WIP: Portals subdirectory

qiita_core/configuration_manager.py

@@ -105,6 +105,10 @@ class ConfigurationManager(object):
         The VAMPS URL
     conf_fp : str
         The filepath for the configuration file that is loaded
+    portal : str
+        The portal under the Qiita instance is running under
+    portal_dir : str
+        The portal subdirectory used in the URL
     portal_fp : str
         The filepath to the portal styling config file
     plugin_launcher : str
@@ -161,7 +165,6 @@ def _get_main(self, config):
                              self.working_dir)
         self.max_upload_size = config.getint('main', 'MAX_UPLOAD_SIZE')
         self.require_approval = config.getboolean('main', 'REQUIRE_APPROVAL')
-        self.portal = config.get('main', 'PORTAL')
         self.plugin_launcher = config.get('main', 'PLUGIN_LAUNCHER')
 
         self.valid_upload_extension = [ve.strip() for ve in config.get(
@@ -240,3 +243,12 @@ def _get_vamps(self, config):
 
     def _get_portal(self, config):
         self.portal_fp = config.get('portal', 'PORTAL_FP')
+        self.portal = config.get('portal', 'PORTAL')
+        self.portal_dir = config.get('portal', 'PORTAL_DIR')
+        if self.portal_dir:
+            if not self.portal_dir.startswith('/'):
+                self.portal_dir = "/%s" % self.portal_dir
+            if self.portal_dir.endswith('/'):
+                self.portal_dir = self.portal_dir[:-1]
+        else:
+            self.portal_dir = ""

qiita_core/support_files/config_test.cfg

@@ -39,9 +39,6 @@ BASE_DATA_DIR =
 # Valid upload extension, comma separated. Empty for no uploads
 VALID_UPLOAD_EXTENSION = fastq,fastq.gz,txt,tsv,sff,fna,qual
 
-# Portal the site is working under
-PORTAL = QIITA
-
 # Script used for launching plugins
 PLUGIN_LAUNCHER = qiita-plugin-launcher
 
@@ -144,5 +141,12 @@ URL = https://vamps.mbl.edu/mobe_workshop/getfile.php
 
 # ----------------------------- Portal settings -----------------------------
 [portal]
+
+# Portal the site is working under
+PORTAL = QIITA
+
+# Portal subdirectory
+PORTAL_DIR =
+
 # Full path to portal styling config file
 PORTAL_FP =

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])
@@ -981,27 +977,15 @@ def _build_mapping_file(self, samples, rename_dup_samples=False):
         """Builds the combined mapping file for all samples
            Code modified slightly from qiime.util.MetadataMap.__add__"""
         with qdb.sql_connection.TRN:
-            # query to get the latest qiime mapping file
-            sql = """SELECT filepath
-                     FROM qiita.filepath
-                        JOIN qiita.prep_template_filepath USING (filepath_id)
-                        JOIN qiita.prep_template USING (prep_template_id)
-                        JOIN qiita.filepath_type USING (filepath_type_id)
-                     WHERE filepath_type = 'qiime_map'
-                        AND artifact_id IN (SELECT *
-                                            FROM qiita.find_artifact_roots(%s))
-                     ORDER BY filepath_id DESC LIMIT 1"""
-            _, fp = qdb.util.get_mountpoint('templates')[0]
-
             all_ids = set()
             to_concat = []
             for aid, samps in viewitems(samples):
-                qdb.sql_connection.TRN.add(sql, [aid])
-                qm_fp = qdb.sql_connection.TRN.execute_fetchindex()[0][0]
+                qiime_map_fp = qdb.artifact.Artifact(
+                    aid).prep_templates[0].qiime_map_fp
 
                 # Parse the mapping file
                 qm = qdb.metadata_template.util.load_template_to_dataframe(
-                    join(fp, qm_fp), index='#SampleID')
+                    qiime_map_fp, index='#SampleID')
 
                 # if we are not going to merge the duplicated samples
                 # append the aid to the sample name

qiita_db/processing_job.py

@@ -306,9 +306,12 @@ def _generate_cmd(self):
         software = self.command.software
         plugin_start_script = software.start_script
         plugin_env_script = software.environment_script
+        # Appending the portal URL so the job requests the information from the
+        # portal server that submitted the job
+        url = "%s%s" % (qiita_config.base_url, qiita_config.portal_dir)
         cmd = '%s "%s" "%s" "%s" "%s" "%s"' % (
             qiita_config.plugin_launcher, plugin_env_script,
-            plugin_start_script, qiita_config.base_url, self.id, job_dir)
+            plugin_start_script, url, self.id, job_dir)
         return cmd
 
     def submit(self):

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

@@ -17,25 +17,29 @@
 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
 from qiita_db.logger import LogEntry
 from qiita_db.reference import Reference
 from qiita_core.util import execute_as_transaction
+from qiita_core.qiita_settings import qiita_config
 
 SELECT_SAMPLES = 2
 SELECT_COMMANDS = 3
@@ -127,11 +131,13 @@ def post(self, analysis_id):
         cmd_split = [x.split("#") for x in command_args]
 
         moi_user_id = get_id_from_user(self.current_user.id)
-        moi_group = create_info(analysis_id, 'group', url='/analysis/',
-                                parent=moi_user_id, store=True)
+        moi_group = create_info(
+            analysis_id, 'group', url='%s/analysis/' % qiita_config.portal_dir,
+            parent=moi_user_id, store=True)
         moi_name = ("Creating %s... When finished, please click the 'Success' "
                     "link to the right" % analysis.name)
-        moi_result_url = '/analysis/results/%d' % analysis_id
+        moi_result_url = '%s/analysis/results/%d' % (qiita_config.portal_dir,
+                                                     analysis_id)
 
         submit(ctx_default, moi_group['id'], moi_name,
                moi_result_url, run_analysis, analysis_id, cmd_split,
@@ -172,10 +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
@@ -206,7 +215,8 @@ def post(self, analysis_id):
             LogEntry.create('Runtime', "Couldn't remove analysis ID %d: %s" %
                             (analysis_id, e))
 
-        self.redirect(u"/analysis/show/?level=%s&message=%s" % (level, msg))
+        self.redirect(u"%s/analysis/show/?level=%s&message=%s"
+                      % (qiita_config.portal_dir, level, msg))
 
 
 class ShowAnalysesHandler(BaseHandler):
@@ -271,7 +281,8 @@ def post(self):
             LogEntry.create('Runtime', "Couldn't remove analysis ID %d: %s" %
                             (analysis_id, e))
 
-        self.redirect(u"/analysis/show/?level=%s&message=%s" % (level, msg))
+        self.redirect(u"%s/analysis/show/?level=%s&message=%s"
+                      % (qiita_config.portal_dir, level, msg))
 
 
 class ResultsHandler(StaticFileHandler, BaseHandler):
@@ -349,3 +360,50 @@ 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="%s/analysis/results/%d">\'%s\'</a> '
+                    'has been shared with you.' %
+                    (qiita_config.portal_dir, 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/auth_handlers.py

@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 from tornado.escape import url_escape, json_encode
 from tornado.web import HTTPError
 
@@ -46,19 +44,21 @@ def post(self):
             try:
                 send_email(username, "QIITA: Verify Email Address", "Please "
                            "click the following link to verify email address: "
-                           "%s/auth/verify/%s?email=%s"
-                           % (qiita_config.base_url, info['user_verify_code'],
-                              url_escape(username)))
+                           "%s/%s/auth/verify/%s?email=%s"
+                           % (qiita_config.base_url, qiita_config.portal_dir,
+                              info['user_verify_code'], url_escape(username)))
             except:
                 msg = ("Unable to send verification email. Please contact the "
                        "qiita developers at <a href='mailto:qiita-help"
                        "@gmail.com'>qiita-help@gmail.com</a>")
-                self.redirect(u"/?level=danger&message=" + url_escape(msg))
+                self.redirect(u"%s/?level=danger&message=%s"
+                              % (qiita_config.portal_dir, url_escape(msg)))
                 return
-            self.redirect(u"/")
+            self.redirect(u"%s/" % qiita_config.portal_dir)
         else:
             error_msg = u"?error=" + url_escape(msg)
-            self.redirect(u"/auth/create/" + error_msg)
+            self.redirect(u"%s/auth/create/%s"
+                          % (qiita_config.portal_dir, error_msg))
 
 
 class AuthVerifyHandler(BaseHandler):
@@ -78,7 +78,7 @@ def get(self, code):
 class AuthLoginHandler(BaseHandler):
     """user login, no page necessary"""
     def get(self):
-        self.redirect("/")
+        self.redirect("%s/" % qiita_config.portal_dir)
 
     @execute_as_transaction
     def post(self):
@@ -92,7 +92,7 @@ def post(self):
             if "auth/" not in self.request.headers['Referer']:
                 nextpage = self.request.headers['Referer']
             else:
-                nextpage = "/"
+                nextpage = "%s/" % qiita_config.portal_dir
 
         msg = ""
         # check the user level
@@ -110,7 +110,7 @@ def post(self):
             # means DB not available, so set maintenance mode and failover
             r_client.set("maintenance", "Database connection unavailable, "
                          "please try again later.")
-            self.redirect("/")
+            self.redirect("%s/" % qiita_config.portal_dir)
             return
 
         # Check the login information
@@ -142,4 +142,4 @@ class AuthLogoutHandler(BaseHandler):
     """Logout handler, no page necessary"""
     def get(self):
         self.clear_cookie("user")
-        self.redirect("/")
+        self.redirect("%s/" % qiita_config.portal_dir)

qiita_pet/handlers/compute.py

@@ -8,6 +8,7 @@
 from qiita_ware.context import submit
 from qiita_ware.dispatchable import create_raw_data, copy_raw_data
 from qiita_core.util import execute_as_transaction
+from qiita_core.qiita_settings import qiita_config
 from qiita_db.util import get_mountpoint
 from qiita_db.metadata_template.prep_template import PrepTemplate
 
@@ -23,7 +24,7 @@ def get(self, job_id):
             # TODO: something smart
             pass
 
-        self.redirect('/')
+        self.redirect('%s/' % qiita_config.portal_dir)
 
 
 class CreateRawData(BaseHandler):
@@ -82,5 +83,6 @@ def post(self):
         self.render('compute_wait.html',
                     job_id=job_id, title='Adding raw data',
                     completion_redirect=(
-                        '/study/description/%s?top_tab=prep_template_tab'
-                        '&sub_tab=%s' % (study_id, pt_id)))
+                        '%s/study/description/%s?top_tab=prep_template_tab'
+                        '&sub_tab=%s'
+                        % (qiita_config.portal_dir, study_id, pt_id)))