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Merge branch 'release_16.10' into dev

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This commit is contained in:
Nicola Soranzo
2016-12-05 18:11:39 +00:00
parent 982a35df08 622f299737
commit 5b1b191f2e
5 changed files with 103 additions and 25 deletions
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lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+7
View File
@@ -1112,6 +1112,11 @@ class AdminToolshed( AdminGalaxy ):
shed_tool_conf_select_field = tool_util.build_shed_tool_conf_select_field( trans.app )
tool_path = suc.get_tool_path_by_shed_tool_conf_filename( trans.app, shed_tool_conf )
tool_panel_section_select_field = tool_util.build_tool_panel_section_select_field( trans.app )
tool_requirements = suc.get_tool_shed_repo_requirements(app=trans.app,
tool_shed_url=tool_shed_url,
repo_info_dicts=repo_info_dicts)
view = views.DependencyResolversView(self.app)
requirements_status = view.get_requirements_status(tool_requirements)
if len( repo_info_dicts ) == 1:
# If we're installing or updating a single repository, see if it contains a readme or
# dependencies that we can display.
@@ -1230,6 +1235,7 @@ class AdminToolshed( AdminGalaxy ):
shed_tool_conf_select_field=shed_tool_conf_select_field,
tool_panel_section_select_field=tool_panel_section_select_field,
tool_shed_url=tool_shed_url,
requirements_status=requirements_status,
message=message,
status=status )
else:
@@ -1256,6 +1262,7 @@ class AdminToolshed( AdminGalaxy ):
shed_tool_conf_select_field=shed_tool_conf_select_field,
tool_panel_section_select_field=tool_panel_section_select_field,
tool_shed_url=tool_shed_url,
tool_requirements=tool_requirements,
message=message,
status=status )
lib/tool_shed/util/shed_util_common.py
+31 -14
View File
@@ -8,11 +8,15 @@ import string
import sqlalchemy.orm.exc
from sqlalchemy import and_, false, true
import tool_shed.util.repository_util
from galaxy import util
from galaxy.util import checkers
from galaxy.web import url_for
from tool_shed.util import basic_util, common_util, hg_util
from tool_shed.util import (
basic_util,
common_util,
hg_util,
repository_util
)
log = logging.getLogger( __name__ )
@@ -178,21 +182,34 @@ def get_category_by_name( app, name ):
return None
def get_tool_shed_repo_requirements(app, tool_shed_url, repository):
def get_tool_shed_repo_requirements(app, tool_shed_url, repositories=None, repo_info_dicts=None):
"""
Contact tool_shed_url for a list of requirements for a repository or a list of repositories.
Returns a list of requirements, where each requirement is a dictionary with name and version as keys.
"""
if not isinstance(repository, list):
repositories = [repository]
if not repositories and not repo_info_dicts:
raise Exception("Need to pass either repository or repo_info_dicts")
if repositories:
if not isinstance(repositories, list):
repositories = [repositories]
repository_params = [{'name': repository.name,
'owner': repository.owner,
'changeset_revision': repository.changeset_revision} for repository in repositories]
else:
repositories = repository
if not isinstance(repo_info_dicts, list):
repo_info_dicts = [repo_info_dicts]
repository_params = []
for repo_info_dict in repo_info_dicts:
for name, repo_info_tuple in repo_info_dict.items():
# repo_info_tuple is a list, but keep terminology
owner = repo_info_tuple[4]
changeset_revision = repo_info_tuple[2]
repository_params.append({'name': name,
'owner': owner,
'changeset_revision': changeset_revision})
pathspec = ["api", "repositories", "get_repository_revision_install_info"]
tools = []
for repository in repositories:
params = {"name": repository.name,
"owner": repository.owner,
"changeset_revision": repository.changeset_revision}
for params in repository_params:
response = util.url_get(tool_shed_url,
password_mgr=app.tool_shed_registry.url_auth( tool_shed_url ),
pathspec=pathspec,
@@ -355,7 +372,7 @@ def get_repository_from_refresh_on_change( app, **kwd ):
changeset_revision_str = 'changeset_revision_'
if k.startswith( changeset_revision_str ):
repository_id = app.security.encode_id( int( k.lstrip( changeset_revision_str ) ) )
repository = tool_shed.util.repository_util.get_repository_in_tool_shed( app, repository_id )
repository = repository_util.get_repository_in_tool_shed( app, repository_id )
if repository.tip( app ) != v:
return v, repository
# This should never be reached - raise an exception?
@@ -458,7 +475,7 @@ def handle_email_alerts( app, host, repository, content_alert_str='', new_repo_a
"""
sa_session = app.model.context.current
repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False )
sharable_link = tool_shed.util.repository_util.generate_sharable_link_for_repository_in_tool_shed( repository, changeset_revision=None )
sharable_link = repository_util.generate_sharable_link_for_repository_in_tool_shed( repository, changeset_revision=None )
smtp_server = app.config.smtp_server
if smtp_server and ( new_repo_alert or repository.email_alerts ):
# Send email alert to users that want them.
@@ -560,7 +577,7 @@ def is_path_within_repo( app, path, repository_id ):
Detect whether the given path is within the repository folder on the disk.
Use to filter malicious symlinks targeting outside paths.
"""
repo_path = os.path.abspath( tool_shed.util.repository_util.get_repository_by_id( app, repository_id ).repo_path( app ) )
repo_path = os.path.abspath( repository_util.get_repository_by_id( app, repository_id ).repo_path( app ) )
resolved_path = os.path.realpath( path )
return os.path.commonprefix( [ repo_path, resolved_path ] ) == repo_path
@@ -610,7 +627,7 @@ def set_image_paths( app, encoded_repository_id, text ):
return the path to it that will enable the caller to open the file.
"""
if text:
if tool_shed.util.repository_util.is_tool_shed_client( app ):
if repository_util.is_tool_shed_client( app ):
route_to_images = 'admin_toolshed/static/images/%s' % encoded_repository_id
else:
# We're in the tool shed.
templates/admin/tool_shed_repository/common.mako
+4 -2
View File
@@ -65,7 +65,7 @@
</script>
</%def>
<%def name="render_dependencies_section( install_resolver_dependencies_check_box, repository_dependencies_check_box, install_tool_dependencies_check_box, containers_dict, revision_label=None, export=False )">
<%def name="render_dependencies_section( install_resolver_dependencies_check_box, repository_dependencies_check_box, install_tool_dependencies_check_box, containers_dict, revision_label=None, export=False, requirements_status=None )">
<style type="text/css">
#dependency_table{ table-layout:fixed;
width:100%;
@@ -126,6 +126,8 @@
Display Details
</button>
</p>
<p>
</p>
</div>
%if export:
<div class="form-row">
@@ -216,7 +218,7 @@
</div>
%endif
<div style="clear: both"></div>
%if install_resolver_dependencies_check_box:
%if requirements_status and install_resolver_dependencies_check_box:
<div class="form-row">
<label>When available, install <a href="https://docs.galaxyproject.org/en/master/admin/conda_faq.html" target="_blank">Conda</a> managed tool dependencies?</label>
${install_resolver_dependencies_check_box.get_html()}
templates/admin/tool_shed_repository/select_tool_panel_section.mako
+38 -2
View File
@@ -65,6 +65,7 @@
<div class="form-row">
<input type="hidden" name="includes_tools" value="${includes_tools}" />
<input type="hidden" name="includes_tool_dependencies" value="${includes_tool_dependencies}" />
<input type="hidden" name="requirements_status" value="${requirements_status}" />
<input type="hidden" name="includes_tools_for_display_in_tool_panel" value="${includes_tools_for_display_in_tool_panel}" />
<input type="hidden" name="tool_shed_url" value="${tool_shed_url}" />
<input type="hidden" name="encoded_repo_info_dicts" value="${encoded_repo_info_dicts}" />
@@ -85,13 +86,48 @@
${render_readme_section( containers_dict )}
<div style="clear: both"></div>
%endif
%if can_display_repository_dependencies or can_display_tool_dependencies or can_display_resolver_installation:
<%
if requirements_status and install_resolver_dependencies_check_box or includes_tool_dependencies:
display_dependency_confirmation = True
else:
display_dependency_confirmation = False
%>
%if requirements_status:
%if not install_resolver_dependencies_check_box and not includes_tool_dependencies:
<div class="form-row">
<table class="colored" width="100%">
<head>
<th>
<img src="${h.url_for('/static')}/images/icon_error_sml.gif" title='Cannot install dependencies'/>
This repository requires dependencies that cannot be installed through the Tool Shed
</th>
</head>
</table>
</div>
<div class="form-row">
<p>This repository defines tool requirements that cannot be installed through the Tool Shed.</p>
<p>Please activate Conda dependency resolution, activate Docker dependency resolution, setup Environment Modules
or manually satisfy the dependencies listed below.</p>
<p>For details see <a target="_blank" href="https://docs.galaxyproject.org/en/latest/admin/dependency_resolvers.html">the dependency resolver documentation.</a></p>
</div>
%endif
<div class="form-row">
<table class="colored" width="100%">
<th bgcolor="#EBD9B2">The following tool dependencies are required by the current repository</th>
</table>
</div>
<div class="form-row">
${render_tool_dependency_resolver( requirements_status, prepare_for_install=True )}
</div>
<div style="clear: both"></div>
%endif
%if can_display_repository_dependencies or display_dependency_confirmation:
<div class="form-row">
<table class="colored" width="100%">
<th bgcolor="#EBD9B2">Confirm dependency installation</th>
</table>
</div>
${render_dependencies_section( install_resolver_dependencies_check_box, install_repository_dependencies_check_box, install_tool_dependencies_check_box, containers_dict, revision_label=None, export=False )}
${render_dependencies_section( install_resolver_dependencies_check_box, install_repository_dependencies_check_box, install_tool_dependencies_check_box, containers_dict, revision_label=None, export=False, requirements_status=requirements_status )}
<div style="clear: both"></div>
%endif
%if shed_tool_conf_select_field:
templates/webapps/tool_shed/repository/common.mako
+23 -7
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@@ -1026,7 +1026,7 @@
%>
</%def>
<%def name="render_tool_dependency_resolver( requirements_status )">
<%def name="render_tool_dependency_resolver( requirements_status, prepare_for_install=False )">
<tr class="datasetRow">
<td style="padding-left: 20 px;">
<table class="grid" id="module_resolver_environment">
@@ -1034,9 +1034,11 @@
<tr>
<th>Dependency</th>
<th>Version</th>
<th>Resolver</th>
<th>Exact version</th>
<th>Status<th>
%if not prepare_for_install:
<th>Resolver</th>
<th>Exact version</th>
%endif
<th>Current Installation Status<th>
</tr>
</head>
<body>
@@ -1044,18 +1046,32 @@
<tr>
<td>${dependency['name'] | h}</td>
<td>${dependency['version'] | h}</td>
<td>${dependency['dependency_type'] | h}</td>
<td>${dependency['exact'] | h}</td>
%if not prepare_for_install:
%if dependency['dependency_type']:
<td>${dependency['dependency_type'].title() | h}</td>
%else:
<td>${dependency['dependency_type'] | h}</td>
%endif
<td>${dependency['exact'] | h}</td>
%endif
%if dependency['dependency_type'] == None:
<td>
<img src="${h.url_for('/static')}/images/icon_error_sml.gif" title='Dependency not resolved'/>
%if prepare_for_install:
Not Installed
%endif
</td>
%elif not dependency['exact']:
<td>
<img src="${h.url_for('/static')}/images/icon_warning_sml.gif" title='Dependency resolved, but version ${dependency['version']} not found'/>
</td>
%else:
<td><img src="${h.url_for('/static')}/june_2007_style/blue/ok_small.png"/></td>
<td>
<img src="${h.url_for('/static')}/june_2007_style/blue/ok_small.png"/>
%if prepare_for_install:
Installed through ${dependency['dependency_type'].title() | h}
%endif
</td>
%endif
</tr>
%endfor