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denis-yuen committed Jul 7, 2021
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7 changes: 6 additions & 1 deletion .circleci/config.yml
Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,11 @@ jobs:
command: bash -i -c 'npm run test-dev-no-auth'
environment:
MOCHA_FILE: nightly-test-results/junit/test-dev-no-auth-[hash].xml
- run:
name: Run remote verification of WAF against dev
command: bash -i -c 'npm run test-dev-waf'
environment:
MOCHA_FILE: nightly-test-results/junit/test-dev-waf-[hash].xml
- upload_nightly_artifacts
- slack/status:
fail_only: true
Expand Down Expand Up @@ -219,7 +224,7 @@ jobs:
command: bash -i -c 'npm config set dockstore-ui2:webservice_version develop'
- run:
name: Build
command: bash -i -c 'npm run build'
command: NODE_OPTIONS="--max-old-space-size=1610" bash -i -c 'npm run build.prod'

workflows:
version: 2
Expand Down
12 changes: 1 addition & 11 deletions README.md
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Expand Up @@ -2,7 +2,7 @@
[![Build Status](https://travis-ci.org/dockstore/dockstore-ui2.svg?branch=develop)](https://travis-ci.org/dockstore/dockstore-ui2)
[![codecov](https://codecov.io/gh/dockstore/dockstore-ui2/branch/develop/graph/badge.svg)](https://codecov.io/gh/dockstore/dockstore-ui2)

Please file issues for this repository and Web site at [the ga4gh/dockstore repository](https://github.com/ga4gh/dockstore/issues)!
Please file issues for this repository and Web site at [the dockstore/dockstore repository](https://github.com/dockstore/dockstore/issues)!

Table of Contents
=================
Expand Down Expand Up @@ -212,16 +212,6 @@ Before running the tests make sure you:
- serve the app via `ng serve` or similar.
- have the Dockstore webservice jar in the root directory and run it (see scripts/run-webservice-script.sh for guideline)

## Documentation Generation

This should eventually be done automatically on the master branch and have GitHub pages point to the docs folder.
To manually run it:
```
npm install -g @compodoc/compodoc
npm run compodoc
```
Then open `docs/index.html` with browser

## Further help

To get more help on the Angular CLI use `ng help` or go check out the [Angular CLI README](https://github.com/angular/angular-cli/blob/master/README.md).
Expand Down
701 changes: 363 additions & 338 deletions THIRD-PARTY-LICENSES.csv

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7 changes: 1 addition & 6 deletions angular.json
Original file line number Diff line number Diff line change
Expand Up @@ -24,9 +24,7 @@
],
"styles": [
"node_modules/bootstrap/dist/css/bootstrap.css",
"node_modules/font-awesome/css/font-awesome.css",
"node_modules/bootstrap-social/bootstrap-social.css",
"src/styles.css",
"node_modules/academicons/css/academicons.css",
"src/styles.scss",
"src/material.scss"
],
Expand Down Expand Up @@ -133,9 +131,6 @@
],
"styles": [
"node_modules/bootstrap/dist/css/bootstrap.css",
"node_modules/font-awesome/css/font-awesome.css",
"node_modules/bootstrap-social/bootstrap-social.css",
"src/styles.css",
"src/styles.scss",
"src/material.scss"
],
Expand Down
78 changes: 78 additions & 0 deletions cypress/fixtures/doiResponse.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,78 @@
[
{
"aliases": null,
"author": null,
"commitID": null,
"dbUpdateDate": 1622246514895,
"description": null,
"descriptionSource": null,
"dirtyBit": false,
"doiStatus": "NOT_REQUESTED",
"doiURL": "10.5072/zenodo.841014",
"email": null,
"frozen": true,
"hidden": false,
"id": 13,
"images": null,
"input_file_formats": [],
"last_modified": 1480374117003,
"legacyVersion": true,
"name": "master",
"output_file_formats": [],
"reference": "master",
"referenceType": "UNSET",
"subClass": null,
"synced": false,
"valid": true,
"validations": null,
"verified": false,
"verifiedSource": null,
"verifiedSources": [],
"versionEditor": null,
"versionMetadata": {
"id": 13,
"orcidPutCode": null,
"parsedInformationSet": []
},
"workflow_path": "/1st-workflow.cwl",
"workingDirectory": ""
},
{
"aliases": null,
"author": null,
"commitID": null,
"dbUpdateDate": 1480374117003,
"description": null,
"descriptionSource": null,
"dirtyBit": false,
"doiStatus": "NOT_REQUESTED",
"doiURL": null,
"email": null,
"frozen": false,
"hidden": true,
"id": 14,
"images": null,
"input_file_formats": [],
"last_modified": 1480374117003,
"legacyVersion": true,
"name": "test",
"output_file_formats": [],
"reference": "test",
"referenceType": "UNSET",
"subClass": null,
"synced": true,
"valid": true,
"validations": null,
"verified": false,
"verifiedSource": null,
"verifiedSources": [],
"versionEditor": null,
"versionMetadata": {
"id": 14,
"orcidPutCode": null,
"parsedInformationSet": []
},
"workflow_path": "/1st-workflow.cwl",
"workingDirectory": ""
}
]
2 changes: 1 addition & 1 deletion cypress/fixtures/myWorkflows.json
Original file line number Diff line number Diff line change
@@ -1 +1 @@
[{"type":"BioWorkflow","descriptorType":"CWL","aliases":null,"author":null,"checker_id":null,"conceptDoi":null,"dbCreateDate":1465409196000,"dbUpdateDate":1465409196000,"defaultTestParameterFilePath":"/test.json","defaultVersion":null,"description":null,"descriptorTypeSubclass":"NOT_APPLICABLE","email":null,"full_workflow_path":"github.com/A/l","gitUrl":"[email protected]:A/l.git","has_checker":false,"id":11,"input_file_formats":[],"is_checker":false,"is_published":true,"labels":[],"lastUpdated":1480363257688,"last_modified":null,"last_modified_date":null,"mode":"FULL","organization":"A","output_file_formats":[],"parent_id":null,"path":"github.com/A/l","repository":"l","sourceControl":"github.com","source_control_provider":"GITHUB","starredUsers":[],"topicId":null,"users":null,"workflowName":null,"workflowVersions":[],"workflow_path":"/1st-workflow.cwl"},{"type":"BioWorkflow","descriptorType":"CWL","aliases":null,"author":null,"checker_id":null,"conceptDoi":null,"dbCreateDate":1465409196000,"dbUpdateDate":1465409196000,"defaultTestParameterFilePath":"/test.json","defaultVersion":null,"description":null,"descriptorTypeSubclass":"NOT_APPLICABLE","email":null,"full_workflow_path":"github.com/A/addedthisworkflowviasync","gitUrl":"[email protected]:A/addedthisworkflowviasync.git","has_checker":false,"id":11,"input_file_formats":[],"is_checker":false,"is_published":true,"labels":[],"lastUpdated":1480363257688,"last_modified":null,"last_modified_date":null,"mode":"FULL","organization":"A","output_file_formats":[],"parent_id":null,"path":"github.com/A/addedthisworkflowviasync","repository":"addedthisworkflowviasync","sourceControl":"github.com","source_control_provider":"GITHUB","starredUsers":[],"topicId":null,"users":null,"workflowName":null,"workflowVersions":[],"workflow_path":"/1st-workflow.cwl"},{"type":"BioWorkflow","descriptorType":"CWL","aliases":null,"author":null,"checker_id":null,"conceptDoi":null,"dbCreateDate":1578510396000,"dbUpdateDate":1578510396000,"defaultTestParameterFilePath":"/test.json","defaultVersion":null,"description":null,"descriptorTypeSubclass":"NOT_APPLICABLE","email":null,"full_workflow_path":"github.com/B/z","gitUrl":"[email protected]:B/z.git","has_checker":false,"id":30,"input_file_formats":[],"is_checker":false,"is_published":false,"labels":[],"lastUpdated":1580241657315,"last_modified":null,"last_modified_date":null,"mode":"DOCKSTORE_YML","organization":"B","output_file_formats":[],"parent_id":null,"path":"github.com/B/z","repository":"z","sourceControl":"github.com","source_control_provider":"GITHUB","starredUsers":[],"topicId":null,"users":null,"workflowName":null,"workflowVersions":[],"workflow_path":"/Dockstore.cwl"},{"type":"BioWorkflow","descriptorType":"WDL","aliases":null,"author":null,"checker_id":null,"conceptDoi":null,"dbCreateDate":1465409196000,"dbUpdateDate":1465409196000,"defaultTestParameterFilePath":"/test.json","defaultVersion":null,"description":null,"descriptorTypeSubclass":"NOT_APPLICABLE","email":null,"full_workflow_path":"dockstore.org/A/hosted-workflow","gitUrl":"[email protected]:workflows/dockstore.org/A/hosted-workflow.git","has_checker":false,"id":21,"input_file_formats":[],"is_checker":false,"is_published":false,"labels":[],"lastUpdated":1480363257315,"last_modified":null,"last_modified_date":null,"mode":"HOSTED","organization":"A","output_file_formats":[],"parent_id":null,"path":"dockstore.org/A/hosted-workflow","repository":"hosted-workflow","sourceControl":"dockstore.org","source_control_provider":"DOCKSTORE","starredUsers":[],"topicId":null,"users":null,"workflowName":null,"workflowVersions":[],"workflow_path":"/Dockstore.wdl"}]
[{"type":"BioWorkflow","descriptorType":"CWL","aliases":null,"author":null,"checker_id":null,"conceptDoi":null,"dbCreateDate":1465409196000,"dbUpdateDate":1465409196000,"defaultTestParameterFilePath":"/test.json","defaultVersion":null,"description":null,"descriptorTypeSubclass":"NOT_APPLICABLE","email":null,"full_workflow_path":"github.com/A/l","gitUrl":"[email protected]:A/l.git","has_checker":false,"id":11,"input_file_formats":[],"isChecker":false,"is_published":true,"labels":[],"lastUpdated":1480363257688,"last_modified":null,"last_modified_date":null,"mode":"FULL","organization":"A","output_file_formats":[],"parent_id":null,"path":"github.com/A/l","repository":"l","sourceControl":"github.com","source_control_provider":"GITHUB","starredUsers":[],"topicId":null,"users":null,"workflowName":null,"workflowVersions":[],"workflow_path":"/1st-workflow.cwl"},{"type":"BioWorkflow","descriptorType":"CWL","aliases":null,"author":null,"checker_id":null,"conceptDoi":null,"dbCreateDate":1465409196000,"dbUpdateDate":1465409196000,"defaultTestParameterFilePath":"/test.json","defaultVersion":null,"description":null,"descriptorTypeSubclass":"NOT_APPLICABLE","email":null,"full_workflow_path":"github.com/A/addedthisworkflowviasync","gitUrl":"[email protected]:A/addedthisworkflowviasync.git","has_checker":false,"id":11,"input_file_formats":[],"isChecker":false,"is_published":true,"labels":[],"lastUpdated":1480363257688,"last_modified":null,"last_modified_date":null,"mode":"FULL","organization":"A","output_file_formats":[],"parent_id":null,"path":"github.com/A/addedthisworkflowviasync","repository":"addedthisworkflowviasync","sourceControl":"github.com","source_control_provider":"GITHUB","starredUsers":[],"topicId":null,"users":null,"workflowName":null,"workflowVersions":[],"workflow_path":"/1st-workflow.cwl"},{"type":"BioWorkflow","descriptorType":"CWL","aliases":null,"author":null,"checker_id":null,"conceptDoi":null,"dbCreateDate":1578510396000,"dbUpdateDate":1578510396000,"defaultTestParameterFilePath":"/test.json","defaultVersion":null,"description":null,"descriptorTypeSubclass":"NOT_APPLICABLE","email":null,"full_workflow_path":"github.com/B/z","gitUrl":"[email protected]:B/z.git","has_checker":false,"id":30,"input_file_formats":[],"isChecker":false,"is_published":false,"labels":[],"lastUpdated":1580241657315,"last_modified":null,"last_modified_date":null,"mode":"DOCKSTORE_YML","organization":"B","output_file_formats":[],"parent_id":null,"path":"github.com/B/z","repository":"z","sourceControl":"github.com","source_control_provider":"GITHUB","starredUsers":[],"topicId":null,"users":null,"workflowName":null,"workflowVersions":[],"workflow_path":"/Dockstore.cwl"},{"type":"BioWorkflow","descriptorType":"WDL","aliases":null,"author":null,"checker_id":null,"conceptDoi":null,"dbCreateDate":1465409196000,"dbUpdateDate":1465409196000,"defaultTestParameterFilePath":"/test.json","defaultVersion":null,"description":null,"descriptorTypeSubclass":"NOT_APPLICABLE","email":null,"full_workflow_path":"dockstore.org/A/hosted-workflow","gitUrl":"[email protected]:workflows/dockstore.org/A/hosted-workflow.git","has_checker":false,"id":21,"input_file_formats":[],"isChecker":false,"is_published":false,"labels":[],"lastUpdated":1480363257315,"last_modified":null,"last_modified_date":null,"mode":"HOSTED","organization":"A","output_file_formats":[],"parent_id":null,"path":"dockstore.org/A/hosted-workflow","repository":"hosted-workflow","sourceControl":"dockstore.org","source_control_provider":"DOCKSTORE","starredUsers":[],"topicId":null,"users":null,"workflowName":null,"workflowVersions":[],"workflow_path":"/Dockstore.wdl"}]
2 changes: 1 addition & 1 deletion cypress/fixtures/refreshedAslashl.json
Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@
"has_checker": false,
"id": 11,
"input_file_formats": [],
"is_checker": false,
"isChecker": false,
"is_published": true,
"labels": [],
"lastUpdated": 1480374057688,
Expand Down
4 changes: 2 additions & 2 deletions cypress/fixtures/refreshedChecker.json
Original file line number Diff line number Diff line change
Expand Up @@ -15,11 +15,11 @@
"full_workflow_path": "github.com\/A\/l\/_cwl_checker",
"gitUrl": "[email protected]:A\/l.git",
"has_checker": false,
"id": 103,
"id": 102,
"input_file_formats": [

],
"is_checker": true,
"isChecker": true,
"is_published": true,
"labels": [

Expand Down
2 changes: 1 addition & 1 deletion cypress/fixtures/searchTableResponse.json
Original file line number Diff line number Diff line change
Expand Up @@ -272,7 +272,7 @@
"aliases": {},
"is_published": true,
"last_modified_date": null,
"is_checker": false,
"isChecker": false,
"checker_id": null,
"repository": "l",
"source_control_provider": "GITHUB",
Expand Down
34 changes: 34 additions & 0 deletions cypress/fixtures/tokens.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,34 @@
[
{
"dbCreateDate": 1595275995928,
"dbUpdateDate": 1595275995928,
"id": 129838,
"tokenSource": "dockstore",
"userId": 1,
"username": "coverbeck"
},
{
"dbCreateDate": 1618604954189,
"dbUpdateDate": 1618604954189,
"id": 135488,
"tokenSource": "orcid.org",
"userId": 1,
"username": "Charles Overbeck"
},
{
"dbCreateDate": 1618602772856,
"dbUpdateDate": 1618602772856,
"id": 135438,
"tokenSource": "zenodo.org",
"userId": 1,
"username": "coverbeck"
},
{
"dbCreateDate": 1595275995936,
"dbUpdateDate": 1620412026948,
"id": 129888,
"tokenSource": "github.com",
"userId": 1,
"username": "coverbeck"
}
]
2 changes: 2 additions & 0 deletions cypress/integration/group1/checkerWorkflowFromTools.ts
Original file line number Diff line number Diff line change
Expand Up @@ -99,6 +99,7 @@ describe('Checker workflow test from my-tools', () => {
// cy.url().should('eq','/my-tools/quay.io/A2/b3')
cy.get('#publishToolButton').should('be.visible').should('contain', 'Unpublish').click();
cy.get('#publishToolButton').should('be.visible').should('contain', 'Publish');
cy.wait(250);
cy.get('#viewCheckerWorkflowButton').should('be.visible').click();

// In the checker workflow right now
Expand All @@ -112,6 +113,7 @@ describe('Checker workflow test from my-tools', () => {
cy.url().should('eq', Cypress.config().baseUrl + '/my-tools/quay.io/A2/b3');
cy.get('#publishToolButton').should('be.visible').should('contain', 'Publish').click();
cy.get('#publishToolButton').should('be.visible').should('contain', 'Unpublish');
cy.wait(250);
cy.get('#viewCheckerWorkflowButton').should('be.visible').click();

// in the checker workflow right now
Expand Down
2 changes: 2 additions & 0 deletions cypress/integration/group1/checkerWorkflowFromWorkflow.ts
Original file line number Diff line number Diff line change
Expand Up @@ -67,6 +67,7 @@ describe('Checker workflow test from my-workflows', () => {
cy.contains('github.com/A/l/_cwl_checker');
cy.get('#addCheckerWorkflowButton').should('not.be.visible');
cy.get('#viewParentEntryButton').should('be.visible').click();
cy.wait(300);
cy.get('#workflow-path').contains('github.com/A/l');
cy.url().should('eq', Cypress.config().baseUrl + '/my-workflows/github.com/A/l');
cy.get('#viewParentEntryButton').should('not.be.visible');
Expand All @@ -81,6 +82,7 @@ describe('Checker workflow test from my-workflows', () => {
goToTab('Launch');
cy.get('#launchCheckerWorkflow').should('be.visible');
goToTab('Info');
cy.wait(300);
cy.get('#viewCheckerWorkflowButton').should('be.visible').click();

// In the checker workflow right now
Expand Down
8 changes: 4 additions & 4 deletions cypress/integration/group1/hostedTools.ts
Original file line number Diff line number Diff line change
Expand Up @@ -161,14 +161,14 @@ describe('Dockstore hosted tools', () => {
});
});

describe('Should not be able to edit unpublished tools', () => {
it('Should return an error when editing an unpublished hosted tool', () => {
describe('Should be able to edit unpublished tools', () => {
it('Should not return an error when editing an unpublished hosted tool', () => {
getTool();
goToTab('Versions');
cy.get('[data-cy=actionsButton]').first().click();
cy.get('[data-cy=editTagButton]').click();
cy.get('.alert').should('exist');
cy.get('.error-output').contains('[HTTP 403] Forbidden: Entry not published').should('exist');
cy.get('.alert').should('not.exist');
cy.get('[data-cy=editToolVersionDialog]').should('exist');
});
it('Should not return an error when editing a published hosted tool', () => {
getTool();
Expand Down
46 changes: 45 additions & 1 deletion cypress/integration/group1/hostedWorkflows.ts
Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,9 @@ describe('Dockstore hosted workflows', () => {
goToUnexpandedSidebarEntry('dockstore.org/A', /hosted/);
}

// using an ugly name to flex workflow naming functionality a bit
const NEW_WORKFLOW_NAME = 'new_Hosted-workflow-8_part-2';

// Ensure tabs are correct for the hosted workflow, try adding a version
describe('Should be able to register a hosted workflow and add files to it', () => {
it('Register the workflow', () => {
Expand All @@ -46,7 +49,7 @@ describe('Dockstore hosted workflows', () => {
cy.get('#publishButton').should('be.disabled');

// Check content of the info tab
cy.contains('Mode: HOSTED');
cy.contains('Mode: Hosted');

// Should not be able to download zip
cy.get('#downloadZipButton').should('not.be.visible');
Expand All @@ -59,6 +62,7 @@ describe('Dockstore hosted workflows', () => {
goToTab('Files');
cy.get('#editFilesButton').click();
cy.contains('Add File').click();
cy.wait(100);
cy.window().then(function (window: any) {
cy.document().then((doc) => {
const editors = doc.getElementsByClassName('ace_editor');
Expand Down Expand Up @@ -145,5 +149,45 @@ describe('Dockstore hosted workflows', () => {
goToTab('Files');
cy.contains('/Dockstore.wdl').should('be.visible');
});
it('Create a new hosted workflow', () => {
cy.get('#registerWorkflowButton').should('be.visible').should('be.enabled').click();
cy.get('#3-register-workflow-option').should('be.visible').click();
cy.contains('button', 'Next').click();
cy.get('#hostedWorkflowRepository').type(NEW_WORKFLOW_NAME);
cy.contains('button', 'Register Workflow').click();
});
it('Add files to hosted workflow', () => {
// navigate to workflow
cy.get('.mat-expanded');
cy.contains('dockstore.org/user_A').click();
cy.contains('a', NEW_WORKFLOW_NAME).click();

// Check content of the info tab
cy.contains('Mode: Hosted');

// Add a new version with 3 descriptors
goToTab('Files');
cy.get('#editFilesButton').click();

// there should be no descriptors files
cy.get('app-code-editor').should('have.length', 0);

// add first file. This will be the primary descriptor, so we wont need to give it a custom name
cy.contains('Add File').click();

// add a bunch of new files
for (let i = 0; i < 3; i++) {
cy.contains('Add File').click();
cy.wait(100); // focus is pulled to the content box of the editor shortly after adding a file, wait for this to occur
cy.get('.editor-file-name').last().type(`{selectall}{backspace}/${i}.cwl{enter}`);
}

// save as a new version
cy.get('#saveNewVersionButton').click();
cy.wait(1000); // have to wait for the response from the webservice, otherwise you may get a false positive

// should have 4 descriptors.
cy.get('app-code-editor').should('have.length', 4);
});
});
});
2 changes: 1 addition & 1 deletion cypress/integration/group2/mytools.ts
Original file line number Diff line number Diff line change
Expand Up @@ -65,7 +65,7 @@ describe('Dockstore my tools', () => {
cy.contains('Last Build');
cy.contains('Last Updated');
cy.contains('Build Mode');
cy.contains('Fully-Automated');
cy.contains('Fully automated');
cy.contains('/Dockstore.cwl');
// Change the dockerfile path
cy.contains('button', ' Edit ').click();
Expand Down
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