Merge pull request #12811 from mvdbeek/show_tool_source_in_tool_form

Display tool source in tool form

client/package.json

@@ -27,6 +27,7 @@
     "@johmun/vue-tags-input": "^2.1.0",
     "@sentry/browser": "^5.20.1",
     "axios": "^0.21.1",
+    "babel-runtime": "^6.26.0",
     "backbone": "1.4.0",
     "bootstrap": "4.5.0",
     "bootstrap-vue": "^2.21.2",
@@ -89,6 +90,7 @@
     "vue-infinite-scroll": "^2.0.2",
     "vue-multiselect": "^2.1.0",
     "vue-observe-visibility": "^1.0.0",
+    "vue-prismjs": "^1.2.0",
     "vue-router": "^3.5.2",
     "vue-rx": "^6.2.0",
     "vue-scrollto": "^2.20.0",
@@ -97,7 +99,8 @@
     "vuex": "^3.4.0",
     "vuex-cache": "^3.2.0",
     "vuex-persist": "^3.1.3",
-    "vuex-persistedstate": "^4.1.0"
+    "vuex-persistedstate": "^4.1.0",
+    "xml-beautifier": "^0.5.0"
   },
   "scripts": {
     "watch": "gulp && yarn run save-build-hash && yarn run webpack-watch",

client/src/components/Tool/ToolCard.test.js

@@ -32,6 +32,9 @@ describe("ToolCard", () => {
                 messageVariant: "warning",
                 disabled: false,
             },
+            stubs: {
+                ToolSourceMenuItem: { template: "<div></div>" },
+            },
             localVue,
         });
     });

client/src/components/Tool/ToolCard.vue

@@ -26,6 +26,7 @@
                         <b-dropdown-item v-if="showDownload" @click="onDownload"
                             ><span class="fa fa-download" /><span v-localize>Download</span>
                         </b-dropdown-item>
+                        <ToolSourceMenuItem :tool-id="id" />
                         <b-dropdown-item v-if="showLink" @click="onLink"
                             ><span class="fa fa-external-link" /><span v-localize
                                 >See in Tool Shed</span
@@ -87,6 +88,7 @@
                     </span>
                 </div>
             </div>
+
             <div class="portlet-content">
                 <FormMessage :message="errorText" variant="danger" :persistent="true" />
                 <FormMessage :message="messageText" :variant="messageVariant" />
@@ -114,6 +116,7 @@ import { copyLink, downloadTool, openLink } from "./utilities";
 import FormMessage from "components/Form/FormMessage";
 import ToolFooter from "components/Tool/ToolFooter";
 import ToolHelp from "components/Tool/ToolHelp";
+import ToolSourceMenuItem from "components/Tool/ToolSourceMenuItem";
 import Webhooks from "mvc/webhooks";
 import { addFavorite, removeFavorite } from "components/Tool/services";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
@@ -128,6 +131,7 @@ export default {
         FormMessage,
         ToolFooter,
         ToolHelp,
+        ToolSourceMenuItem,
     },
     props: {
         id: {

client/src/components/Tool/ToolSource.vue

@@ -0,0 +1,30 @@
+<template>
+    <ToolSourceProvider :id="toolId" v-slot="{ result, loading, error }">
+        <loading-span v-if="loading" message="Waiting on tool source" />
+        <alert v-else-if="error" :message="error" variant="error" />
+        <prism v-else :language="result.language" :code="result.source" :plugins="['normalize-whitespace']"></prism>
+    </ToolSourceProvider>
+</template>
+<script>
+import Alert from "components/Alert";
+import LoadingSpan from "components/LoadingSpan";
+import { ToolSourceProvider } from "components/providers/ToolSourceProvider";
+import Prism from "vue-prismjs";
+import "prismjs/themes/prism.css";
+import "prismjs/plugins/normalize-whitespace/prism-normalize-whitespace.js";
+
+export default {
+    components: {
+        Alert,
+        LoadingSpan,
+        Prism,
+        ToolSourceProvider,
+    },
+    props: {
+        toolId: {
+            type: String,
+            required: true,
+        },
+    },
+};
+</script>

client/src/components/Tool/ToolSourceMenuItem.vue

@@ -0,0 +1,39 @@
+<template>
+    <CurrentUser v-slot="{ user }">
+        <ConfigProvider v-slot="{ config }">
+            <div v-if="config.enable_tool_source_display || (user && user.is_admin)">
+                <b-dropdown-item v-b-modal.tool-source-viewer
+                    ><span class="fa fa-eye" /><span v-localize>View Tool source</span>
+                </b-dropdown-item>
+                <b-modal
+                    id="tool-source-viewer"
+                    :title="`Tool Source for ${toolId}`"
+                    size="lg"
+                    ok-only
+                    ok-title="Close"
+                >
+                    <ToolSource :tool-id="toolId" />
+                </b-modal>
+            </div>
+        </ConfigProvider>
+    </CurrentUser>
+</template>
+<script>
+import ConfigProvider from "components/providers/ConfigProvider";
+import CurrentUser from "components/providers/CurrentUser";
+import ToolSource from "components/Tool/ToolSource";
+
+export default {
+    components: {
+        ConfigProvider,
+        CurrentUser,
+        ToolSource,
+    },
+    props: {
+        toolId: {
+            type: String,
+            required: true,
+        },
+    },
+};
+</script>

client/src/components/providers/SingleQueryProvider.js

@@ -2,9 +2,9 @@ import hash from "object-hash";
 
 /**
  * Builds a provider that gets its result from a single promise-based query function and
- * caches the result of lookup for subsequent instantitations.
+ * caches the result of lookup for subsequent instantiations.
  *
- * @param   {Function}  lookup  async function that loads the result, paramters will be an object
+ * @param   {Function}  lookup  async function that loads the result, parameters will be an object
  *                              whose properties are the attributes assigned to the provider component
  * @return  {VueComponentOptions} Vue component options definition
  */

client/src/components/providers/ToolSourceProvider.js

@@ -0,0 +1,24 @@
+import axios from "axios";
+import { getAppRoot } from "onload/loadConfig";
+import { SingleQueryProvider } from "components/providers/SingleQueryProvider";
+import { rethrowSimple } from "utils/simple-error";
+import beautify from "xml-beautifier";
+
+async function toolSource({ id }) {
+    const url = `${getAppRoot()}api/tools/${id}/raw_tool_source`;
+    try {
+        const { data, headers } = await axios.get(url);
+        const result = {};
+        result.language = headers.language;
+        if (headers.language === "xml") {
+            result.source = beautify(data);
+        } else {
+            result.source = data;
+        }
+        return result;
+    } catch (e) {
+        rethrowSimple(e);
+    }
+}
+
+export const ToolSourceProvider = SingleQueryProvider(toolSource);

client/yarn.lock

@@ -2729,6 +2729,14 @@ babel-preset-jest@^27.2.0:
     babel-plugin-jest-hoist "^27.2.0"
     babel-preset-current-node-syntax "^1.0.0"
 
+babel-runtime@^6.26.0:
+  version "6.26.0"
+  resolved "https://registry.yarnpkg.com/babel-runtime/-/babel-runtime-6.26.0.tgz#965c7058668e82b55d7bfe04ff2337bc8b5647fe"
+  integrity sha1-llxwWGaOgrVde/4E/yM3vItWR/4=
+  dependencies:
+    core-js "^2.4.0"
+    regenerator-runtime "^0.11.0"
+
 [email protected]:
   version "3.0.0-canary-5"
   resolved "https://registry.yarnpkg.com/babel-walk/-/babel-walk-3.0.0-canary-5.tgz#f66ecd7298357aee44955f235a6ef54219104b11"
@@ -3831,6 +3839,11 @@ core-js-pure@^3.0.0:
   resolved "https://registry.yarnpkg.com/core-js-pure/-/core-js-pure-3.18.3.tgz#7eed77dcce1445ab68fd68715856633e2fb3b90c"
   integrity sha512-qfskyO/KjtbYn09bn1IPkuhHl5PlJ6IzJ9s9sraJ1EqcuGyLGKzhSM1cY0zgyL9hx42eulQLZ6WaeK5ycJCkqw==
 
+core-js@^2.4.0:
+  version "2.6.12"
+  resolved "https://registry.yarnpkg.com/core-js/-/core-js-2.6.12.tgz#d9333dfa7b065e347cc5682219d6f690859cc2ec"
+  integrity sha512-Kb2wC0fvsWfQrgk8HU5lW6U/Lcs8+9aaYcy4ZFc6DDlo4nZ7n70dEgE5rtR0oG6ufKDUnrwfWL1mXR5ljDatrQ==
+
 core-js@^3.19.1:
   version "3.19.1"
   resolved "https://registry.yarnpkg.com/core-js/-/core-js-3.19.1.tgz#f6f173cae23e73a7d88fa23b6e9da329276c6641"
@@ -10070,7 +10083,7 @@ pretty@^2.0.0:
     extend-shallow "^2.0.1"
     js-beautify "^1.6.12"
 
-prismjs@^1.17.1, prismjs@^1.23.0:
+prismjs@^1.17.1, prismjs@^1.23.0, prismjs@^1.6.0:
   version "1.25.0"
   resolved "https://registry.yarnpkg.com/prismjs/-/prismjs-1.25.0.tgz#6f822df1bdad965734b310b315a23315cf999756"
   integrity sha512-WCjJHl1KEWbnkQom1+SzftbtXMKQoezOCYs5rECqMN+jP+apI7ftoflyqigqzopSO3hMhTEb0mFClA8lkolgEg==
@@ -10736,6 +10749,11 @@ regenerate@^1.4.0, regenerate@^1.4.2:
   resolved "https://registry.yarnpkg.com/regenerate/-/regenerate-1.4.2.tgz#b9346d8827e8f5a32f7ba29637d398b69014848a"
   integrity sha512-zrceR/XhGYU/d/opr2EKO7aRHUeiBI8qjtfHqADTwZd6Szfy16la6kqD0MIUs5z5hx6AaKa+PixpPrR289+I0A==
 
+regenerator-runtime@^0.11.0:
+  version "0.11.1"
+  resolved "https://registry.yarnpkg.com/regenerator-runtime/-/regenerator-runtime-0.11.1.tgz#be05ad7f9bf7d22e056f9726cee5017fbf19e2e9"
+  integrity sha512-MguG95oij0fC3QV3URf4V2SDYGJhJnJGqvIIgdECeODCT98wSWDAJ94SSuVpYQUoTcGUIL6L4yNB7j1DFFHSBg==
+
 regenerator-runtime@^0.13.4, regenerator-runtime@^0.13.7, regenerator-runtime@^0.13.9:
   version "0.13.9"
   resolved "https://registry.yarnpkg.com/regenerator-runtime/-/regenerator-runtime-0.13.9.tgz#8925742a98ffd90814988d7566ad30ca3b263b52"
@@ -10867,7 +10885,7 @@ repeat-element@^1.1.2:
   resolved "https://registry.yarnpkg.com/repeat-element/-/repeat-element-1.1.4.tgz#be681520847ab58c7568ac75fbfad28ed42d39e9"
   integrity sha512-LFiNfRcSu7KK3evMyYOuCzv3L10TW7yC1G2/+StMjK8Y6Vqd2MG7r/Qjw4ghtuCOjFvlnms/iMmLqpvW/ES/WQ==
 
-repeat-string@^1.0.0, repeat-string@^1.6.1:
+repeat-string@1.6.1, repeat-string@^1.0.0, repeat-string@^1.6.1:
   version "1.6.1"
   resolved "https://registry.yarnpkg.com/repeat-string/-/repeat-string-1.6.1.tgz#8dcae470e1c88abc2d600fff4a776286da75e637"
   integrity sha1-jcrkcOHIirwtYA//Sndihtp15jc=
@@ -12933,6 +12951,13 @@ vue-observe-visibility@^1.0.0:
   resolved "https://registry.yarnpkg.com/vue-observe-visibility/-/vue-observe-visibility-1.0.0.tgz#17cf1b2caf74022f0f3c95371468ddf2b9573152"
   integrity sha512-s5TFh3s3h3Mhd3jaz3zGzkVHKHnc/0C/gNr30olO99+yw2hl3WBhK3ng3/f9OF+qkW4+l7GkmwfAzDAcY3lCFg==
 
+vue-prismjs@^1.2.0:
+  version "1.2.0"
+  resolved "https://registry.yarnpkg.com/vue-prismjs/-/vue-prismjs-1.2.0.tgz#b137f5ed958685ce1fd55ca6b068289f3359b8b7"
+  integrity sha512-1mICbMknMiKw4mfM1AU7vkFT3VX4Cq8ySyDU7IBr9tYW1fzxIPkfLoERkRMbQLBc+J74K3FIiuuZ+WfBjO3SCQ==
+  dependencies:
+    prismjs "^1.6.0"
+
 vue-router@^3.5.2:
   version "3.5.2"
   resolved "https://registry.yarnpkg.com/vue-router/-/vue-router-3.5.2.tgz#5f55e3f251970e36c3e8d88a7cd2d67a350ade5c"
@@ -13544,6 +13569,13 @@ ws@~7.4.2:
   resolved "https://registry.yarnpkg.com/ws/-/ws-7.4.6.tgz#5654ca8ecdeee47c33a9a4bf6d28e2be2980377c"
   integrity sha512-YmhHDO4MzaDLB+M9ym/mDA5z0naX8j7SIlT8f8z+I0VtzsRbekxEutHSme7NPS2qE8StCYQNUnfWdXta/Yu85A==
 
+xml-beautifier@^0.5.0:
+  version "0.5.0"
+  resolved "https://registry.yarnpkg.com/xml-beautifier/-/xml-beautifier-0.5.0.tgz#476fd7118b972c2ec5863babca6812934d34bb56"
+  integrity sha512-QG/qiHeolHUd1tAtM+5zHxTzDprb8qvhmIYUYV1E9QK/jTFlrAa1Mz7QQqJPeqc3uuFAGzTOhjvbdx2hOP6bHw==
+  dependencies:
+    repeat-string "1.6.1"
+
 xml-name-validator@^3.0.0:
   version "3.0.0"
   resolved "https://registry.yarnpkg.com/xml-name-validator/-/xml-name-validator-3.0.0.tgz#6ae73e06de4d8c6e47f9fb181f78d648ad457c6a"

doc/source/admin/galaxy_options.rst

@@ -3908,6 +3908,20 @@
 :Type: bool
 
 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``enable_tool_source_display``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    This option allows users to view the tool wrapper source code.
+    This is safe to enable if you have not hardcoded any secrets in
+    any of the tool wrappers installed on this Galaxy server. If you
+    have only installed tool wrappers from  public tool sheds and
+    tools shipped with Galaxy there you can enable this option.
+:Default: ``false``
+:Type: bool
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``job_metrics_config_file``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~

lib/galaxy/config/sample/galaxy.yml.sample

@@ -1912,6 +1912,13 @@ galaxy:
   # see dataset paths.
   #expose_dataset_path: false
 
+  # This option allows users to view the tool wrapper source code. This
+  # is safe to enable if you have not hardcoded any secrets in any of
+  # the tool wrappers installed on this Galaxy server. If you have only
+  # installed tool wrappers from  public tool sheds and tools shipped
+  # with Galaxy there you can enable this option.
+  #enable_tool_source_display: false
+
   # XML config file that contains the job metric collection
   # configuration.
   # The value of this option will be resolved with respect to

lib/galaxy/managers/configuration.py

@@ -208,6 +208,7 @@ def _config_is_truthy(item, key, **context):
             'upload_from_form_button': _use_config,
             'release_doc_base_url': _use_config,
             'expose_user_email': _use_config,
+            'enable_tool_source_display': _use_config,
             'user_library_import_dir_available': lambda item, key, **context: bool(item.get('user_library_import_dir')),
             'welcome_directory': _use_config,
         }

lib/galaxy/tool_util/parser/cwl.py

@@ -21,6 +21,8 @@
 
 class CwlToolSource(ToolSource):
 
+    language = 'yaml'
+
     def __init__(self, tool_file, strict_cwl_validation=True):
         self._cwl_tool_file = tool_file
         self._id, _ = os.path.splitext(os.path.basename(tool_file))

lib/galaxy/tool_util/parser/interface.py

@@ -19,6 +19,7 @@ class ToolSource(metaclass=ABCMeta):
     information from.
     """
     default_is_multi_byte = False
+    language: str
 
     @abstractmethod
     def parse_id(self):

lib/galaxy/tool_util/parser/xml.py

@@ -50,6 +50,8 @@ class XmlToolSource(ToolSource):
     """ Responsible for parsing a tool from classic Galaxy representation.
     """
 
+    language = 'xml'
+
     def __init__(self, xml_tree, source_path=None, macro_paths=None):
         self.xml_tree = xml_tree
         self.root = xml_tree.getroot()

lib/galaxy/tool_util/parser/yaml.py

@@ -23,6 +23,8 @@
 
 class YamlToolSource(ToolSource):
 
+    language = 'yaml'
+
     def __init__(self, root_dict, source_path=None):
         self.root_dict = root_dict
         self._source_path = source_path

lib/galaxy/webapps/galaxy/api/tools.py

@@ -18,6 +18,7 @@
     expose_api_anonymous_and_sessionless,
     expose_api_raw_anonymous_and_sessionless,
 )
+from galaxy.web.framework.decorators import expose_api_raw
 from galaxy.webapps.base.controller import UsesVisualizationMixin
 from galaxy.webapps.base.webapp import GalaxyWebTransaction
 from . import BaseGalaxyAPIController, depends
@@ -490,6 +491,15 @@ def download(self, trans: GalaxyWebTransaction, id, **kwds):
         trans.response.headers["Content-Disposition"] = f'attachment; filename="{id}.tgz"'
         return download_file
 
+    @expose_api_raw
+    def raw_tool_source(self, trans: GalaxyWebTransaction, id, **kwds):
+        """Returns tool source. ``language`` is included in the response header."""
+        if not trans.app.config.enable_tool_source_display and not trans.user_is_admin:
+            raise exceptions.InsufficientPermissionsException("Only administrators may display tool sources on this Galaxy server.")
+        tool = self._get_tool(id, user=trans.user, tool_version=kwds.get('tool_version'))
+        trans.response.headers['language'] = tool.tool_source.language
+        return tool.tool_source.to_string()
+
     @expose_api_anonymous
     def fetch(self, trans: GalaxyWebTransaction, payload, **kwd):
         """Adapt clean API to tool-constrained API.

lib/galaxy/webapps/galaxy/buildapp.py

@@ -434,6 +434,7 @@ def populate_api_routes(webapp, app):
     webapp.mapper.connect('/api/tools/{tool_id:.+?}/convert', action='conversion', controller="tools", conditions=dict(method=["POST"]))
     webapp.mapper.connect('/api/tools/{id:.+?}/xrefs', action='xrefs', controller="tools")
     webapp.mapper.connect('/api/tools/{id:.+?}/download', action='download', controller="tools")
+    webapp.mapper.connect('/api/tools/{id:.+?}/raw_tool_source', action='raw_tool_source', controller="tools")
     webapp.mapper.connect('/api/tools/{id:.+?}/requirements', action='requirements', controller="tools")
     webapp.mapper.connect('/api/tools/{id:.+?}/install_dependencies', action='install_dependencies', controller="tools", conditions=dict(method=["POST"]))
     webapp.mapper.connect('/api/tools/{id:.+?}/dependencies', action='install_dependencies', controller="tools", conditions=dict(method=["POST"]))

lib/galaxy/webapps/galaxy/config_schema.yml

@@ -2821,6 +2821,17 @@ mapping:
           Details" option in the history. This option also exposes the command line to
           non-administrative users. Administrators can always see dataset paths.
 
+      enable_tool_source_display:
+        type: bool
+        default: false
+        required: false
+        desc: |
+          This option allows users to view the tool wrapper source code. This is
+          safe to enable if you have not hardcoded any secrets in any of the tool
+          wrappers installed on this Galaxy server. If you have only installed tool
+          wrappers from  public tool sheds and tools shipped with Galaxy there you
+          can enable this option.
+
       job_metrics_config_file:
         type: str
         default: job_metrics_conf.xml