Analysis refactor gui part3 (#2078)

* 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

* Fixing typo

* Addressing @antgonza's comments

* Addressing @antgonza's comments

Author: josenavas

qiita_db/analysis.py

@@ -514,6 +514,26 @@ def pmid(self, pmid):
             qdb.sql_connection.TRN.add(sql, [pmid, self._id])
             qdb.sql_connection.TRN.execute()
 
+    @property
+    def can_be_publicized(self):
+        """Returns whether the analysis can be made public
+
+        Returns
+        -------
+        bool
+            Whether the analysis can be publicized or not
+        """
+        # The analysis can be made public if all the artifacts used
+        # to get the samples from are public
+        with qdb.sql_connection.TRN:
+            sql = """SELECT DISTINCT artifact_id
+                     FROM qiita.analysis_sample
+                     WHERE analysis_id = %s"""
+            qdb.sql_connection.TRN.add(sql, [self.id])
+            return all(
+                [qdb.artifact.Artifact(aid).visibility == 'public'
+                 for aid in qdb.sql_connection.TRN.execute_fetchflatten()])
+
     def add_artifact(self, artifact):
         """Adds an artifact to the analysis
 
@@ -570,6 +590,24 @@ def has_access(self, user):
             return self in Analysis.get_by_status('public') | \
                 user.private_analyses | user.shared_analyses
 
+    def can_edit(self, user):
+        """Returns whether the given user can edit the analysis
+
+        Parameters
+        ----------
+        user : User object
+            User we are checking edit permissions for
+
+        Returns
+        -------
+        bool
+            Whether user can edit the study or not
+        """
+        # The analysis is editable only if the user is the owner, is in the
+        # shared list or the user is an admin
+        return (user.level in {'superuser', 'admin'} or self.owner == user or
+                user in self.shared_with)
+
     def summary_data(self):
         """Return number of studies, artifacts, and samples selected
 

qiita_db/handlers/artifact.py

@@ -79,6 +79,7 @@ def get(self, artifact_id):
         """
         with qdb.sql_connection.TRN:
             artifact = _get_artifact(artifact_id)
+            study = artifact.study
             response = {
                 'name': artifact.name,
                 'timestamp': str(artifact.timestamp),
@@ -89,7 +90,7 @@ def get(self, artifact_id):
                 'can_be_submitted_to_vamps':
                     artifact.can_be_submitted_to_vamps,
                 'prep_information': [p.id for p in artifact.prep_templates],
-                'study': artifact.study.id}
+                'study': study.id if study else None}
             params = artifact.processing_parameters
             response['processing_parameters'] = (
                 params.values if params is not None else None)

qiita_db/test/test_analysis.py

@@ -125,6 +125,27 @@ def test_get_by_status(self):
         self.assertEqual(
             qdb.analysis.Analysis.get_by_status('public'), set([]))
 
+    def test_can_be_publicized(self):
+        analysis = qdb.analysis.Analysis(1)
+        self.assertFalse(analysis.can_be_publicized)
+        a4 = qdb.artifact.Artifact(4)
+        a5 = qdb.artifact.Artifact(5)
+        a6 = qdb.artifact.Artifact(6)
+
+        a4.visibility = 'public'
+        self.assertFalse(analysis.can_be_publicized)
+
+        a5.visibility = 'public'
+        self.assertFalse(analysis.can_be_publicized)
+
+        a6.visibility = 'public'
+        self.assertTrue(analysis.can_be_publicized)
+
+        a4.visibility = 'private'
+        a5.visibility = 'private'
+        a6.visibility = 'private'
+        self.assertFalse(analysis.can_be_publicized)
+
     def test_add_artifact(self):
         obs = self._create_analyses_with_samples()
         exp = qdb.artifact.Artifact(4)
@@ -162,6 +183,13 @@ def test_has_access_no_access(self):
         self.assertFalse(
             self.analysis.has_access(qdb.user.User("demo@microbio.me")))
 
+    def test_can_edit(self):
+        a = qdb.analysis.Analysis(1)
+        self.assertTrue(a.can_edit(qdb.user.User('test@foo.bar')))
+        self.assertTrue(a.can_edit(qdb.user.User('shared@foo.bar')))
+        self.assertTrue(a.can_edit(qdb.user.User('admin@foo.bar')))
+        self.assertFalse(a.can_edit(qdb.user.User('demo@microbio.me')))
+
     def test_create_nonqiita_portal(self):
         qiita_config.portal = "EMP"
         obs = qdb.analysis.Analysis.create(

qiita_pet/exceptions.py

@@ -7,9 +7,28 @@
 # -----------------------------------------------------------------------------
 
 from __future__ import division
+
+from tornado.web import HTTPError
+
 from qiita_core.exceptions import QiitaError
 
 
+class QiitaHTTPError(HTTPError):
+    def __init__(self, status_code=500, log_message=None, *args, **kwargs):
+        super(QiitaHTTPError, self).__init__(
+            status_code, log_message, *args, **kwargs)
+        # The HTTPError has an attribute named "reason" that will get send to
+        # the requester if specified. However, the developer need to
+        # specifically pass the keyword "reason" when raising the exception.
+        # The vast majority of our code it is not using the keyword "reason"
+        # but we are using "log_message". By setting up the attribute reason
+        # with the value in log_message, we make sure that when the answer
+        # is sent to the requester, it will contain a useful error message,
+        # rather than a generic error message.
+        if not self.reason:
+            self.reason = log_message
+
+
 class QiitaPetAuthorizationError(QiitaError):
     """When a user tries to access a resource without proper authorization"""
     def __init__(self, user_id, resource_name_str):

qiita_pet/handlers/analysis_handlers/tests/test_base_handlers.py

@@ -11,13 +11,15 @@
 
 from tornado.web import HTTPError
 
+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)
 
 
+@qiita_test_checker()
 class TestBaseHandlersUtils(TestCase):
     def test_analyisis_graph_handler_get_request(self):
         obs = analyisis_graph_handler_get_request(1, User('test@foo.bar'))

qiita_pet/handlers/artifact_handlers/__init__.py

@@ -0,0 +1,11 @@
+# -----------------------------------------------------------------------------
+# Copyright (c) 2014--, The Qiita Development Team.
+#
+# Distributed under the terms of the BSD 3-clause License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# -----------------------------------------------------------------------------
+
+from .base_handlers import ArtifactSummaryAJAX, ArtifactAJAX
+
+__all__ = ['ArtifactSummaryAJAX', 'ArtifactAJAX']