From aaf9aa7fa4414f74faba508a9c4bd280860298f5 Mon Sep 17 00:00:00 2001 From: janani Date: Sat, 13 Jul 2019 16:27:21 +0200 Subject: [PATCH 01/60] Issue#8105: Make tool favourite query a toggle - The favourite button has been changed to toggle between clearing the search and showing the favourites --- .../galaxy/scripts/entry/panels/tool-panel.js | 18 +++++++++++++++--- 1 file changed, 15 insertions(+), 3 deletions(-) diff --git a/client/galaxy/scripts/entry/panels/tool-panel.js b/client/galaxy/scripts/entry/panels/tool-panel.js index 47b1ab4cfbe..4c0798608a6 100644 --- a/client/galaxy/scripts/entry/panels/tool-panel.js +++ b/client/galaxy/scripts/entry/panels/tool-panel.js @@ -52,9 +52,21 @@ const ToolPanel = Backbone.View.extend({ title: _l("Show favorites"), icon: "fa fa-star-o", onclick: e => { - $("#tool-search-query") - .val("#favorites") - .trigger("change"); + $(".panel-header-button .fa").toggleClass("fa-star-o fa-star"); + //hide the tooltip + $(".panel-header-button").tooltip('hide'); + if($("#tool-search-query").val().indexOf("#favorites")!= -1) + { + $("#tool-search-query").val(""); + $("#tool-search-query").keyup(); + $(".panel-header-button").attr("title",""); + } + else + { + $("#tool-search-query") + .val("#favorites") + .trigger("change"); + } } }); panel_buttons.push(this.favorite_button); From 6e1504b0df503d2c5c945a6cd8b4816bdd891493 Mon Sep 17 00:00:00 2001 From: janani Date: Wed, 17 Jul 2019 02:48:39 +0200 Subject: [PATCH 02/60] Code updated for Issue#8105: Make tool favourite query a toggle --- .../galaxy/scripts/entry/panels/tool-panel.js | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/client/galaxy/scripts/entry/panels/tool-panel.js b/client/galaxy/scripts/entry/panels/tool-panel.js index 4c0798608a6..eb133b53fae 100644 --- a/client/galaxy/scripts/entry/panels/tool-panel.js +++ b/client/galaxy/scripts/entry/panels/tool-panel.js @@ -52,20 +52,21 @@ const ToolPanel = Backbone.View.extend({ title: _l("Show favorites"), icon: "fa fa-star-o", onclick: e => { + var search_query = $("#tool-search-query"); + var header_btn = $(".panel-header-button"); $(".panel-header-button .fa").toggleClass("fa-star-o fa-star"); //hide the tooltip - $(".panel-header-button").tooltip('hide'); - if($("#tool-search-query").val().indexOf("#favorites")!= -1) + header_btn.tooltip('hide'); + if(search_query.val().indexOf("#favorites")!= -1) { - $("#tool-search-query").val(""); - $("#tool-search-query").keyup(); - $(".panel-header-button").attr("title",""); + search_query.val(""); + search_query.keyup(); + header_btn.attr("title",""); } else { - $("#tool-search-query") - .val("#favorites") - .trigger("change"); + search_query.val("#favorites").trigger("change"); + } } }); From 079c6586b3cfbda9eb0290652f5b3c51edd3d91a Mon Sep 17 00:00:00 2001 From: janani Date: Wed, 17 Jul 2019 14:30:18 +0200 Subject: [PATCH 03/60] Code updated for Issue#8105: Make tool favourite query a toggle --- client/galaxy/scripts/entry/panels/tool-panel.js | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/client/galaxy/scripts/entry/panels/tool-panel.js b/client/galaxy/scripts/entry/panels/tool-panel.js index eb133b53fae..4753209dfd3 100644 --- a/client/galaxy/scripts/entry/panels/tool-panel.js +++ b/client/galaxy/scripts/entry/panels/tool-panel.js @@ -52,8 +52,8 @@ const ToolPanel = Backbone.View.extend({ title: _l("Show favorites"), icon: "fa fa-star-o", onclick: e => { - var search_query = $("#tool-search-query"); - var header_btn = $(".panel-header-button"); + const search_query = $("#tool-search-query"); + const header_btn = $(".panel-header-button"); $(".panel-header-button .fa").toggleClass("fa-star-o fa-star"); //hide the tooltip header_btn.tooltip('hide'); @@ -66,7 +66,6 @@ const ToolPanel = Backbone.View.extend({ else { search_query.val("#favorites").trigger("change"); - } } }); From b7cb02664ec9ba3d6610ca7387fb70cf75d19249 Mon Sep 17 00:00:00 2001 From: will Date: Mon, 22 Jul 2019 14:18:13 -0400 Subject: [PATCH 04/60] Use bootstrap classes to fix css issue --- client/galaxy/scripts/mvc/ui/ui-select-content.js | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/client/galaxy/scripts/mvc/ui/ui-select-content.js b/client/galaxy/scripts/mvc/ui/ui-select-content.js index d9baa250c59..a913a806434 100644 --- a/client/galaxy/scripts/mvc/ui/ui-select-content.js +++ b/client/galaxy/scripts/mvc/ui/ui-select-content.js @@ -346,7 +346,6 @@ const View = Backbone.View.extend({ this.button_dialog = new Ui.Button({ icon: "fa-folder-open-o", tooltip: "Browse Datasets", - cls: "ml-2", onclick: () => { const current = this.model.get("current"); const cnf = this.config[current]; @@ -364,10 +363,10 @@ const View = Backbone.View.extend({ }); // append views - const $fields = $("
").addClass("w-100"); + const $fields = $("
").addClass("flex-fill"); this.$el .empty() - .addClass("d-flex flex-row") + .addClass("d-flex flex-row flex-wrap") .append($("
").append(this.button_type.$el)) .append($fields) .append($("
").append(this.button_dialog.$el)); From 924dedd734eae4efad1ba7dbfbb54619922383da Mon Sep 17 00:00:00 2001 From: will Date: Mon, 22 Jul 2019 14:24:24 -0400 Subject: [PATCH 05/60] add right margin for form field --- client/galaxy/scripts/mvc/ui/ui-select-content.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/client/galaxy/scripts/mvc/ui/ui-select-content.js b/client/galaxy/scripts/mvc/ui/ui-select-content.js index a913a806434..c26745fcc43 100644 --- a/client/galaxy/scripts/mvc/ui/ui-select-content.js +++ b/client/galaxy/scripts/mvc/ui/ui-select-content.js @@ -363,7 +363,7 @@ const View = Backbone.View.extend({ }); // append views - const $fields = $("
").addClass("flex-fill"); + const $fields = $("
").addClass("flex-fill mr-2"); this.$el .empty() .addClass("d-flex flex-row flex-wrap") From ae535f83075f50aebe05a73a9c175d56cbd24a71 Mon Sep 17 00:00:00 2001 From: guerler Date: Wed, 24 Jul 2019 15:52:22 -0400 Subject: [PATCH 06/60] Identify visualization static path from absolute path --- lib/galaxy/visualization/plugins/plugin.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/lib/galaxy/visualization/plugins/plugin.py b/lib/galaxy/visualization/plugins/plugin.py index ee51b2fbd5d..e0f5d494dee 100644 --- a/lib/galaxy/visualization/plugins/plugin.py +++ b/lib/galaxy/visualization/plugins/plugin.py @@ -5,6 +5,7 @@ from a query string and render a webpage based on those data. import copy import logging import os +import re import mako.lookup @@ -72,7 +73,7 @@ class VisualizationPlugin(ServesTemplatesPluginMixin): self.config = config base_url = context.get('base_url', '') self.base_url = '/'.join([base_url, self.name]) if base_url else self.name - self.static_path = os.path.join(self.path.replace('./config', './static'), 'static') + self.static_path = self._get_static_path(self.path) if os.path.exists(os.path.join(self.static_path, 'logo.png')): self.config['logo'] = '/'.join([self.static_path, 'logo.png']) template_cache_dir = context.get('template_cache_dir', None) @@ -127,6 +128,12 @@ class VisualizationPlugin(ServesTemplatesPluginMixin): return url_for(controller='visualization', action=self.name) return url_for('visualization_plugin', visualization_name=self.name) + def _get_static_path(self, path): + match = re.match(r'.*/config/(.*)', path) + if match: + return os.path.join('./static', match.group(1), 'static') + return None + def _get_saved_visualization_config(self, visualization, revision=None, **kwargs): """ Return the config of a saved visualization and revision. From 58d4bea616239714f9bb52868ea4d151a8011921 Mon Sep 17 00:00:00 2001 From: will Date: Wed, 24 Jul 2019 18:58:50 -0400 Subject: [PATCH 07/60] add margin in between ui select buttons when they wrap vertically --- client/galaxy/scripts/mvc/ui/ui-select-content.js | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/client/galaxy/scripts/mvc/ui/ui-select-content.js b/client/galaxy/scripts/mvc/ui/ui-select-content.js index c26745fcc43..79e37e73886 100644 --- a/client/galaxy/scripts/mvc/ui/ui-select-content.js +++ b/client/galaxy/scripts/mvc/ui/ui-select-content.js @@ -335,7 +335,7 @@ const View = Backbone.View.extend({ this.button_type = new Ui.RadioButton.View({ value: this.model.get("current"), data: this.button_data, - cls: "mr-2", + cls: "mr-2 mt-2", onchange: function(value) { self.model.set("current", value); self.trigger("change"); @@ -346,6 +346,7 @@ const View = Backbone.View.extend({ this.button_dialog = new Ui.Button({ icon: "fa-folder-open-o", tooltip: "Browse Datasets", + cls: "mt-2", onclick: () => { const current = this.model.get("current"); const cnf = this.config[current]; @@ -363,10 +364,10 @@ const View = Backbone.View.extend({ }); // append views - const $fields = $("
").addClass("flex-fill mr-2"); + const $fields = $("
").addClass("flex-fill mr-2 mt-2"); this.$el .empty() - .addClass("d-flex flex-row flex-wrap") + .addClass("d-flex flex-row flex-wrap mt-n2") .append($("
").append(this.button_type.$el)) .append($fields) .append($("
").append(this.button_dialog.$el)); From 31e99a932e0280d08bc6d935f3df8b0e5b47a896 Mon Sep 17 00:00:00 2001 From: guerler Date: Wed, 24 Jul 2019 20:54:45 -0400 Subject: [PATCH 08/60] Validate static path before joining path extensions --- lib/galaxy/visualization/plugins/plugin.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/visualization/plugins/plugin.py b/lib/galaxy/visualization/plugins/plugin.py index e0f5d494dee..d033c424f77 100644 --- a/lib/galaxy/visualization/plugins/plugin.py +++ b/lib/galaxy/visualization/plugins/plugin.py @@ -74,7 +74,7 @@ class VisualizationPlugin(ServesTemplatesPluginMixin): base_url = context.get('base_url', '') self.base_url = '/'.join([base_url, self.name]) if base_url else self.name self.static_path = self._get_static_path(self.path) - if os.path.exists(os.path.join(self.static_path, 'logo.png')): + if self.static_path and os.path.exists(os.path.join(self.static_path, 'logo.png')): self.config['logo'] = '/'.join([self.static_path, 'logo.png']) template_cache_dir = context.get('template_cache_dir', None) additional_template_paths = context.get('additional_template_paths', []) From 27971c094374764f916b649fe05fde0d93e289f5 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Thu, 25 Jul 2019 13:33:26 +0200 Subject: [PATCH 09/60] Fix exception thrown with invalid session key Move session lookup into try/except, user will then just get a new session. Fixes ``` 127.0.0.1 - - [25/Jul/2019:13:24:23 +0200] "GET / HTTP/1.1" 500 - "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_13_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/75.0.3770.142 Safari/537.36" Traceback (most recent call last): File "lib/galaxy/web/framework/middleware/error.py", line 154, in __call__ app_iter = self.application(environ, sr_checker) File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "lib/galaxy/web/framework/base.py", line 143, in __call__ return self.handle_request(environ, start_response) File "lib/galaxy/web/framework/base.py", line 199, in handle_request trans = self.transaction_factory(environ) File "lib/galaxy/web/framework/webapp.py", line 82, in self.set_transaction_factory(lambda e: self.transaction_chooser(e, galaxy_app, session_cookie)) File "lib/galaxy/web/framework/webapp.py", line 115, in transaction_chooser return GalaxyWebTransaction(environ, galaxy_app, self, session_cookie) File "lib/galaxy/web/framework/webapp.py", line 219, in __init__ self._ensure_valid_session(session_cookie) File "lib/galaxy/web/framework/webapp.py", line 446, in _ensure_valid_session self.app.model.GalaxySession.table.c.is_valid == true())).options(joinedload("user")).first() File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3222, in first ret = list(self[0:1]) File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3012, in __getitem__ return list(res) File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3324, in __iter__ return self._execute_and_instances(context) File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3349, in _execute_and_instances result = conn.execute(querycontext.statement, self._params) File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 988, in execute return meth(self, multiparams, params) File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.7/site-packages/sqlalchemy/sql/elements.py", line 287, in _execute_on_connection return connection._execute_clauseelement(self, multiparams, params) File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1107, in _execute_clauseelement distilled_params, File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1248, in _execute_context e, statement, parameters, cursor, context File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1468, in _handle_dbapi_exception util.reraise(*exc_info) File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 154, in reraise raise value File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1244, in _execute_context cursor, statement, parameters, context File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 550, in do_execute cursor.execute(statement, parameters) ValueError: A string literal cannot contain NUL (0x00) characters. The above exception was the direct cause of the following exception: Traceback (most recent call last): File "lib/galaxy/web/framework/middleware/batch.py", line 80, in __call__ return self.application(environ, start_response) File "lib/galaxy/web/framework/middleware/request_id.py", line 15, in __call__ return self.app(environ, start_response) File "lib/galaxy/web/framework/middleware/xforwardedhost.py", line 23, in __call__ return self.app(environ, start_response) File "lib/galaxy/web/framework/middleware/translogger.py", line 71, in __call__ return self.application(environ, replacement_start_response) File "lib/galaxy/web/framework/middleware/error.py", line 164, in __call__ exc_info) File "lib/galaxy/web/framework/middleware/translogger.py", line 70, in replacement_start_response return start_response(status, headers, exc_info) SystemError: returned a result with an error set ``` Which can be provoked by switching between python 3 and python 2. --- lib/galaxy/web/framework/webapp.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/lib/galaxy/web/framework/webapp.py b/lib/galaxy/web/framework/webapp.py index 569a0c0a3f4..e7d7e2cf7c7 100644 --- a/lib/galaxy/web/framework/webapp.py +++ b/lib/galaxy/web/framework/webapp.py @@ -436,14 +436,14 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, # Decode the cookie value to get the session_key try: session_key = self.security.decode_guid(secure_id) + if session_key: + # Retrieve the galaxy_session id via the unique session_key + galaxy_session = self.sa_session.query(self.app.model.GalaxySession) \ + .filter(and_(self.app.model.GalaxySession.table.c.session_key == session_key, + self.app.model.GalaxySession.table.c.is_valid == true())).options(joinedload("user")).first() except Exception: # We'll end up creating a new galaxy_session session_key = None - if session_key: - # Retrieve the galaxy_session id via the unique session_key - galaxy_session = self.sa_session.query(self.app.model.GalaxySession) \ - .filter(and_(self.app.model.GalaxySession.table.c.session_key == session_key, - self.app.model.GalaxySession.table.c.is_valid == true())).options(joinedload("user")).first() # If remote user is in use it can invalidate the session and in some # cases won't have a cookie set above, so we need to to check some # things now. From 70363cd0b33a9a80c973676670e30f6e938fe681 Mon Sep 17 00:00:00 2001 From: guerler Date: Thu, 25 Jul 2019 14:00:39 -0400 Subject: [PATCH 10/60] Add error logging and use avoid usage of regex --- lib/galaxy/visualization/plugins/plugin.py | 11 ++++++----- lib/galaxy/visualization/plugins/registry.py | 2 ++ 2 files changed, 8 insertions(+), 5 deletions(-) diff --git a/lib/galaxy/visualization/plugins/plugin.py b/lib/galaxy/visualization/plugins/plugin.py index d033c424f77..db64e028e3e 100644 --- a/lib/galaxy/visualization/plugins/plugin.py +++ b/lib/galaxy/visualization/plugins/plugin.py @@ -5,10 +5,10 @@ from a query string and render a webpage based on those data. import copy import logging import os -import re import mako.lookup +from galaxy.exceptions import MessageException from galaxy.managers import api_keys from galaxy.visualization.plugins import ( interactive_environments, @@ -129,10 +129,11 @@ class VisualizationPlugin(ServesTemplatesPluginMixin): return url_for('visualization_plugin', visualization_name=self.name) def _get_static_path(self, path): - match = re.match(r'.*/config/(.*)', path) - if match: - return os.path.join('./static', match.group(1), 'static') - return None + if '/config/' in path: + match = path.split('/config/')[-1] + return os.path.join('./static', match, 'static') + else: + raise MessageException('Failed to determine static path: %s.' % path) def _get_saved_visualization_config(self, visualization, revision=None, **kwargs): """ diff --git a/lib/galaxy/visualization/plugins/registry.py b/lib/galaxy/visualization/plugins/registry.py index 8442484bad2..95983ab7c7f 100644 --- a/lib/galaxy/visualization/plugins/registry.py +++ b/lib/galaxy/visualization/plugins/registry.py @@ -189,6 +189,8 @@ class VisualizationsRegistry(object): if config is not None: plugin = self._build_plugin(plugin_name, plugin_path, config) return plugin + else: + raise ObjectNotFound('Visualization XML not found: %s.' % config_file) def _build_plugin(self, plugin_name, plugin_path, config): # TODO: as builder not factory From 5c7fddc15cb3d26a59cbea88b75e8ef00cbdff1a Mon Sep 17 00:00:00 2001 From: guerler Date: Thu, 25 Jul 2019 17:00:47 -0400 Subject: [PATCH 11/60] Replace message exception with log statement, a static path is optional --- lib/galaxy/visualization/plugins/plugin.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/visualization/plugins/plugin.py b/lib/galaxy/visualization/plugins/plugin.py index db64e028e3e..95c459f6635 100644 --- a/lib/galaxy/visualization/plugins/plugin.py +++ b/lib/galaxy/visualization/plugins/plugin.py @@ -133,7 +133,7 @@ class VisualizationPlugin(ServesTemplatesPluginMixin): match = path.split('/config/')[-1] return os.path.join('./static', match, 'static') else: - raise MessageException('Failed to determine static path: %s.' % path) + log.debug('Visualization has no static path: %s.' % path) def _get_saved_visualization_config(self, visualization, revision=None, **kwargs): """ From 766d0d062c88060c7c50b78ca3201a62a706ac65 Mon Sep 17 00:00:00 2001 From: guerler Date: Thu, 25 Jul 2019 17:15:37 -0400 Subject: [PATCH 12/60] Remove unused import --- lib/galaxy/visualization/plugins/plugin.py | 1 - 1 file changed, 1 deletion(-) diff --git a/lib/galaxy/visualization/plugins/plugin.py b/lib/galaxy/visualization/plugins/plugin.py index 95c459f6635..5435f180562 100644 --- a/lib/galaxy/visualization/plugins/plugin.py +++ b/lib/galaxy/visualization/plugins/plugin.py @@ -8,7 +8,6 @@ import os import mako.lookup -from galaxy.exceptions import MessageException from galaxy.managers import api_keys from galaxy.visualization.plugins import ( interactive_environments, From 49ef5f48da393cb4235bf621d050a19c74684614 Mon Sep 17 00:00:00 2001 From: M Bernt Date: Mon, 29 Jul 2019 13:19:43 +0200 Subject: [PATCH 13/60] univa runner: fix check for drmaa python module the runner name was changed at some point and we forgot to change it here (also looks much better now) --- lib/galaxy/dependencies/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/dependencies/__init__.py b/lib/galaxy/dependencies/__init__.py index e3c614ecdb0..b255ef91236 100644 --- a/lib/galaxy/dependencies/__init__.py +++ b/lib/galaxy/dependencies/__init__.py @@ -136,7 +136,7 @@ class ConditionalDependencies(object): def check_drmaa(self): return ("galaxy.jobs.runners.drmaa:DRMAAJobRunner" in self.job_runners or "galaxy.jobs.runners.slurm:SlurmJobRunner" in self.job_runners or - "galaxy.jobs.runners.drmaauniva:DRMAAUnivaJobRunner" in self.job_runners) + "galaxy.jobs.runners.univa:UnivaJobRunner" in self.job_runners) def check_galaxycloudrunner(self): return ("galaxycloudrunner.rules" in self.job_rule_modules) From 955018e79c329d191338092ddba1b5bc85647575 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Mon, 29 Jul 2019 13:28:10 -0400 Subject: [PATCH 14/60] Better isolation of embedded Pulsar tests. --- lib/galaxy/jobs/runners/pulsar.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/jobs/runners/pulsar.py b/lib/galaxy/jobs/runners/pulsar.py index 6ea38d13cd2..29fa1c06dda 100644 --- a/lib/galaxy/jobs/runners/pulsar.py +++ b/lib/galaxy/jobs/runners/pulsar.py @@ -231,9 +231,9 @@ class PulsarJobRunner(AsynchronousJobRunner): if "job_metrics_config_file" not in conf: conf["job_metrics"] = self.app.job_metrics if "staging_directory" not in conf: - conf["staging_directory"] = "database/pulsar_staging" + conf["staging_directory"] = os.path.join(self.app.config.data_dir, "pulsar_staging") if "persistence_directory" not in conf: - conf["persistence_directory"] = "database/pulsar_persisted_data" + conf["persistence_directory"] = os.path.join(self.app.config.data_dir, "pulsar_persisted_data") if "galaxy_home" not in conf: conf["galaxy_home"] = galaxy_directory() self.pulsar_app = pulsar.core.PulsarApp(**conf) From 308b376a77a67667ff86a456cc05daff0e72e5f2 Mon Sep 17 00:00:00 2001 From: guerler Date: Sat, 6 Jul 2019 09:22:45 +0200 Subject: [PATCH 15/60] Refactor theming, improve color contrast relationships between text and background --- .../galaxy/scripts/components/PluginList.vue | 6 +- client/galaxy/scripts/layout/page.js | 4 +- .../galaxy/scripts/mvc/workflow/workflow.js | 8 +- client/galaxy/style/scss/base.scss | 426 +++++++----------- client/galaxy/style/scss/charts.scss | 7 +- client/galaxy/style/scss/dataset.scss | 12 +- client/galaxy/style/scss/frame.scss | 2 +- client/galaxy/style/scss/history.scss | 37 +- client/galaxy/style/scss/job.scss | 4 +- client/galaxy/style/scss/library.scss | 2 +- client/galaxy/style/scss/list-item.scss | 14 +- client/galaxy/style/scss/overrides.scss | 45 +- client/galaxy/style/scss/theme/blue.scss | 50 +- client/galaxy/style/scss/ui.scss | 22 +- client/galaxy/style/scss/ui/icon-btn.scss | 1 - client/galaxy/style/scss/ui/search-input.scss | 5 +- client/galaxy/style/scss/upload.scss | 1 + 17 files changed, 296 insertions(+), 350 deletions(-) diff --git a/client/galaxy/scripts/components/PluginList.vue b/client/galaxy/scripts/components/PluginList.vue index 2f70becf0c7..a9402ed4fdf 100644 --- a/client/galaxy/scripts/components/PluginList.vue +++ b/client/galaxy/scripts/components/PluginList.vue @@ -20,15 +20,15 @@
-
{{ plugin.html }}
-
{{ plugin.description }}
+
{{ plugin.html }}
+
{{ plugin.description }}
-
Select a dataset to visualize:
+
Select a dataset to visualize:
Create diff --git a/client/galaxy/scripts/components/xrefs.vue b/client/galaxy/scripts/components/xrefs.vue index 13c005243ba..97c0529bdd1 100644 --- a/client/galaxy/scripts/components/xrefs.vue +++ b/client/galaxy/scripts/components/xrefs.vue @@ -5,10 +5,10 @@ - +
- {{xref.reftype}}: - {{ xref.reftype }}: