.dispatchable import delete_artifact
 from qiita_db.artifact import Artifact
 from qiita_db.software import Command, Parameters
 from qiita_db.processing_job import ProcessingJob
+from qiita_db.util import get_visibilities
+
+
+PREP_TEMPLATE_KEY_FORMAT = 'prep_template_%s'
 
 
 def check_artifact_access(user, artifact):
@@ -131,7 +139,7 @@ def artifact_summary_get_request(user, artifact_id):
         # If the artifact is part of an analysis, we don't require admin
         # approval, and the artifact can be made public only if all the
         # artifacts used to create the initial artifact set are public
-        if analysis.can_be_publicized:
+        if analysis.can_be_publicized and visibility != 'public':
             buttons.append(btn_base % ('make public', 'public', 'Make public'))
 
     else:
@@ -145,13 +153,12 @@ def artifact_summary_get_request(user, artifact_id):
                 buttons.append(
                     btn_base % ('request approval for', 'awaiting_approval',
                                 'Request approval'))
-
-        elif user.level == 'admin' and visibility == 'awaiting_approval':
-            # The approve artifact button only appears if the user is an admin
-            # the artifact is waiting to be approvaed and the qiita config
-            # requires artifact approval
-            buttons.append(btn_base % ('approve', 'private',
-                                       'Approve artifact'))
+            elif user.level == 'admin' and visibility == 'awaiting_approval':
+                # The approve artifact button only appears if the user is an
+                # admin the artifact is waiting to be approvaed and the qiita
+                # config requires artifact approval
+                buttons.append(btn_base % ('approve', 'private',
+                                           'Approve artifact'))
 
         if visibility == 'private':
             # The make public button only appears if the artifact is private
@@ -206,8 +213,7 @@ def artifact_summary_get_request(user, artifact_id):
             'processing_jobs': processing_jobs,
             'summary': summary,
             'job': job_info,
-            'errored_jobs': errored_jobs
-            }
+            'errored_jobs': errored_jobs}
 
 
 def artifact_summary_post_request(user, artifact_id):
@@ -311,6 +317,23 @@ def artifact_patch_request(user, artifact_id, req_op, req_path, req_value=None,
         if attribute == 'name':
             artifact.name = req_value
             return
+        elif attribute == 'visibility':
+            if req_value not in get_visibilities():
+                raise QiitaHTTPError(400, 'Unknown visibility value: %s'
+                                          % req_value)
+            # Set the approval to private if needs approval and admin
+            if req_value == 'private':
+                if not qiita_config.require_approval:
+                    artifact.visibility = 'private'
+                # Set the approval to private if approval not required
+                elif user.level == 'admin':
+                    artifact.visibility = 'private'
+                # Trying to set approval without admin privileges
+                else:
+                    raise QiitaHTTPError(403, 'User does not have permissions '
+                                              'to approve change')
+            else:
+                artifact.visibility = req_value
         else:
             # We don't understand the attribute so return an error
             raise QiitaHTTPError(404, 'Attribute "%s" not found. Please, '
@@ -320,7 +343,40 @@ def artifact_patch_request(user, artifact_id, req_op, req_path, req_value=None,
                                   'supported operations: replace' % req_op)
 
 
+def artifact_post_req(user, artifact_id):
+    """Deletes the artifact
+
+    Parameters
+    ----------
+    user : qiita_db.user.User
+        The user requesting the action
+    artifact_id : int
+        Id of the artifact being deleted
+    """
+    artifact_id = int(artifact_id)
+    artifact = Artifact(artifact_id)
+    check_artifact_access(user, artifact)
+
+    analysis = artifact.analysis
+
+    if analysis:
+        # Do something when deleting in the analysis part to keep track of it
+        redis_key = "analysis_%s" % analysis.id
+    else:
+        pt_id = artifact.prep_templates[0].id
+        redis_key = PREP_TEMPLATE_KEY_FORMAT % pt_id
+
+    job_id = safe_submit(user.id, delete_artifact, artifact_id)
+    r_client.set(redis_key, dumps({'job_id': job_id, 'is_qiita_job': False}))
+
+
 class ArtifactAJAX(BaseHandler):
+    @authenticated
+    def post(self, artifact_id):
+        with safe_execution():
+            artifact_post_req(self.current_user, artifact_id)
+        self.finish()
+
     @authenticated
     def patch(self, artifact_id):
         """Patches a prep template in the system
diff --git a/qiita_pet/handlers/artifact_handlers/tests/test_base_handlers.py b/qiita_pet/handlers/artifact_handlers/tests/test_base_handlers.py
@@ -252,9 +252,10 @@ def test_artifact_summary_post_request(self):
 
     def test_artifact_patch_request(self):
         a = Artifact(1)
+        test_user = User('test@foo.bar')
         self.assertEqual(a.name, 'Raw data 1')
 
-        artifact_patch_request(User('test@foo.bar'), 1, 'replace', '/name/',
+        artifact_patch_request(test_user, 1, 'replace', '/name/',
                                req_value='NEW_NAME')
         self.assertEqual(a.name, 'NEW_NAME')
 
@@ -268,24 +269,44 @@ def test_artifact_patch_request(self):
 
         # Incorrect path parameter
         with self.assertRaises(QiitaHTTPError):
-            artifact_patch_request(User('test@foo.bar'), 1, 'replace',
+            artifact_patch_request(test_user, 1, 'replace',
                                    '/name/wrong/', req_value='NEW_NAME')
 
         # Missing value
         with self.assertRaises(QiitaHTTPError):
-            artifact_patch_request(User('test@foo.bar'), 1, 'replace',
-                                   '/name/')
+            artifact_patch_request(test_user, 1, 'replace', '/name/')
 
         # Wrong attribute
         with self.assertRaises(QiitaHTTPError):
-            artifact_patch_request(User('test@foo.bar'), 1, 'replace',
+            artifact_patch_request(test_user, 1, 'replace',
                                    '/wrong/', req_value='NEW_NAME')
 
         # Wrong operation
         with self.assertRaises(QiitaHTTPError):
-            artifact_patch_request(User('test@foo.bar'), 1, 'add', '/name/',
+            artifact_patch_request(test_user, 1, 'add', '/name/',
                                    req_value='NEW_NAME')
 
+        # Changing visibility
+        self.assertEqual(a.visibility, 'private')
+        artifact_patch_request(test_user, 1, 'replace', '/visibility/',
+                               req_value='sandbox')
+        self.assertEqual(a.visibility, 'sandbox')
+
+        # Admin can change to private
+        artifact_patch_request(User('admin@foo.bar'), 1, 'replace',
+                               '/visibility/', req_value='private')
+        self.assertEqual(a.visibility, 'private')
+
+        # Test user can't change to private
+        with self.assertRaises(QiitaHTTPError):
+            artifact_patch_request(test_user, 1, 'replace', '/visibility/',
+                                   req_value='private')
+
+        # Unkown req value
+        with self.assertRaises(QiitaHTTPError):
+            artifact_patch_request(test_user, 1, 'replace', '/visibility/',
+                                   req_value='wrong')
+
 
 class TestBaseHandlers(TestHandlerBase):
     def test_get_artifact_summary_ajax_handler(self):
diff --git a/qiita_pet/templates/analysis_description.html b/qiita_pet/templates/analysis_description.html
@@ -2,6 +2,29 @@
 {% block head %}
 <script type="text/javascript">
 
+  /**
+   *
+   * This function is needed by the artifact subsection of the page. Since the
+   * artifact can be either embedded in the analysis pipeline or in the study
+   * pipeline, we take advantage of the templating system to abstract the way
+   * the graph should be updated. In the analysis pipeline (current) the graph
+   * is reloaded by calling the update_graph function of the Vue component.
+   */
+  function reload_graph() {
+    $("#analysis-network-div").data('data-graph-vue').update_graph();
+  }
+
+  /**
+   *
+   * This function is needed by the artifact subsection of the page. After the
+   * artifact is sent for deletion, we need to reload the current page to
+   * update the UI.
+   *
+   */
+  function reload_UI_post_artifact_delete() {
+      location.reload();
+  }
+
   /**
    * Creates the HTML with the job information and adds it to `target`
    *
@@ -170,6 +193,9 @@
 
     // Add the vue object to the div, so we avoid to have global variables
     $("#analysis-network-div").data('data-graph-vue', vueGraph);
+    {% if alert_msg %}
+      bootstrapAlert("{{alert_msg}}", "{{alert_type}}");
+    {% end %}
   });
 </script>
 <style>
diff --git a/qiita_pet/templates/artifact_ajax/artifact_summary.html b/qiita_pet/templates/artifact_ajax/artifact_summary.html
diff --git a/qiita_pet/templates/study_ajax/prep_summary.html b/qiita_pet/templates/study_ajax/prep_summary.html
