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jmchiltonjmchilton
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[WIP] Use tool request API from the tool form.
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12 files changed

+1635
-99
lines changed

12 files changed

+1635
-99
lines changed

‎client/src/api/jobs.ts‎

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@@ -39,4 +39,5 @@ export interface ResponseVal {
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jobDef: JobDef;
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jobResponse: JobResponse;
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toolName: string;
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usedToolRequest: boolean;
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}

‎client/src/api/tools.ts‎

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@@ -72,3 +72,12 @@ export function fetchJobErrorMessage(jobDetails: ShowFullJobResponse): string |
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}
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return errorMessage;
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}
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export async function getToolInputs(tool_id: string, tool_version: string) {
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return GalaxyApi().GET(`/api/tools/{tool_id}/inputs`, {
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params: {
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query: { tool_version },
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path: { tool_id },
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},
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});
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}

‎client/src/components/Tool/ToolForm.vue‎

Lines changed: 202 additions & 89 deletions
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‎client/src/components/Tool/ToolSuccess.vue‎

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@@ -20,6 +20,8 @@ const router = useRouter();
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const jobDef = computed(() => latestResponse.value?.jobDef);
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const jobResponse = computed(() => latestResponse.value?.jobResponse);
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const responseVal = computed(() => jobStore.latestResponse);
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const usedToolRequest = computed(() => responseVal.value?.usedToolRequest);
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const showRecommendation = computed(() => config.value.enable_tool_recommendations);
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const toolName = computed(() => latestResponse.value?.toolName);
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@@ -38,7 +40,10 @@ if (!latestResponse.value || Object.keys(latestResponse.value).length === 0) {
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<div v-if="jobResponse?.produces_entry_points">
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<ToolEntryPoints v-for="job in jobResponse.jobs" :key="job.id" :job-id="job.id" />
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</div>
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<ToolSuccessMessage :job-response="jobResponse" :tool-name="toolName || '...'" />
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<ToolSuccessMessage
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:job-response="jobResponse"
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:tool-name="toolName || '...'"
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:used-tool-request="usedToolRequest || false" />
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<Webhook v-if="jobDef" type="tool" :tool-id="jobDef.tool_id" />
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<ToolRecommendation v-if="showRecommendation && jobDef" :tool-id="jobDef.tool_id" />
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</div>

‎client/src/components/Tool/ToolSuccessMessage.test.ts‎

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@@ -38,6 +38,7 @@ describe("ToolSuccessMessage", () => {
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propsData: {
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jobResponse: TEST_JOB_RESPONSE,
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toolName: TEST_TOOL_NAME,
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usedToolRequest: false,
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},
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stubs: {
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FontAwesomeIcon: true,

‎client/src/components/Tool/ToolSuccessMessage.vue‎

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Original file line numberDiff line numberDiff line change
@@ -9,6 +9,7 @@ import ExternalLink from "../ExternalLink.vue";
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const props = defineProps<{
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jobResponse: JobResponse;
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toolName: string;
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usedToolRequest: boolean;
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}>();
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const outputs = computed(() => props.jobResponse.outputs.concat(props.jobResponse.output_collections));
@@ -22,15 +23,23 @@ const nOutputsText = computed(() => (outputs.value.length > 1 ? `${outputs.value
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<template>
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<div class="donemessagelarge">
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<p>
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Started tool <b>{{ props.toolName }}</b> and successfully added {{ nJobsText }} to the queue.
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</p>
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<p>It produces {{ nOutputsText }}:</p>
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<ul data-description="list of outputs">
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<li v-for="item of outputs" :key="item.hid">
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<b>{{ item.hid }}: {{ item.name }}</b>
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</li>
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</ul>
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<div v-if="usedToolRequest">
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You used the fancy new API... something new will be here.
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<img
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src="https://www.animatedimages.org/data/media/695/animated-under-construction-image-0055.gif"
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alt="90s style under construction" />
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</div>
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<div v-else>
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<p>
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Started tool <b>{{ props.toolName }}</b> and successfully added {{ nJobsText }} to the queue.
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</p>
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<p>It produces {{ nOutputsText }}:</p>
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<ul data-description="list of outputs">
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<li v-for="item of outputs" :key="item.hid">
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<b>{{ item.hid }}: {{ item.name }}</b>
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</li>
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</ul>
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</div>
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<p>
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You can check the status of queued jobs and view the resulting data by refreshing the History panel. When
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the job has been run the status will change from 'running' to 'finished' if completed successfully or

‎client/src/components/Tool/parameterModels.ts‎

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@@ -0,0 +1,305 @@
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/* tslint:disable */
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/* eslint-disable */
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/**
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/* This file was automatically generated from pydantic models by running pydantic2ts.
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/* Do not modify it by hand - just update the pydantic models and then re-run the script
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*/
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export type ToolParameterModel =
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| TextParameterModel
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| IntegerParameterModel
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| FloatParameterModel
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| BooleanParameterModel
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| HiddenParameterModel
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| SelectParameterModel
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| DataParameterModel
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| DataCollectionParameterModel
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| DirectoryUriParameterModel
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| RulesParameterModel
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| ColorParameterModel
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| ConditionalParameterModel
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| RepeatParameterModel
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| CwlIntegerParameterModel
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| CwlFloatParameterModel
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| CwlStringParameterModel
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| CwlBooleanParameterModel
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| CwlNullParameterModel
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| CwlFileParameterModel
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| CwlDirectoryParameterModel
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| CwlUnionParameterModel;
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export interface BaseGalaxyToolParameterModelDefinition {
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name: string;
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parameter_type: string;
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hidden?: boolean;
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label?: string;
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help?: string;
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argument?: string;
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refresh_on_change?: boolean;
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optional?: boolean;
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is_dynamic?: boolean;
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}
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export interface BaseToolParameterModelDefinition {
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name: string;
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parameter_type: string;
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}
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export interface BooleanParameterModel {
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name: string;
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parameter_type?: "gx_boolean";
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hidden?: boolean;
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label?: string;
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help?: string;
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argument?: string;
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refresh_on_change?: boolean;
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optional?: boolean;
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is_dynamic?: boolean;
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value?: boolean;
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truevalue?: string;
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falsevalue?: string;
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}
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export interface ColorParameterModel {
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name: string;
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parameter_type?: "gx_color";
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hidden?: boolean;
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label?: string;
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help?: string;
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argument?: string;
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refresh_on_change?: boolean;
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optional?: boolean;
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is_dynamic?: boolean;
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}
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export interface ConditionalParameterModel {
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name: string;
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parameter_type?: "gx_conditional";
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hidden?: boolean;
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label?: string;
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help?: string;
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argument?: string;
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refresh_on_change?: boolean;
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optional?: boolean;
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is_dynamic?: boolean;
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test_parameter: BooleanParameterModel | SelectParameterModel;
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whens: ConditionalWhen[];
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}
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export interface SelectParameterModel {
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name: string;
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parameter_type?: "gx_select";
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hidden?: boolean;
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label?: string;
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help?: string;
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argument?: string;
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refresh_on_change?: boolean;
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optional?: boolean;
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is_dynamic?: boolean;
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options?: LabelValue[];
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multiple: boolean;
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}
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export interface LabelValue {
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label: string;
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value: string;
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}
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export interface ConditionalWhen {
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discriminator: boolean | string;
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parameters: ToolParameterModel[];
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}
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export interface TextParameterModel {
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name: string;
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parameter_type?: "gx_text";
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hidden?: boolean;
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label?: string;
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help?: string;
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argument?: string;
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refresh_on_change?: boolean;
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optional?: boolean;
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is_dynamic?: boolean;
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area?: boolean;
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value?: string;
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default_options?: LabelValue[];
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}
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export interface IntegerParameterModel {
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name: string;
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parameter_type?: "gx_integer";
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hidden?: boolean;
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label?: string;
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help?: string;
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argument?: string;
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refresh_on_change?: boolean;
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optional: boolean;
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is_dynamic?: boolean;
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value?: number;
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min?: number;
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max?: number;
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}
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export interface FloatParameterModel {
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name: string;
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parameter_type?: "gx_float";
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hidden?: boolean;
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label?: string;
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help?: string;
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argument?: string;
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refresh_on_change?: boolean;
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optional?: boolean;
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is_dynamic?: boolean;
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value?: number;
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min?: number;
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max?: number;
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}
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export interface HiddenParameterModel {
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name: string;
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parameter_type?: "gx_hidden";
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hidden?: boolean;
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label?: string;
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help?: string;
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argument?: string;
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refresh_on_change?: boolean;
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optional?: boolean;
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is_dynamic?: boolean;
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}
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export interface DataParameterModel {
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name: string;
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parameter_type?: "gx_data";
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hidden?: boolean;
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label?: string;
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help?: string;
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argument?: string;
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refresh_on_change?: boolean;
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optional?: boolean;
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is_dynamic?: boolean;
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extensions?: string[];
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multiple?: boolean;
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min?: number;
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max?: number;
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}
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export interface DataCollectionParameterModel {
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name: string;
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parameter_type?: "gx_data_collection";
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hidden?: boolean;
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label?: string;
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help?: string;
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argument?: string;
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refresh_on_change?: boolean;
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optional?: boolean;
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is_dynamic?: boolean;
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collection_type?: string;
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extensions?: string[];
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}
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export interface DirectoryUriParameterModel {
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name: string;
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parameter_type: "gx_directory_uri";
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hidden?: boolean;
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label?: string;
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help?: string;
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argument?: string;
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refresh_on_change?: boolean;
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optional?: boolean;
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is_dynamic?: boolean;
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value?: string;
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}
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export interface RulesParameterModel {
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name: string;
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parameter_type?: "gx_rules";
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hidden?: boolean;
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label?: string;
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help?: string;
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argument?: string;
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refresh_on_change?: boolean;
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optional?: boolean;
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is_dynamic?: boolean;
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}
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export interface RepeatParameterModel {
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name: string;
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parameter_type?: "gx_repeat";
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hidden?: boolean;
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label?: string;
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help?: string;
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argument?: string;
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refresh_on_change?: boolean;
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optional?: boolean;
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is_dynamic?: boolean;
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parameters: ToolParameterModel[];
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}
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export interface CwlIntegerParameterModel {
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name: string;
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parameter_type?: "cwl_integer";
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}
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export interface CwlFloatParameterModel {
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name: string;
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parameter_type?: "cwl_float";
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}
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export interface CwlStringParameterModel {
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name: string;
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parameter_type?: "cwl_string";
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}
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export interface CwlBooleanParameterModel {
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name: string;
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parameter_type?: "cwl_boolean";
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}
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export interface CwlNullParameterModel {
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name: string;
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parameter_type?: "cwl_null";
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}
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export interface CwlFileParameterModel {
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name: string;
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parameter_type?: "cwl_file";
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hidden?: boolean;
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label?: string;
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help?: string;
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argument?: string;
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refresh_on_change?: boolean;
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optional?: boolean;
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is_dynamic?: boolean;
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}
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export interface CwlDirectoryParameterModel {
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name: string;
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parameter_type?: "cwl_directory";
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hidden?: boolean;
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label?: string;
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help?: string;
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argument?: string;
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refresh_on_change?: boolean;
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optional?: boolean;
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is_dynamic?: boolean;
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}
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export interface CwlUnionParameterModel {
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name: string;
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parameter_type?: "cwl_union";
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parameters: ToolParameterModel[];
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}
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export interface DataCollectionRequest {
269+
src: "hdca";
270+
id: string;
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}
272+
export interface DataCollectionRequestInternal {
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src: "hdca";
274+
id: number;
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}
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export interface DataRequest {
277+
src: "hda" | "ldda";
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id: string;
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}
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export interface DataRequestInteranl {
281+
src: "hda" | "ldda";
282+
id: number;
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}
284+
export interface MultiDataInstance {
285+
src: "hda" | "ldda" | "hdca";
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id: string;
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}
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export interface MultiDataInstanceInternal {
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src: "hda" | "ldda" | "hdca";
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id: number;
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}
292+
export interface RulesMapping {
293+
type: string;
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columns: number[];
295+
}
296+
export interface RulesModel {
297+
rules: {
298+
[k: string]: unknown;
299+
}[];
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mappings: RulesMapping[];
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}
302+
export interface StrictModel {}
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export interface ToolParameterBundleModel {
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input_models: ToolParameterModel[];
305+
}

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