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Merge pull request #11762 from mvdbeek/assorted_tool_shed_fixes

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[21.01] Assorted tool shed fixes
This commit is contained in:
John Chilton
2021-04-01 10:46:38 -04:00
committed by GitHub
parent a6f3b255cb f0e299cb9b
commit 950856002f
7 changed files with 34 additions and 13 deletions
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lib/tool_shed/grids/repository_grids.py
+2 -1
View File
@@ -1,3 +1,4 @@
import json
import logging
from markupsafe import escape as escape_html
@@ -180,7 +181,7 @@ class RepositoryGrid(grids.Grid):
class EmailAlertsColumn(grids.TextColumn):
def get_value(self, trans, grid, repository):
if trans.user and trans.user.email in repository.email_alerts:
if trans.user and repository.email_alerts and trans.user.email in json.loads(repository.email_alerts):
return 'yes'
return ''
lib/tool_shed/util/commit_util.py
+3 -1
View File
@@ -1,5 +1,6 @@
import bz2
import gzip
import json
import logging
import os
import shutil
@@ -71,7 +72,8 @@ def check_file_contents_for_email_alerts(app):
admin_users = app.config.get("admin_users", "").split(",")
for repository in sa_session.query(app.model.Repository) \
.filter(app.model.Repository.table.c.email_alerts != null()):
for user_email in repository.email_alerts:
email_alerts = json.loads(repository.email_alerts)
for user_email in email_alerts:
if user_email in admin_users:
return True
return False
lib/tool_shed/util/shed_util_common.py
+1 -1
View File
@@ -385,7 +385,7 @@ def handle_email_alerts(app, host, repository, content_alert_str='', new_repo_al
email_alerts.append(user.email)
else:
subject = "Galaxy tool shed update alert for repository named %s" % str(repository.name)
email_alerts = repository.email_alerts
email_alerts = json.loads(repository.email_alerts)
for email in email_alerts:
to = email.strip()
# Send it
lib/tool_shed/webapp/controllers/repository.py
+23 -7
View File
@@ -1658,6 +1658,10 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
alerts = kwd.get('alerts', '')
alerts_checked = CheckboxField.is_checked(alerts)
category_ids = util.listify(kwd.get('category_id', ''))
if repository.email_alerts:
email_alerts = json.loads(repository.email_alerts)
else:
email_alerts = []
allow_push = kwd.get('allow_push', '')
error = False
user = trans.user
@@ -1710,12 +1714,14 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
elif kwd.get('receive_email_alerts_button', False):
flush_needed = False
if alerts_checked:
if user.email not in repository.email_alerts:
repository.email_alerts.append(user.email)
if user.email not in email_alerts:
email_alerts.append(user.email)
repository.email_alerts = json.dumps(email_alerts)
flush_needed = True
else:
if user.email in repository.email_alerts:
repository.email_alerts.remove(user.email)
if user.email in email_alerts:
email_alerts.remove(user.email)
repository.email_alerts = json.dumps(email_alerts)
flush_needed = True
if flush_needed:
trans.sa_session.add(repository)
@@ -1737,7 +1743,7 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
for obj in options:
label = obj.username
allow_push_select_field.add_option(label, trans.security.encode_id(obj.id))
checked = alerts_checked or user.email in repository.email_alerts
checked = alerts_checked or user.email in email_alerts
alerts_check_box = CheckboxField('alerts', value=checked)
changeset_revision_select_field = grids_util.build_changeset_revision_select_field(trans,
repository,
@@ -2267,14 +2273,19 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
flush_needed = False
for repository_id in repository_ids:
repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id)
email_alerts = repository.email_alerts
if repository.email_alerts:
email_alerts = json.loads(repository.email_alerts)
else:
email_alerts = []
if user.email in email_alerts:
email_alerts.remove(user.email)
repository.email_alerts = json.dumps(email_alerts)
trans.sa_session.add(repository)
flush_needed = True
total_alerts_removed += 1
else:
email_alerts.append(user.email)
repository.email_alerts = json.dumps(email_alerts)
trans.sa_session.add(repository)
flush_needed = True
total_alerts_added += 1
@@ -2557,7 +2568,10 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
display_reviews = kwd.get('display_reviews', False)
alerts = kwd.get('alerts', '')
alerts_checked = CheckboxField.is_checked(alerts)
email_alerts = repository.email_alerts
if repository.email_alerts:
email_alerts = json.loads(repository.email_alerts)
else:
email_alerts = []
repository_dependencies = None
user = trans.user
if user and kwd.get('receive_email_alerts_button', False):
@@ -2565,10 +2579,12 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
if alerts_checked:
if user.email not in email_alerts:
email_alerts.append(user.email)
repository.email_alerts = json.dumps(email_alerts)
flush_needed = True
else:
if user.email in email_alerts:
email_alerts.remove(user.email)
repository.email_alerts = json.dumps(email_alerts)
flush_needed = True
if flush_needed:
trans.sa_session.add(repository)
lib/tool_shed/webapp/model/__init__.py
+1 -1
View File
@@ -183,7 +183,7 @@ class Repository(Dictifiable, _HasTable):
dict_collection_visible_keys = ['id', 'name', 'type', 'remote_repository_url', 'homepage_url', 'description', 'user_id', 'private', 'deleted',
'times_downloaded', 'deprecated', 'create_time']
dict_element_visible_keys = ['id', 'name', 'type', 'remote_repository_url', 'homepage_url', 'description', 'long_description', 'user_id', 'private',
'deleted', 'times_downloaded', 'deprecated', 'create_time', 'ratings', 'reviews', 'reviewers']
'deleted', 'times_downloaded', 'deprecated', 'create_time']
file_states = Bunch(NORMAL='n',
NEEDS_MERGING='m',
MARKED_FOR_REMOVAL='r',
lib/tool_shed/webapp/model/mapping.py
+1 -1
View File
@@ -118,7 +118,7 @@ Repository.table = Table("repository", metadata,
Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
Column("private", Boolean, default=False),
Column("deleted", Boolean, index=True, default=False),
Column("email_alerts", JSONType, nullable=True, default=list),
Column("email_alerts", JSONType, nullable=True),
Column("times_downloaded", Integer),
Column("deprecated", Boolean, default=False))
lib/tool_shed/webapp/search/tool_search.py
+3 -1
View File
@@ -13,6 +13,7 @@ from whoosh.qparser import MultifieldParser
from galaxy import exceptions
from galaxy.exceptions import ObjectNotFound
from galaxy.util import unicodify
log = logging.getLogger(__name__)
@@ -82,7 +83,8 @@ class ToolSearch:
hit_dict['repo_name'] = hit.get('repo_name')
hit_dict['name'] = hit.get('name')
hit_dict['description'] = hit.get('description')
results['hits'].append({'tool': hit_dict, 'matched_terms': hit.matched_terms(), 'score': hit.score})
matched_terms = {k: unicodify(v) for k, v in hit.matched_terms()}
results['hits'].append({'tool': hit_dict, 'matched_terms': matched_terms, 'score': hit.score})
return results
finally:
searcher.close()