Portals artifacts

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

@@ -977,27 +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_pet/handlers/analysis_handlers.py

@@ -36,6 +36,7 @@
 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 +128,13 @@ 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,
@@ -206,7 +209,8 @@ 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 +275,8 @@ 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):

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):
@@ -77,7 +77,7 @@ 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):
@@ -91,7 +91,7 @@ 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
@@ -109,7 +109,7 @@ 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
@@ -141,4 +141,4 @@ 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)))

qiita_pet/handlers/study_handlers/edit_handlers.py

@@ -11,6 +11,7 @@
 from wtforms import (Form, StringField, SelectField, SelectMultipleField,
                      TextAreaField, validators)
 
+from qiita_core.qiita_settings import qiita_config
 from qiita_db.study import Study, StudyPerson
 from qiita_db.util import get_timeseries_types, get_environmental_packages
 from qiita_db.exceptions import QiitaDBUnknownIDError
@@ -261,18 +262,20 @@ def post(self, study=None):
             the_study.title = study_title
             the_study.info = info
 
-            msg = ('Study <a href="/study/description/%d">%s</a> '
+            msg = ('Study <a href="%s/study/description/%d">%s</a> '
                    'successfully updated' %
-                   (the_study.id, form_data.data['study_title'][0]))
+                   (qiita_config.portal_dir, the_study.id,
+                    form_data.data['study_title'][0]))
         else:
             # create the study
             # TODO: Fix this EFO once ontology stuff from emily is added
             the_study = Study.create(self.current_user, study_title,
                                      efo=[1], info=info)
 
-            msg = ('Study <a href="/study/description/%d">%s</a> '
+            msg = ('Study <a href="%s/study/description/%d">%s</a> '
                    'successfully created' %
-                   (the_study.id, form_data.data['study_title'][0]))
+                   (qiita_config.portal_dir, the_study.id,
+                    form_data.data['study_title'][0]))
 
         # Add the environmental packages, this attribute can only be edited
         # if the study is not public, otherwise this cannot be changed