Merge pull request #1768 from squirrelo/share-analyses

Share analyses

Author: antgonza

qiita_db/analysis.py

@@ -683,13 +683,11 @@ def share(self, user):
         user: User object
             The user to share the analysis with
         """
-        with qdb.sql_connection.TRN:
-            self._lock_check()
-
-            # Make sure the analysis is not already shared with the given user
-            if user.id in self.shared_with:
-                return
+        # Make sure the analysis is not already shared with the given user
+        if user.id == self.owner or user.id in self.shared_with:
+            return
 
+        with qdb.sql_connection.TRN:
             sql = """INSERT INTO qiita.analysis_users (analysis_id, email)
                      VALUES (%s, %s)"""
             qdb.sql_connection.TRN.add(sql, [self._id, user.id])
@@ -704,8 +702,6 @@ def unshare(self, user):
             The user to unshare the analysis with
         """
         with qdb.sql_connection.TRN:
-            self._lock_check()
-
             sql = """DELETE FROM qiita.analysis_users
                      WHERE analysis_id = %s AND email = %s"""
             qdb.sql_connection.TRN.add(sql, [self._id, user.id])

qiita_db/support_files/populate_test_db.sql

@@ -427,7 +427,7 @@ INSERT INTO qiita.job (data_type_id, job_status_id, command_id, options, input_f
 INSERT INTO qiita.job_results_filepath (job_id, filepath_id) VALUES (1, 13), (2, 14);
 
 -- Insert Analysis
-INSERT INTO qiita.analysis (email, name, description, analysis_status_id, pmid) VALUES ('test@foo.bar', 'SomeAnalysis', 'A test analysis', 1, '121112'), ('test@foo.bar', 'SomeSecondAnalysis', 'Another test analysis', 1, '22221112');
+INSERT INTO qiita.analysis (email, name, description, analysis_status_id, pmid) VALUES ('test@foo.bar', 'SomeAnalysis', 'A test analysis', 1, '121112'), ('admin@foo.bar', 'SomeSecondAnalysis', 'Another test analysis', 1, '22221112');
 INSERT INTO qiita.analysis_portal (analysis_id, portal_type_id) VALUES (1, 1), (2, 1);
 -- Insert Analysis Workflow
 INSERT INTO qiita.analysis_workflow (analysis_id, step) VALUES (1, 3), (2, 3);

qiita_db/test/test_user.py

@@ -261,7 +261,7 @@ def test_get_shared_studies(self):
     def test_get_private_analyses(self):
         user = qdb.user.User('test@foo.bar')
         qiita_config.portal = "QIITA"
-        exp = {qdb.analysis.Analysis(1), qdb.analysis.Analysis(2)}
+        exp = {qdb.analysis.Analysis(1)}
         self.assertEqual(user.private_analyses, exp)
 
         qiita_config.portal = "EMP"

qiita_pet/handlers/analysis_handlers.py

@@ -17,19 +17,22 @@
 from functools import partial
 
 from tornado.web import authenticated, HTTPError, StaticFileHandler
+from tornado.gen import coroutine, Task
 from moi import ctx_default, r_client
 from moi.job import submit
 from moi.group import get_id_from_user, create_info
 
 from qiita_pet.util import is_localhost
 from qiita_pet.handlers.base_handlers import BaseHandler
-from qiita_pet.handlers.util import download_link_or_path
+from qiita_pet.handlers.util import (
+    download_link_or_path, get_shared_links)
 from qiita_pet.exceptions import QiitaPetAuthorizationError
 from qiita_ware.dispatchable import run_analysis
 from qiita_db.analysis import Analysis
 from qiita_db.artifact import Artifact
 from qiita_db.job import Command
-from qiita_db.util import (get_db_files_base_dir,
+from qiita_db.user import User
+from qiita_db.util import (get_db_files_base_dir, add_message,
                            check_access_to_analysis_result,
                            filepath_ids_to_rel_paths, get_filepath_id)
 from qiita_db.exceptions import QiitaDBUnknownIDError
@@ -175,10 +178,13 @@ def get(self, analysis_id):
             data_type = proc_data.data_type
             dropped[data_type].append((proc_data.study.title, len(samples),
                                        ', '.join(samples)))
+        share_access = (self.current_user.id in analysis.shared_with or
+                        self.current_user.id == analysis.owner)
 
         self.render("analysis_results.html", analysis_id=analysis_id,
                     jobres=jobres, aname=analysis.name, dropped=dropped,
-                    basefolder=get_db_files_base_dir())
+                    basefolder=get_db_files_base_dir(),
+                    share_access=share_access)
 
     @authenticated
     @execute_as_transaction
@@ -354,3 +360,49 @@ class AnalysisSummaryAJAX(BaseHandler):
     def get(self):
         info = self.current_user.default_analysis.summary_data()
         self.write(dumps(info))
+
+
+class ShareAnalysisAJAX(BaseHandler):
+    @execute_as_transaction
+    def _get_shared_for_study(self, analysis, callback):
+        shared_links = get_shared_links(analysis)
+        users = [u.email for u in analysis.shared_with]
+        callback((users, shared_links))
+
+    @execute_as_transaction
+    def _share(self, analysis, user, callback):
+        user = User(user)
+        add_message('Analysis <a href="/analysis/results/%d">\'%s\'</a> '
+                    'has been shared with you.' %
+                    (analysis.id, analysis.name), [user])
+        callback(analysis.share(user))
+
+    @execute_as_transaction
+    def _unshare(self, analysis, user, callback):
+        user = User(user)
+        add_message('Analysis \'%s\' has been unshared from you.' %
+                    analysis.name, [user])
+        callback(analysis.unshare(user))
+
+    @authenticated
+    @coroutine
+    @execute_as_transaction
+    def get(self):
+        analysis_id = int(self.get_argument('id'))
+        analysis = Analysis(analysis_id)
+        if self.current_user != analysis.owner:
+            raise HTTPError(403, 'User %s does not have permissions to share '
+                            'analysis %s' % (
+                                self.current_user.id, analysis.id))
+
+        selected = self.get_argument('selected', None)
+        deselected = self.get_argument('deselected', None)
+
+        if selected is not None:
+            yield Task(self._share, analysis, selected)
+        if deselected is not None:
+            yield Task(self._unshare, analysis, deselected)
+
+        users, links = yield Task(self._get_shared_for_study, analysis)
+
+        self.write(dumps({'users': users, 'links': links}))

qiita_pet/handlers/study_handlers/listing_handlers.py

@@ -23,28 +23,13 @@
 from qiita_db.logger import LogEntry
 from qiita_db.exceptions import QiitaDBIncompatibleDatatypeError
 from qiita_db.reference import Reference
-from qiita_db.util import get_pubmed_ids_from_dois
+from qiita_db.util import get_pubmed_ids_from_dois, add_message
 from qiita_core.exceptions import IncompetentQiitaDeveloperError
 from qiita_core.util import execute_as_transaction
 from qiita_pet.handlers.base_handlers import BaseHandler
 from qiita_pet.handlers.util import (
-    study_person_linkifier, doi_linkifier, pubmed_linkifier, check_access)
-
-
-@execute_as_transaction
-def _get_shared_links_for_study(study):
-    shared = []
-    for person in study.shared_with:
-        name = person.info['name']
-        email = person.email
-        # Name is optional, so default to email if non existant
-        if name:
-            shared.append(study_person_linkifier(
-                (email, name)))
-        else:
-            shared.append(study_person_linkifier(
-                (email, email)))
-    return ", ".join(shared)
+    study_person_linkifier, doi_linkifier, pubmed_linkifier, check_access,
+    get_shared_links)
 
 
 @execute_as_transaction
@@ -83,7 +68,7 @@ def _build_single_study_info(study, info, study_proc, proc_samples):
         info['pmid'] = ""
     if info["number_samples_collected"] is None:
         info["number_samples_collected"] = 0
-    info["shared"] = _get_shared_links_for_study(study)
+    info["shared"] = get_shared_links(study)
     # raw data is any artifact that is not Demultiplexed or BIOM
 
     info["num_raw_data"] = len([a for a in study.artifacts()
@@ -258,25 +243,30 @@ def get(self):
 class ShareStudyAJAX(BaseHandler):
     @execute_as_transaction
     def _get_shared_for_study(self, study, callback):
-        shared_links = _get_shared_links_for_study(study)
+        shared_links = get_shared_links(study)
         users = [u.email for u in study.shared_with]
         callback((users, shared_links))
 
     @execute_as_transaction
     def _share(self, study, user, callback):
         user = User(user)
+        add_message('Study <a href="/study/description/%d">\'%s\'</a> '
+                    'has been shared with you.' %
+                    (study.id, study.title), [user])
         callback(study.share(user))
 
     @execute_as_transaction
     def _unshare(self, study, user, callback):
         user = User(user)
+        add_message('Study \'%s\' has been unshared from you.' %
+                    study.title, [user])
         callback(study.unshare(user))
 
     @authenticated
     @coroutine
     @execute_as_transaction
     def get(self):
-        study_id = int(self.get_argument('study_id'))
+        study_id = int(self.get_argument('id'))
         study = Study(study_id)
         check_access(self.current_user, study, no_public=True,
                      raise_error=True)

qiita_pet/handlers/study_handlers/tests/test_listing_handlers.py

@@ -18,8 +18,7 @@
 from qiita_db.user import User
 from qiita_pet.test.tornado_test_base import TestHandlerBase
 from qiita_pet.handlers.study_handlers.listing_handlers import (
-    _get_shared_links_for_study, _build_study_info, _build_single_study_info,
-    _build_single_proc_data_info)
+    _build_study_info, _build_single_study_info, _build_single_proc_data_info)
 from qiita_pet.handlers.base_handlers import BaseHandler
 
 
@@ -135,11 +134,6 @@ def setUp(self):
         }
         self.exp = [self.single_exp]
 
-    def test_get_shared_links_for_study(self):
-        obs = _get_shared_links_for_study(Study(1))
-        exp = '<a target="_blank" href="mailto:shared@foo.bar">Shared</a>'
-        self.assertEqual(obs, exp)
-
     def test_build_single_study_info(self):
         study_proc = {1: {'18S': [4, 5, 6]}}
         proc_samples = {4: self.proc_data_exp[0]['samples'],
@@ -237,18 +231,23 @@ class TestShareStudyAjax(TestHandlerBase):
     def test_get_deselected(self):
         s = Study(1)
         u = User('shared@foo.bar')
-        args = {'deselected': u.id, 'study_id': s.id}
+        args = {'deselected': u.id, 'id': s.id}
         self.assertEqual(s.shared_with, [u])
         response = self.get('/study/sharing/', args)
         self.assertEqual(response.code, 200)
         exp = {'users': [], 'links': ''}
         self.assertEqual(loads(response.body), exp)
         self.assertEqual(s.shared_with, [])
 
+        # Make sure unshared message added to the system
+        self.assertEqual('Study \'Identification of the Microbiomes for '
+                         'Cannabis Soils\' has been unshared from you.',
+                         u.messages()[0][1])
+
     def test_get_selected(self):
         s = Study(1)
         u = User('admin@foo.bar')
-        args = {'selected': u.id, 'study_id': s.id}
+        args = {'selected': u.id, 'id': s.id}
         response = self.get('/study/sharing/', args)
         self.assertEqual(response.code, 200)
         exp = {
@@ -259,6 +258,12 @@ def test_get_selected(self):
         self.assertEqual(loads(response.body), exp)
         self.assertEqual(s.shared_with, [User('shared@foo.bar'), u])
 
+        # Make sure shared message added to the system
+        self.assertEqual('Study <a href="/study/description/1">'
+                         '\'Identification of the Microbiomes for Cannabis '
+                         'Soils\'</a> has been shared with you.',
+                         u.messages()[0][1])
+
     def test_get_no_access(self):
         # Create a new study belonging to the 'shared' user, so 'test' doesn't
         # have access
@@ -275,7 +280,7 @@ def test_get_no_access(self):
         s = Study.create(u, 'test_study', efo=[1], info=info)
         self.assertEqual(s.shared_with, [])
 
-        args = {'selected': 'test@foo.bar', 'study_id': s.id}
+        args = {'selected': 'test@foo.bar', 'id': s.id}
         response = self.get('/study/sharing/', args)
         self.assertEqual(response.code, 403)
         self.assertEqual(s.shared_with, [])

qiita_pet/handlers/util.py

@@ -89,3 +89,32 @@ def to_int(value):
     except ValueError:
         raise HTTPError(400, "%s cannot be converted to an integer" % value)
     return res
+
+
+@execute_as_transaction
+def get_shared_links(obj):
+    """Creates email links for the users obj is shared with
+
+    Parameters
+    ----------
+    obj : QiitaObject
+        A qiita object with a 'shared_with' property that returns a list of
+        User objects
+
+    Returns
+    -------
+    str
+        Email links for each person obj is shared with
+    """
+    shared = []
+    for person in obj.shared_with:
+        name = person.info['name']
+        email = person.email
+        # Name is optional, so default to email if non existant
+        if name:
+            shared.append(study_person_linkifier(
+                (email, name)))
+        else:
+            shared.append(study_person_linkifier(
+                (email, email)))
+    return ", ".join(shared)

qiita_pet/static/js/sharing.js

@@ -1,5 +1,3 @@
-var current_study = null;
-
 $(document).ready(function () {
   $('#shares-select').select2({
     ajax: {
@@ -18,18 +16,18 @@ $(document).ready(function () {
   });
 
   $('#shares-select').on("select2:select", function (e) {
-    update_share({selected: e.params.data.text});
+    update_share(e.target.classList[0], {selected: e.params.data.text});
   });
 
   $('#shares-select').on("select2:unselect", function (e) {
-    update_share({deselected: e.params.data.text});
+    update_share(e.target.classList[0], {deselected: e.params.data.text});
   });
 });
 
-function modify_sharing(study_id) {
-var shared_list;
-current_study = study_id;
-$.get('/study/sharing/', {study_id: study_id})
+function modify_sharing(share_type, id) {
+  var shared_list;
+  $('#shares-select').attr('data-current-id', id);
+  $.get('/' + share_type + '/sharing/', {id: id})
     .done(function(data) {
       var users_links = JSON.parse(data);
       var users = users_links.users;
@@ -43,13 +41,14 @@ $.get('/study/sharing/', {study_id: study_id})
     });
 }
 
-function update_share(params) {
+function update_share(share_type, params) {
+  share_id = $('#shares-select').attr('data-current-id');
   data = params || {};
-  data.study_id = current_study;
-  $.get('/study/sharing/', data)
+  data.id = share_id;
+  $.get('/' + share_type + '/sharing/', data)
     .done(function(data) {
       users_links = JSON.parse(data);
       links = users_links.links;
-      $("#shared_html_"+current_study).html(links);
+      $("#shared_html_"+share_id).html(links);
     });
 }