An out of date export is ready .
diff --git a/client/src/components/Panels/ToolBox.vue b/client/src/components/Panels/ToolBox.vue
index 3af9756d9b7..5abc1cd1701 100644
--- a/client/src/components/Panels/ToolBox.vue
+++ b/client/src/components/Panels/ToolBox.vue
@@ -166,8 +166,9 @@ export default {
} else if (tool.form_style === "regular") {
evt.preventDefault();
const Galaxy = getGalaxyInstance();
+ // encode spaces in tool.id
Galaxy.router.push("/", {
- tool_id: tool.id,
+ tool_id: tool.id.replace(/ /g, "%20"),
version: tool.version,
});
}
diff --git a/client/src/store/index.js b/client/src/store/index.js
index b6b06ed2963..734d60ffb22 100644
--- a/client/src/store/index.js
+++ b/client/src/store/index.js
@@ -5,7 +5,8 @@
import Vue from "vue";
import Vuex from "vuex";
import createCache from "vuex-cache";
-import createPersistedState from "vuex-persistedstate";
+import VuexPersistence from "vuex-persist";
+import localForage from "localforage";
import config from "config";
@@ -35,19 +36,28 @@ import { syncVuextoGalaxy } from "./syncVuextoGalaxy";
Vue.use(Vuex);
-const panelsState = createPersistedState({
- paths: ["panels"],
+const galaxyStorage = localForage.createInstance({});
+galaxyStorage.config({
+ driver: [localForage.INDEXEDDB, localForage.LOCALSTORAGE],
+ name: "galaxyIndexedDB",
+ version: 1.0,
+ storeName: "galaxyStore",
+});
+
+const panelsPersistence = new VuexPersistence({
+ storage: galaxyStorage,
+ asyncStorage: true,
+ modules: ["panels"],
});
export function createStore() {
const storeConfig = {
- plugins: [createCache(), panelsState],
+ plugins: [createCache(), panelsPersistence.plugin],
modules: {
user: userStore,
config: configStore,
betaHistory: betaHistoryStore,
panels: panelStore,
-
// TODO: please namespace all store modules
gridSearch: gridSearchStore,
histories: historyStore,
diff --git a/client/src/ui/search-input.js b/client/src/ui/search-input.js
index 21c36f4e7dd..06acd5ce212 100644
--- a/client/src/ui/search-input.js
+++ b/client/src/ui/search-input.js
@@ -152,6 +152,18 @@ function searchInput(parentNode, options) {
.popover("show");
});
}
+ // Hack to hide the advanced search popover when clicking outside
+ $("body").on("click", function (e) {
+ $('[data-toggle="advSearchPopover"]').each(function () {
+ if (
+ !$(this).is(e.target) &&
+ $(this).has(e.target).length === 0 &&
+ $(".popover").has(e.target).length === 0
+ ) {
+ $(this).popover("hide");
+ }
+ });
+ });
// .................................................................... loadingIndicator rendering
// a button for clearing the search bar, placed on the right hand side
diff --git a/client/yarn.lock b/client/yarn.lock
index 5c98a827544..f5412e2ff8e 100644
--- a/client/yarn.lock
+++ b/client/yarn.lock
@@ -4625,10 +4625,15 @@ flat-cache@^3.0.4:
flatted "^3.1.0"
rimraf "^3.0.2"
-flatted@^3.0.5, flatted@^3.1.0, flatted@^3.2.4:
- version "3.2.5"
- resolved "https://registry.yarnpkg.com/flatted/-/flatted-3.2.5.tgz#76c8584f4fc843db64702a6bd04ab7a8bd666da3"
- integrity sha512-WIWGi2L3DyTUvUrwRKgGi9TwxQMUEqPOPQBVi71R96jZXJdFskXEmf54BoZaS1kknGODoIGASGEzBUYdyMCBJg==
+flatted@^2.0.0:
+ version "2.0.2"
+ resolved "https://registry.yarnpkg.com/flatted/-/flatted-2.0.2.tgz#4575b21e2bcee7434aa9be662f4b7b5f9c2b5138"
+ integrity sha512-r5wGx7YeOwNWNlCA0wQ86zKyDLMQr+/RB8xy74M4hTphfmjlijTSSXGuH8rnvKZnfT9i+75zmd8jcKdMR4O6jA==
+
+flatted@^3.1.0, flatted@^3.2.4:
+ version "3.2.4"
+ resolved "https://registry.yarnpkg.com/flatted/-/flatted-3.2.4.tgz#28d9969ea90661b5134259f312ab6aa7929ac5e2"
+ integrity sha512-8/sOawo8tJ4QOBX8YlQBMxL8+RLZfxMQOif9o0KUKTNTjMYElWPE0r/m5VNFxTRd0NSw8qSy8dajrwX4RYI1Hw==
flush-promises@^1.0.2:
version "1.0.2"
@@ -5216,6 +5221,11 @@ imask@^6.4.0:
resolved "https://registry.yarnpkg.com/imask/-/imask-6.4.0.tgz#76e48e6bbf5306f7de058f8a1b90fd2282d446bc"
integrity sha512-iXXgSQA6TJX/RSKivKoTYYoCc4ZmVseMcoDIxMrlW1JPpc8LU9FtCp3f80vg1eUQvmVfEQbh+vybFVDRt2o9TQ==
+immediate@~3.0.5:
+ version "3.0.6"
+ resolved "https://registry.yarnpkg.com/immediate/-/immediate-3.0.6.tgz#9db1dbd0faf8de6fbe0f5dd5e56bb606280de69b"
+ integrity sha1-nbHb0Pr43m++D13V5Wu2BigN5ps=
+
immutable@^4.0.0:
version "4.0.0"
resolved "https://registry.yarnpkg.com/immutable/-/immutable-4.0.0.tgz#b86f78de6adef3608395efb269a91462797e2c23"
@@ -6556,6 +6566,13 @@ levn@~0.3.0:
prelude-ls "~1.1.2"
type-check "~0.3.2"
+lie@3.1.1:
+ version "3.1.1"
+ resolved "https://registry.yarnpkg.com/lie/-/lie-3.1.1.tgz#9a436b2cc7746ca59de7a41fa469b3efb76bd87e"
+ integrity sha1-mkNrLMd0bKWd56QfpGmz77dr2H4=
+ dependencies:
+ immediate "~3.0.5"
+
liftoff@^3.1.0:
version "3.1.0"
resolved "https://registry.yarnpkg.com/liftoff/-/liftoff-3.1.0.tgz#c9ba6081f908670607ee79062d700df062c52ed3"
@@ -6631,6 +6648,13 @@ loader-utils@^2.0.0:
emojis-list "^3.0.0"
json5 "^2.1.2"
+localforage@^1.10.0:
+ version "1.10.0"
+ resolved "https://registry.yarnpkg.com/localforage/-/localforage-1.10.0.tgz#5c465dc5f62b2807c3a84c0c6a1b1b3212781dd4"
+ integrity sha512-14/H1aX7hzBBmmh7sGPd+AOMkkIrHM3Z1PAyGgZigA1H1p5O5ANnMyWzvpAETtG68/dC4pC0ncy3+PPGzXZHPg==
+ dependencies:
+ lie "3.1.1"
+
locate-path@^5.0.0:
version "5.0.0"
resolved "https://registry.yarnpkg.com/locate-path/-/locate-path-5.0.0.tgz#1afba396afd676a6d42504d0a67a3a7eb9f62aa0"
@@ -6718,7 +6742,7 @@ lodash.uniqby@4.5.0:
lodash._baseiteratee "~4.7.0"
lodash._baseuniq "~4.6.0"
-lodash@^4.13.1, lodash@^4.17.14, lodash@^4.17.15, lodash@^4.17.21, lodash@^4.7.0:
+lodash@^4.13.1, lodash@^4.17.14, lodash@^4.17.15, lodash@^4.17.19, lodash@^4.17.21, lodash@^4.7.0:
version "4.17.21"
resolved "https://registry.yarnpkg.com/lodash/-/lodash-4.17.21.tgz#679591c564c3bffaae8454cf0b3df370c3d6911c"
integrity sha512-v2kDEe57lecTulaDIuNTPy3Ry4gLGJ6Z1O3vE1krgXZNrsQ+LFTGHVxVjcXPs17LhbZVGedAJv8XZ1tvj5FvSg==
@@ -7207,12 +7231,17 @@ object-hash@^2.2.0:
resolved "https://registry.yarnpkg.com/object-hash/-/object-hash-2.2.0.tgz#5ad518581eefc443bd763472b8ff2e9c2c0d54a5"
integrity sha512-gScRMn0bS5fH+IuwyIFgnh9zBdo4DV+6GhygmWM9HyNJSgS0hScp1f5vjtm7oIIOiT9trXrShAkLFSc2IqKNgw==
-object-inspect@^1.11.0, object-inspect@^1.9.0:
+object-inspect@^1.11.0:
+ version "1.11.0"
+ resolved "https://registry.yarnpkg.com/object-inspect/-/object-inspect-1.11.0.tgz#9dceb146cedd4148a0d9e51ab88d34cf509922b1"
+ integrity sha512-jp7ikS6Sd3GxQfZJPyH3cjcbJF6GZPClgdV+EFygjFLQ5FmW/dRUnTd9PQ9k0JhoNDabWFbpF1yCdSWCC6gexg==
+
+object-inspect@^1.9.0:
version "1.12.0"
resolved "https://registry.yarnpkg.com/object-inspect/-/object-inspect-1.12.0.tgz#6e2c120e868fd1fd18cb4f18c31741d0d6e776f0"
integrity sha512-Ho2z80bVIvJloH+YzRmpZVQe87+qASmBUKZDWgx9cu+KDrX2ZDH/3tMy+gXbZETVGs2M8YdxObOh7XAtim9Y0g==
-object-is@^1.0.1, object-is@^1.1.4:
+object-is@^1.0.1:
version "1.1.5"
resolved "https://registry.yarnpkg.com/object-is/-/object-is-1.1.5.tgz#b9deeaa5fc7f1846a0faecdceec138e5778f53ac"
integrity sha512-3cyDsyHgtmi7I7DfSSI2LDp6SK2lwvtbg0p0R1e0RvTqF5ceGx+K2dfSjm1bKDMVCFEDAQvy+o8c6a7VujOddw==
@@ -7220,6 +7249,14 @@ object-is@^1.0.1, object-is@^1.1.4:
call-bind "^1.0.2"
define-properties "^1.1.3"
+object-is@^1.1.4:
+ version "1.1.4"
+ resolved "https://registry.yarnpkg.com/object-is/-/object-is-1.1.4.tgz#63d6c83c00a43f4cbc9434eb9757c8a5b8565068"
+ integrity sha512-1ZvAZ4wlF7IyPVOcE1Omikt7UpaFlOQq0HlSti+ZvDH3UiD2brwGMwDbyV43jao2bKJ+4+WdPJHSd7kgzKYVqg==
+ dependencies:
+ call-bind "^1.0.0"
+ define-properties "^1.1.3"
+
object-keys@^1.0.12, object-keys@^1.1.1:
version "1.1.1"
resolved "https://registry.yarnpkg.com/object-keys/-/object-keys-1.1.1.tgz#1c47f272df277f3b1daf061677d9c82e2322c60e"
@@ -8667,11 +8704,6 @@ shebang-regex@^3.0.0:
resolved "https://registry.yarnpkg.com/shebang-regex/-/shebang-regex-3.0.0.tgz#ae16f1644d873ecad843b0307b143362d4c42172"
integrity sha512-7++dFhtcx3353uBaq8DDR4NuxBetBzC7ZQOhmTQInHEd6bSrXdiEyzCvG07Z44UYdLShWUyXt5M/yhz8ekcb1A==
-shvl@^2.0.3:
- version "2.0.3"
- resolved "https://registry.yarnpkg.com/shvl/-/shvl-2.0.3.tgz#eb4bd37644f5684bba1fc52c3010c96fb5e6afd1"
- integrity sha512-V7C6S9Hlol6SzOJPnQ7qzOVEWUQImt3BNmmzh40wObhla3XOYMe4gGiYzLrJd5TFa+cI2f9LKIRJTTKZSTbWgw==
-
side-channel@^1.0.3, side-channel@^1.0.4:
version "1.0.4"
resolved "https://registry.yarnpkg.com/side-channel/-/side-channel-1.0.4.tgz#efce5c8fdc104ee751b25c58d4290011fa5ea2cf"
@@ -9907,21 +9939,13 @@ vuex-cache@^3.4.0:
resolved "https://registry.yarnpkg.com/vuex-cache/-/vuex-cache-3.4.0.tgz#0aec66b7abb370b1a089f678681af8efe5a9289b"
integrity sha512-C0HJvVTEdjn8gq0EXemcJCBgAyPLnms8VGz/kMakrpaF6XNwkZY5KvySkdBJSY6rp0eTdWMoHPVU2Oq+dK7WEQ==
-vuex-persist@^3.1.3:
- version "3.1.3"
- resolved "https://registry.yarnpkg.com/vuex-persist/-/vuex-persist-3.1.3.tgz#518c722a2ca3026bcee5732f99d24f75cee0f3b6"
- integrity sha512-QWOpP4SxmJDC5Y1+0+Yl/F4n7z27syd1St/oP+IYCGe0X0GFio0Zan6kngZFufdIhJm+5dFGDo3VG5kdkCGeRQ==
+vuex-persist@2.3:
+ version "2.3.0"
+ resolved "https://registry.yarnpkg.com/vuex-persist/-/vuex-persist-2.3.0.tgz#f3d21b6d631078667d6834f2f74442ee332ac281"
+ integrity sha512-0QPZQYgQ72SbXkdwctXGFQJhlRiySP0z9wHDBTlyHvNy3CneKvgyJ7Lfob8NUiYbaurJepaC+JFynwshp59FGA==
dependencies:
- deepmerge "^4.2.2"
- flatted "^3.0.5"
-
-vuex-persistedstate@^4.1.0:
- version "4.1.0"
- resolved "https://registry.yarnpkg.com/vuex-persistedstate/-/vuex-persistedstate-4.1.0.tgz#127165f85f5b4534fb3170a5d3a8be9811bd2a53"
- integrity sha512-3SkEj4NqwM69ikJdFVw6gObeB0NHyspRYMYkR/EbhR0hbvAKyR5gksVhtAfY1UYuWUOCCA0QNGwv9pOwdj+XUQ==
- dependencies:
- deepmerge "^4.2.2"
- shvl "^2.0.3"
+ flatted "^2.0.0"
+ lodash "^4.17.19"
vuex@^3.6.2:
version "3.6.2"
diff --git a/lib/galaxy/jobs/runners/univa.py b/lib/galaxy/jobs/runners/univa.py
index 5a3117c6456..c0d2ecb730c 100644
--- a/lib/galaxy/jobs/runners/univa.py
+++ b/lib/galaxy/jobs/runners/univa.py
@@ -32,6 +32,7 @@ import logging
import re
import signal
import time
+from math import inf
from galaxy.jobs.runners.drmaa import DRMAAJobRunner
from galaxy.util import (
@@ -587,8 +588,8 @@ def _parse_native_specs(job_id, native_spec):
specification string passed to GE
return time,mem (or None,None if nothing found)
"""
- tme = None
- mem = None
+ tme = inf
+ mem = inf
# parse time
m = re.search(r"rt=([0-9:]+)[\s,]*", native_spec)
if m is not None:
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 7a076b0397e..23ec3a031a4 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -7085,7 +7085,7 @@ class WorkflowStepConnection(Base, RepresentById):
return self.input_step_input.name
@property
- def input_step(self):
+ def input_step(self) -> Optional[WorkflowStep]:
return self.input_step_input and self.input_step_input.workflow_step
@property
diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index 9f63050c9a6..f1fdf05591d 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -1470,7 +1470,7 @@ class DirectoryModelExportStore(ModelExportStore):
datasets = query.all()
for dataset in datasets:
dataset.annotation = get_item_annotation_str(sa_session, history.user, dataset)
- add_dataset = (not dataset.visible or not include_hidden) and (not dataset.deleted or include_deleted)
+ add_dataset = (dataset.visible or include_hidden) and (not dataset.deleted or include_deleted)
if dataset.id in self.collection_datasets:
add_dataset = True
diff --git a/lib/galaxy/selenium/navigation.yml b/lib/galaxy/selenium/navigation.yml
index ebc97f3e2b7..debfd06a3d9 100644
--- a/lib/galaxy/selenium/navigation.yml
+++ b/lib/galaxy/selenium/navigation.yml
@@ -526,6 +526,9 @@ workflow_run:
subworkflow_step_icon: ".portlet-title-icon.fa-sitemap"
run_workflow: "#run-workflow"
validation_error: ".validation-error"
+ input_select_field:
+ type: xpath
+ selector: '//div[@data-label="${label}"]//span[@class="select2-chosen"]'
workflow_editor:
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index 69b00ff14d3..89e170899ab 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -9,6 +9,7 @@ from typing import (
Any,
cast,
Dict,
+ Iterable,
List,
Optional,
Union,
@@ -27,6 +28,7 @@ from galaxy.job_execution.actions.post import ActionBox
from galaxy.model import (
PostJobAction,
Workflow,
+ WorkflowStepConnection,
)
from galaxy.model.dataset_collections import matching
from galaxy.tool_util.parser.output_objects import ToolExpressionOutput
@@ -817,7 +819,12 @@ class InputDataCollectionModule(InputModule):
]
input_collection_type = TextToolParameter(None, collection_type_source)
tag_source = dict(
- name="tag", label="Tag filter", type="text", value=tag, help="Tags to automatically filter inputs"
+ name="tag",
+ label="Tag filter",
+ type="text",
+ optional="true",
+ value=tag,
+ help="Tags to automatically filter inputs",
)
input_tag = TextToolParameter(None, tag_source)
inputs = {}
@@ -881,7 +888,7 @@ class InputParameterModule(WorkflowModule):
name = "Input parameter"
default_parameter_type = "text"
default_optional = False
- default_default_value = ""
+ default_default_value = None
parameter_type = default_parameter_type
optional = default_optional
default_value = default_default_value
@@ -1097,10 +1104,53 @@ class InputParameterModule(WorkflowModule):
parameter_type_cond.cases = cases
return {"parameter_definition": parameter_type_cond}
- def get_runtime_inputs(self, connections=None, **kwds):
+ def restrict_options(self, connections: Iterable[WorkflowStepConnection], default_value):
+ try:
+ static_options = []
+ # Retrieve possible runtime options for 'select' type inputs
+ for connection in connections:
+ # Well this isn't a great assumption...
+ module = connection.input_step.module # type: ignore[union-attr]
+ tool_inputs = module.tool.inputs # may not be set, but we're catching the Exception below.
+
+ def callback(input, prefixed_name, context, **kwargs):
+ if prefixed_name == connection.input_name and hasattr(input, "get_options"):
+ static_options.append(input.get_options(self.trans, {}))
+
+ visit_input_values(tool_inputs, module.state.inputs, callback)
+
+ options = None
+ if static_options and len(static_options) == 1:
+ # If we are connected to a single option, just use it as is so order is preserved cleanly and such.
+ options = [
+ {"label": o[0], "value": o[1], "selected": bool(default_value and o[1] == default_value)}
+ for o in static_options[0]
+ ]
+ elif static_options:
+ # Intersection based on values of multiple option connections.
+ intxn_vals = set.intersection(*({option[1] for option in options} for options in static_options))
+ intxn_opts = {option for options in static_options for option in options if option[1] in intxn_vals}
+ d = defaultdict(set) # Collapse labels with same values
+ for label, value, _ in intxn_opts:
+ d[value].add(label)
+ options = [
+ {
+ "label": ", ".join(label),
+ "value": value,
+ "selected": bool(default_value and value == default_value),
+ }
+ for value, label in d.items()
+ ]
+
+ return options
+ except Exception:
+ log.debug("Failed to generate options for text parameter, falling back to free text.", exc_info=True)
+
+ def get_runtime_inputs(self, connections: Optional[Iterable[WorkflowStepConnection]] = None, **kwds):
parameter_def = self._parse_state_into_dict()
parameter_type = parameter_def["parameter_type"]
optional = parameter_def["optional"]
+ default_value = parameter_def.get("default", self.default_default_value)
if parameter_type not in ["text", "boolean", "integer", "float", "color"]:
raise ValueError("Invalid parameter type for workflow parameters encountered.")
@@ -1113,41 +1163,12 @@ class InputParameterModule(WorkflowModule):
# Really is just an attempt - tool module may not be available (small problem), get_options may really depend on other
# values we are not setting, so this isn't great. Be sure to just fallback to text in this case.
attemptRestrictOnConnections = is_text and parameter_def.get("restrictOnConnections") and connections
- try:
- if attemptRestrictOnConnections:
- static_options = []
- # Retrieve possible runtime options for 'select' type inputs
- for connection in connections:
- # Well this isn't a great assumption...
- module = connection.input_step.module
- tool_inputs = module.tool.inputs # may not be set, but we're catching the Exception below.
-
- def callback(input, prefixed_name, context, **kwargs):
- if prefixed_name == connection.input_name and hasattr(input, "get_options"):
- static_options.append(input.get_options(self.trans, {}))
-
- visit_input_values(tool_inputs, module.state.inputs, callback)
-
- options = None
- if static_options and len(static_options) == 1:
- # If we are connected to a single option, just use it as is so order is preserved cleanly and such.
- options = [{"label": o[0], "value": o[1]} for o in static_options[0]]
- elif static_options:
- # Intersection based on values of multiple option connections.
- intxn_vals = set.intersection(*({option[1] for option in options} for options in static_options))
- intxn_opts = {option for options in static_options for option in options if option[1] in intxn_vals}
- d = defaultdict(set) # Collapse labels with same values
- for label, value, _ in intxn_opts:
- d[value].add(label)
- options = [
- {"label": ", ".join(label), "value": value, "selected": False} for value, label in d.items()
- ]
-
- if options is not None:
- parameter_kwds["options"] = options
- restricted_inputs = True
- except Exception:
- log.debug("Failed to generate options for text parameter, falling back to free text.", exc_info=True)
+ if attemptRestrictOnConnections:
+ connections = cast(Iterable[WorkflowStepConnection], connections)
+ restricted_options = self.restrict_options(connections=connections, default_value=default_value)
+ if restricted_options is not None:
+ restricted_inputs = True
+ parameter_kwds["options"] = restricted_options
def _parameter_def_list_to_options(parameter_value):
options = []
@@ -1178,8 +1199,10 @@ class InputParameterModule(WorkflowModule):
parameter_class = parameter_types[client_parameter_type]
if optional:
- default_value = parameter_def.get("default", self.default_default_value)
- parameter_kwds["value"] = default_value
+ if client_parameter_type == "select":
+ parameter_kwds["selected"] = default_value
+ else:
+ parameter_kwds["value"] = default_value
if parameter_type == "boolean":
parameter_kwds["checked"] = default_value
diff --git a/lib/galaxy_test/selenium/test_workflow_run.py b/lib/galaxy_test/selenium/test_workflow_run.py
index 977cbbe5a24..208df75e14a 100644
--- a/lib/galaxy_test/selenium/test_workflow_run.py
+++ b/lib/galaxy_test/selenium/test_workflow_run.py
@@ -190,6 +190,34 @@ steps:
content = self.dataset_populator.get_history_dataset_content(history_id, hid=7)
self.assertEqual("10.0\n30.0\n20.0\n40.0\n", content)
+ @selenium_test
+ @managed_history
+ def test_execution_with_text_default_value_connected_to_restricted_select(self):
+ self.open_in_workflow_run(
+ """
+class: GalaxyWorkflow
+inputs:
+ text_param:
+ optional: true
+ default: ex2
+ restrictOnConnections: true
+ type: text
+steps:
+ multi_select:
+ tool_id: multi_select
+ in:
+ select_ex:
+ source: text_param
+"""
+ )
+ element = self.components.workflow_run.input_select_field(label="text_param").wait_for_present()
+ assert element.text == "Ex2"
+ self.workflow_run_submit()
+ history_id = self.current_history_id()
+ self.workflow_populator.wait_for_history_workflows(history_id, expected_invocation_count=1)
+ content = self.dataset_populator.get_history_dataset_content(history_id, hid=1)
+ assert content == "ex2"
+
@selenium_test
@managed_history
def test_execution_with_rules(self):
diff --git a/scripts/common_startup.sh b/scripts/common_startup.sh
index a8b4c2f0a94..9912a908050 100755
--- a/scripts/common_startup.sh
+++ b/scripts/common_startup.sh
@@ -122,7 +122,6 @@ if [ $SET_VENV -eq 1 ] && [ $CREATE_VENV -eq 1 ]; then
conda_activate
fi
virtualenv "$GALAXY_VIRTUAL_ENV"
- setup_gravity_state_dir
else
# If $GALAXY_VIRTUAL_ENV does not exist, and there is no conda available, attempt to create it.
if [ -z "$GALAXY_PYTHON" ]; then
@@ -140,7 +139,6 @@ if [ $SET_VENV -eq 1 ] && [ $CREATE_VENV -eq 1 ]; then
echo "existing environment before starting Galaxy."
if command -v virtualenv >/dev/null; then
virtualenv -p "$GALAXY_PYTHON" "$GALAXY_VIRTUAL_ENV"
- setup_gravity_state_dir
else
vvers=16.7.9
vurl="https://files.pythonhosted.org/packages/source/v/virtualenv/virtualenv-${vvers}.tar.gz"
@@ -167,10 +165,10 @@ urlretrieve('$vurl', '$vsrc')"
tar zxf "$vsrc" -C "$vtmp"
"$GALAXY_PYTHON" "$vtmp/virtualenv-$vvers/virtualenv.py" "$GALAXY_VIRTUAL_ENV"
rm -rf "$vtmp"
- setup_gravity_state_dir
fi
fi
fi
+ setup_gravity_state_dir
fi
# activate virtualenv or conda env, sets $GALAXY_VIRTUAL_ENV and $GALAXY_CONDA_ENV
diff --git a/test/unit/data/model/test_model_store.py b/test/unit/data/model/test_model_store.py
index 0605e4b93fb..220ca73b7f0 100644
--- a/test/unit/data/model/test_model_store.py
+++ b/test/unit/data/model/test_model_store.py
@@ -44,6 +44,30 @@ def test_import_export_history_failed_job():
_assert_simple_cat_job_imported(imported_history, state="error")
+def test_import_export_history_hidden_false_with_hidden_dataset():
+ app = _mock_app()
+
+ u, h, d1, d2, j = _setup_simple_cat_job(app)
+ d2.visible = False
+ app.model.session.flush()
+
+ imported_history = _import_export_history(app, h, export_files="copy", include_hidden=False)
+ assert d1.dataset.get_size() == imported_history.datasets[0].get_size()
+ assert imported_history.datasets[1].get_size() == 0
+
+
+def test_import_export_history_hidden_true_with_hidden_dataset():
+ app = _mock_app()
+
+ u, h, d1, d2, j = _setup_simple_cat_job(app)
+ d2.visible = False
+ app.model.session.flush()
+
+ imported_history = _import_export_history(app, h, export_files="copy", include_hidden=True)
+ assert d1.dataset.get_size() == imported_history.datasets[0].get_size()
+ assert d2.dataset.get_size() == imported_history.datasets[1].get_size()
+
+
def test_import_export_bag_archive():
"""Test a simple job import/export using a BagIt archive."""
dest_parent = mkdtemp()
@@ -488,13 +512,13 @@ def _setup_simple_cat_job(app, state="ok"):
return u, h, d1, d2, j
-def _import_export_history(app, h, dest_export=None, export_files=None):
+def _import_export_history(app, h, dest_export=None, export_files=None, include_hidden=False):
if dest_export is None:
dest_parent = mkdtemp()
dest_export = os.path.join(dest_parent, "moo.tgz")
with store.TarModelExportStore(dest_export, app=app, export_files=export_files) as export_store:
- export_store.export_history(h)
+ export_store.export_history(h, include_hidden=include_hidden)
imported_history = import_archive(dest_export, app, h.user)
assert imported_history