Merge pull request #13394 from dannon/dev

Merge 22.01 -> dev.
2026-09-24 16:30:27 +08:00 · 2022-02-17 09:33:18 +01:00
parent 88b455c953 29a7489590
commit d905fe3fe6
14 changed files with 212 additions and 84 deletions
@@ -57,6 +57,7 @@
    "jspdf": "^2.5.1",
    "linkify-html": "^3.0.5",
    "linkifyjs": "^3.0.5",
+    "localforage": "^1.10.0",
    "markdown-it": "^12.3.2",
    "markdown-it-regexp": "^0.4.0",
    "moment": "2.29.1",
@@ -95,8 +96,7 @@
    "vueisotope": "^3.1.2",
    "vuex": "^3.6.2",
    "vuex-cache": "^3.4.0",
-    "vuex-persist": "^3.1.3",
-    "vuex-persistedstate": "^4.1.0",
+    "vuex-persist": "2.3",
    "xml-beautifier": "^0.5.0"
  },
  "scripts": {
@@ -17,7 +17,11 @@
        <div v-else-if="latestExportReady">
            Link for download ready
            <export-link :history-export="latestExport" />
-            . Use this link to download the archive or import it on another Galaxy server.
+            <p>Use this link to download the archive or import it on another Galaxy server.</p>
+            <b-alert show variant="warning"
+                >History archives are removed at regular intervals. For permanent storage download the archive, export
+                to a remote file or import the archive on another Galaxy server.
+            </b-alert>
        </div>
        <div v-else-if="hasReadyExport">
            <p>An out of date export is ready <export-link :history-export="latestReadyExport" />.</p>
@@ -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,
                });
            }
@@ -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,
@@ -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
@@ -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"
@@ -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:
@@ -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
@@ -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

@@ -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:

@@ -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

@@ -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):
@@ -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
@@ -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