WDL imports #43

ekoltsova · 2017-11-22T15:55:37Z

General idea

Currently pipeline-builder has no support for import statements (https://software.broadinstitute.org/wdl/documentation/spec#import-statements)

The PR resolve this problem

Changes

Added support for sub workflows and import statements:

import "foo.wdl" as Foo and import "bar.wdl" like imports
- In this case additional files can be provided via .zip archive file or baseURI (baseURI + fileName)
http:// and https:// protocols support (like import "http://foo/bar.wdl" as Bar)

Added tests

Acceptance criteria

1st scenario:

Run gulp serve to launch the demo
Type .wdl script in textarea
Click Load zip button and choose .zip file containing .wdl import files

Example:

WDL script with import statements:

import "tasks.wdl"
import "sub_workflow.wdl" as SubWorkflow

workflow RootWorkflow {
    File? wfInput
    File? wfInputTwo
    File? wfInputThree

    call tasks.TaskOne {
        input:
            taskInput = wfInput
    }

    call SubWorkflow.Workflow {
        input:
            wf_input = TaskOne.task_output,
            wf_input_two = wfInput
    }

    call SubWorkflow.Workflow as WorkflowAliasOne {
        input:
            wf_input = TaskOne.task_output,
            wf_input_two = wfInputTwo
    }

    call SubWorkflow.Workflow as WorkflowAliasTwo {
        input:
            wf_input = TaskOne.task_output,
            wf_input_two = wfInputThree
    }

    output {
        String output_1 = WorkflowAliasTwo.output_string
        String? output_2 = Workflow.output_string
        String? output_3 = WorkflowAliasOne.output_string
    }
}

.zip archive containing files for imports:
importsTestArchive.zip

2nd scenario:

Run gulp serve to launch the demo
Type .wdl script in textarea
Type baseURI in corresponding input
Click Build button

Example:

WDL script with import statements:

import "cnv_common_tasks.wdl" as CNVTasks

workflow CNVSomaticPairWorkflow {
    # Workflow input files
    File? targets
    String gatk_jar

    # If no target file is input, then do WGS workflow
    Boolean is_wgs = select_first([targets, ""]) == ""
 
     # docker images
    String gatk_docker
 
    if (!is_wgs) {
        call CNVTasks.PadTargets {
            input:
                targets = targets,
                gatk_jar = gatk_jar,
                gatk_docker = gatk_docker
        }
    }
 
  output {
        String tumor_entity_id = PadTargets.padded_targets
   }
}

baseURI:
https://raw.githubusercontent.com/broadinstitute/gatk/master/scripts/cnv_wdl

3rd scenario:

Run gulp serve to launch the demo
Type .wdl script with http:// URI right in imput statement in textarea
Click Build button

Example:

WDL script with import statements:

import "https://raw.githubusercontent.com/broadinstitute/gatk/master/scripts/cnv_wdl/cnv_common_tasks.wdl" as CNVTasks

workflow CNVSomaticPairWorkflow {
    # Workflow input files
    File? targets
    String gatk_jar

    # If no target file is input, then do WGS workflow
    Boolean is_wgs = select_first([targets, ""]) == ""
 
     # docker images
    String gatk_docker
 
    if (!is_wgs) {
        call CNVTasks.PadTargets {
            input:
                targets = targets,
                gatk_jar = gatk_jar,
                gatk_docker = gatk_docker
        }
    }
 
  output {
        String tumor_entity_id = PadTargets.padded_targets
   }
}

Visualization result for first example should looks like:

Visualization result for last two examples should looks like:

4th scenario:

Run gulp serve to launch the demo
Type .wdl script in textarea
Set sub workflow expanding level (Depth of recursion; default is 0) and sepcified sub workflows to expand according to expanding level (SubWorkflow to be detailed; type sub workflows names as you can see it on graph comma separated or * to expand all sub workflows)
Click Load zip button and choose .zip file containing .wdl import files

Example:

WDL script with import statements:

import "tasks.wdl"
import "sub_workflow.wdl" as SubWorkflow
import "sub_workflow2.wdl" as SubWorkflow2

workflow RootWorkflow {
    File? wfInput
    File? wfInputTwo
    File? wfInputThree

    call tasks.TaskOne {
        input:
            taskInput = wfInput
    }

    call SubWorkflow2.SubWorkflow as wf2{
 	input:
		wf_input = wfInput
    }

    call SubWorkflow.Workflow {
        input:
            wf_input = TaskOne.task_output,
            wf_input_two = wfInput
    }

    call SubWorkflow.Workflow as WorkflowAliasOne {
        input:
            wf_input = TaskOne.task_output,
            wf_input_two = wfInputTwo
    }

    call SubWorkflow.Workflow as WorkflowAliasTwo {
        input:
            wf_input = TaskOne.task_output,
            wf_input_two = wfInputThree
    }

    output {
        String output_1 = WorkflowAliasTwo.output_string
        String? output_2 = Workflow.output_string
        String? output_3 = WorkflowAliasOne.output_string
    }
}

.zip archive containing files for imports:
importsTestArchive2.zip

Visualization result:

Specified parameters:
SubWorkflow to be detailed - *
Depth of recursion - 1

Specified parameters:
SubWorkflow to be detailed - SubWorkflow2_SubWorkflow
Depth of recursion - 1

Example from Broadinstitute running on 1st scenario:

WDL script:

# Workflow for running GATK CNV (and optionally, ACNV) on tumor/normal or tumor-only cases. Supports both WGS and WES.
#
# Notes:
#
# - The target file (targets) is required for the WES workflow and should be a TSV file with the column headers:
#    contig    start    stop    name
#   These targets will be padded on both sides by the amount specified by PadTargets.padding (default 250).
#
# - If a target file is not provided, then the WGS workflow will be run instead and the specified value of
#   wgs_bin_length (default 1000) will be used.
#
# - A normal BAM (normal_bam) is requrired for the tumor/normal workflow.  If not provided, the tumor-only workflow
#   will be run.
#
# - The sites file (common_sites) is required for the ACNV workflow and should be a Picard interval list.
#   If not provided, the ACNV workflow will not be run.
#
# - Example invocation:
#    java -jar cromwell.jar run cnv_somatic_pair_workflow.wdl myParameters.json
#   See cnv_somatic_pair_workflow_template.json for a template json file to modify with your own parameters (please save
#   your modified version with a different filename and do not commit to the gatk repository).
#
#############

import "cnv_common_tasks.wdl" as CNVTasks
import "cnv_somatic_copy_ratio_bam_workflow.wdl" as CopyRatio
import "cnv_somatic_allele_fraction_pair_workflow.wdl" as AlleleFraction
import "cnv_somatic_oncotate.wdl" as Oncotate

workflow CNVSomaticPairWorkflow {
    # Workflow input files
    File? targets
    File? common_sites
    File tumor_bam
    File tumor_bam_idx
    File? normal_bam
    File? normal_bam_idx
    File ref_fasta
    File ref_fasta_dict
    File ref_fasta_fai
    File cnv_panel_of_normals
    String gatk_jar

    # If no target file is input, then do WGS workflow
    Boolean is_wgs = select_first([targets, ""]) == ""
    # If no sites file is input, then do not do ACNV workflow
    Boolean is_cnv_only = select_first([common_sites, ""]) == ""
    # If no normal BAM is input, then do tumor-only workflow
    Boolean is_tumor_only = select_first([normal_bam, ""]) == ""

    Boolean is_run_oncotator = false

    # docker images
    String gatk_docker
    String oncotator_docker="broadinstitute/oncotator:1.9.3.0-eval-gatk-protected"

    if (!is_wgs) {
        call CNVTasks.PadTargets {
            input:
                # The task will fail if targets is not defined when it gets here, but that should not be allowed to happen.
                targets = select_first([targets, ""]),
                gatk_jar = gatk_jar,
                gatk_docker = gatk_docker
        }
    }

    call CopyRatio.CNVSomaticCopyRatioBAMWorkflow as TumorCopyRatioWorkflow {
        input:
            padded_targets = PadTargets.padded_targets,
            bam = tumor_bam,
            bam_idx = tumor_bam_idx,
            ref_fasta = ref_fasta,
            ref_fasta_dict = ref_fasta_dict,
            ref_fasta_fai = ref_fasta_fai,
            cnv_panel_of_normals = cnv_panel_of_normals,
            gatk_jar = gatk_jar,
            gatk_docker = gatk_docker
    }

    if (!is_tumor_only) {
        call CopyRatio.CNVSomaticCopyRatioBAMWorkflow as NormalCopyRatioWorkflow {
            input:
                padded_targets = PadTargets.padded_targets,
                bam = select_first([normal_bam, ""]),
                bam_idx = select_first([normal_bam_idx, ""]),
                ref_fasta = ref_fasta,
                ref_fasta_dict = ref_fasta_dict,
                ref_fasta_fai = ref_fasta_fai,
                cnv_panel_of_normals = cnv_panel_of_normals,
                gatk_jar = gatk_jar,
                gatk_docker = gatk_docker
        }
    }

    if (!is_cnv_only) {
        call AlleleFraction.CNVSomaticAlleleFractionPairWorkflow as TumorAlleleFractionWorkflow {
            input:
                common_sites = select_first([common_sites, ""]),
                tumor_bam = tumor_bam,
                tumor_bam_idx = tumor_bam_idx,
                normal_bam = normal_bam,    # If no normal BAM is input, tumor-only GetBayesianHetCoverage will be run
                normal_bam_idx = normal_bam_idx,
                tumor_tn_coverage = TumorCopyRatioWorkflow.tn_coverage,
                tumor_called_segments = TumorCopyRatioWorkflow.called_segments,
                ref_fasta = ref_fasta,
                ref_fasta_dict = ref_fasta_dict,
                ref_fasta_fai = ref_fasta_fai,
                gatk_jar = gatk_jar,
                gatk_docker = gatk_docker,
                is_wgs = is_wgs
        }
    }

    if (is_run_oncotator) {
        call Oncotate.CNVOncotateCalledSegments as OncotateCalledCNVWorkflow {
            input:
                 called_file=TumorCopyRatioWorkflow.called_segments,
                 oncotator_docker=oncotator_docker
        }
    }

    output {
        String tumor_entity_id = TumorCopyRatioWorkflow.entity_id
        File tumor_tn_coverage = TumorCopyRatioWorkflow.tn_coverage
        File tumor_called_segments = TumorCopyRatioWorkflow.called_segments
        String? normal_entity_id = NormalCopyRatioWorkflow.entity_id
        File? normal_tn_coverage = NormalCopyRatioWorkflow.tn_coverage
        File? normal_called_segments = NormalCopyRatioWorkflow.called_segments
        File? tumor_hets = TumorAlleleFractionWorkflow.tumor_hets
        File? tumor_acnv_segments = TumorAlleleFractionWorkflow.acnv_segments
        File? oncotated_called_file = OncotateCalledCNVWorkflow.oncotated_called_file
    }
}

.zip archive containing files for imports:
broad_cnvSomaticLegacy.zip

Visualization result:

Specified parameters:
SubWorkflow to be detailed - *
Depth of recursion - 1
(Expanding all sub workflows)

Specified parameters:
SubWorkflow to be detailed - AlleleFraction_CNVSomaticAlleleFractionPairWorkflow
Depth of recursion - 1
(Expanding only 1 sub workflow)

…ols for imports. Exceptions added: 'file://' protocol for imports; generation from graph with imports

…into import_wdl

… imports and no import's wdl presented

…into import_wdl

coveralls · 2017-11-22T16:12:03Z

Coverage decreased (-1.3%) to 95.104% when pulling 951b3eb on import_wdl into ac1cf43 on dev.

sidoruka · 2017-11-23T09:24:20Z

@ekoltsova , @TimSPb89 , Thanks for your work!
Several things to improve:

As we see coverage is down by 1.3%, fix that please
Provide a sample wdl with imports and all necessary instruction on loading it, including an expected visualization (this can be added to the PR description)
Update documentation on this feature, where appropriate

coveralls · 2017-11-23T16:08:14Z

Coverage increased (+0.2%) to 96.534% when pulling 71113aa on import_wdl into ac1cf43 on dev.

sidoruka · 2017-11-23T17:03:41Z

That looks great for me as a starting point. Thank you!

@daniilsavchuk , could you please review the code once you'll have time?

daniilsavchuk · 2017-11-23T18:35:35Z

Dear @sidoruka and colleagues,

Looks like the PR is too big to be reviewed just by me. Let me add @paulsmirnov to the reviewers?
Guess that checking 32 commits with 26 files changed will take a while. As well as visual issues to be discussed.

Thank you in advance!

sidoruka · 2017-11-24T12:01:06Z

@daniilsavchuk , indeed I've counted 6 files that are somehow changed (if not counting tests and configuration changes). But if you are busy now, that's fine, I'll ask someone else to perform the review

daniilsavchuk · 2017-11-30T14:36:30Z

I reviewed part of changes in files I responsible for. The code looks quite good, but there are some slight issues (see file changes comments)

…led SubWorkflow; name conflicts resolved in visualisation

paulsmirnov

Thank you for your valuable efforts in making PB to enhance the support of WDL syntax! Import statements are quite important. However, I have a few inline comments for changed files. Please consider revising the changes.

paulsmirnov · 2017-12-01T07:28:10Z

src/app.js

+        flow1 = res.model[0];
+        diagram.attachTo(flow1);
+      } else {
+        throw new Error(res.message, 'wdl parsing error');


I'm not quite sure why do you throw here and where do you catch this exception. When you decide to migrate to a promise-based solution, you should take care of errors differently.

The second argument to Error constructor is a file name. Shouldn't you remove the erroneous argument or use a plus (+) instead of a comma? I think it's an old bug but I've just noticed it.

paulsmirnov · 2017-12-01T07:57:06Z

src/generator/WDL/entities/WorkflowGenerator.js

+
+    return `${res}${EOL}`;
+  }
+


The method genWorkflow() completely duplicates genCall(). Please refactor this.

Generation feature is not part of this PR.

paulsmirnov · 2017-12-01T08:00:39Z

src/dataServices/data-services.js

@@ -0,0 +1,22 @@
+export default function $http(method, url, data) {


The name of a file and its default export should match and describe their purpose. Please decide if it's a single method (then rename both) or a module (then don't use a default export and rename the method properly).

paulsmirnov · 2017-12-01T08:03:20Z

src/parser/WDL/entities/Context.js

@@ -27,6 +28,7 @@ export default class Context {
   * @param {ast} ast - Root ast tree node of parsing result
   */
  buildWorkflowList(ast) {
+    if (ast.attributes.imports && ast.attributes.imports.list.length) this.hasImports = true;


Shouldn't we use a single statement per line for easier debugging and comprehension?

paulsmirnov · 2017-12-01T10:07:02Z

src/app.js

+      } else {
+        throw new Error(res.message, 'wdl parsing error');
+      }
+    });


It seems that this block duplicates the one above.

After changing error handling it's not actual anymore

paulsmirnov · 2017-12-01T11:13:44Z

src/parser/WDL/parse.js

+
+  // check if calls're already in existing tasks
+  calls = calls.filter(call => !tasks.includes(call));
+  if (!calls.length) return result;


Let's stick to using one statement per line.

paulsmirnov · 2017-12-01T11:32:42Z

src/parser/WDL/parse.js

-    ast = ret.ast;
+  const ret = hermesStage(data);
+  result.status = ret.status;
+  result.message = ret.message;


We should consider revising the approach to returning results, as we change parse() method to an async promise-based implementation. Errors should be thrown to be caught in a .catch() clause.

paulsmirnov · 2017-12-01T11:41:05Z

src/parser/parse.js

+      parseWDL(text, opts).then((data) => {
+        resolve(data);
+      });
+    });


Am I right saying that with this implementation we are unable to catch exceptions raised in the parseWDL() function?

I'm not sure that we need a new Promise() here since we already have one from parseWDL() function.

Please test thoroughly if a user can successfully intercept all exceptions by artificially generating them in different parts of code, and then adjust the code correspondingly.

paulsmirnov · 2017-12-01T11:45:01Z

src/visual/VisualWorkflow.js

@@ -13,11 +13,15 @@ export default class VisualWorkflow extends VisualGroup {
    super(_.defaultsDeep(opts, {
      attrs: {
        '.label': {
-          text: opts.step.type,
+          text: `${opts.step.type} ${opts.step.name}`,


Is it really necessary to see a step type on a diagram?

There can be multiple subWorkflows in real WDL examples. So it's better to show name to be able to recognise one subWorkflow from other and show it's type to recognise subWorkflow visualisation from task visualisation

paulsmirnov · 2017-12-01T11:51:37Z

test/parser/parseTest.js

-    })).to.throw(Error);
+    return parse(src, { format: 'cwl' }).catch((e) => {
+      expect(e).to.be.an('Error');
+    });


Unfortunately the logic of the assertion has changed and it tests almost nothing now. If parse() completes successfully the test will succeed (but it should fail). Consider using chai-as-promised plugin for this and other tests to test promise-based interface in more intuitive manner.

daniilsavchuk · 2017-11-30T14:09:21Z

src/app/example3.js

-  return pipeline.parse(wdl, { format: 'wdl' }).model[0];
+async function createFlow() {
+  const res = await pipeline.parse(wdl);
+  return res.model[0];


@paulsmirnov what do you think about compatibility with all supported browsers?

Thanks. I've forgotten to check if polyfills are included in the demo app build. I guess they are not, neither for Promise class, nor for Array/Object methods. We should fix this too then. Of course, library should not have polyfills included, as it is a concern of the final application. We could carefully use babel-polyfill and adjust the docs to make user know about the steps to take.

daniilsavchuk · 2017-11-30T14:12:09Z

src/generator/WDL/entities/WorkflowGenerator.js

@@ -238,6 +241,46 @@ export default class WorkflowGenerator {
    return res;
  }

+  genWorkflow(child) {


Please explain what genWorkflow does? It looks like genCall function.

Generation feature is not part of this PR.

daniilsavchuk · 2017-11-30T14:18:49Z

src/generator/WDL/generate.js

@@ -25,7 +27,11 @@ export default function generate(objectModel) {
  actionSelector(objectModel.children);

  _.forEach(actionsToBeRendered, (action) => {
-    tasks += new TaskGenerator(action).renderTask();
+    if (!!action.type && action.type.toLowerCase() === 'workflow') {


What a generation result?
Users are waiting that WDL script will no differ from original(only spacing) if nothing changed on the diagram after multiple generations performed.
If so, I kindly expect function that generates strings like: " "smthng"" will be implemented as another type of WDL script item class like WorkflowGenerator or TaskGenerator, but not injected to existed one.

Generation feature is not part of this PR.

daniilsavchuk · 2017-11-30T14:20:07Z

src/generator/generate.js

@@ -10,6 +10,9 @@ import generateWDL from './WDL/generate';
 * @returns {string} Textual representation of the workflow.
 */
 function generate(flow, opts = {}) {
+  if (flow.hasImports) {


Does it mean that declared "importing" feature not supported in fact?

Generation feature is not part of this PR.

daniilsavchuk · 2017-11-30T14:30:38Z

src/parser/WDL/parse.js

+}
+
+/** Parse function with WDL imports support */
+async function importParsingStage(firstAst, opts) {


Up to me, this function is a code copy according to existed workflow parser. It is suitable to reuse existed parser. And patch it to support multilevel name accessors like "."

We need you to explain your idea more detailed

daniilsavchuk · 2017-11-30T14:32:49Z

src/visual/VisualWorkflow.js

@@ -13,11 +13,15 @@ export default class VisualWorkflow extends VisualGroup {
    super(_.defaultsDeep(opts, {
      attrs: {
        '.label': {
-          text: opts.step.type,
+          text: `${opts.step.type} ${opts.step.name}`,


Does this solution approved by the final user? It breaks out start ideology to keep just names for steps and just types for groups

Answered above

…ation_detailing' into import_wdl_sub-workflow_visualization_detailing # Conflicts: # src/parser/WDL/parse.js # src/parser/parse.js

coveralls · 2017-12-07T17:11:26Z

Coverage increased (+0.6%) to 96.982% when pulling 9ab68fe on import_wdl into ac1cf43 on dev.

ekoltsova · 2017-12-07T17:24:49Z

Added sub workflow expanding with new examples added to PR body. And updated code according to reviews.

coveralls · 2017-12-08T09:26:39Z

Coverage increased (+0.7%) to 97.1% when pulling 076c3d9 on import_wdl into ac1cf43 on dev.

ekoltsova and others added 28 commits November 13, 2017 11:57

Unzip sub-files

985f63d

Added sub-workflow visualization

90f2a23

Added workflow name to graph. Multiple sub-workflows support added.

cfcd326

minor fix sub-workflow alias conflict

21f982b

implemented WDL's import functionality

6db68dc

code refactoring

5f640a9

baseURI & code refactoring

f30cb77

Load import of Base URL

77f9219

fix test startup fail

8b5a4f9

xhr status handling & fixed existing tests

497721f

Support added: imports without alias; 'http://' and 'https://' protoc…

53fa0d5

…ols for imports. Exceptions added: 'file://' protocol for imports; generation from graph with imports

fixed WDLWorkflow tests failing

d30369e

added data-servicesTest.js

dc1eba7

Merge branch 'import_wdl' of https://github.com/epam/pipeline-builder …

9035e1e

…into import_wdl

parser/WDL/parse() tests added

b093267

Added test parser/parse.js

945e91c

Merge branch 'import_wdl' of https://github.com/epam/pipeline-builder …

2aaedc7

…into import_wdl

added functionality and test for parsing valid wdl script with unused…

cd7bab8

… imports and no import's wdl presented

Added test parser/WDL/parse.js

a9e94a0

Merge branch 'import_wdl' of https://github.com/epam/pipeline-builder …

84d9cdb

…into import_wdl

Changed test parser/WDL/parse.js

61feeb8

"file://" and "http://" protocols in import statements tests added

f6a0ea2

Added test Context.js

3dc2dc7

Merge branch 'import_wdl' of https://github.com/epam/pipeline-builder …

0378d01

…into import_wdl

Changed test data-services.js and parser/WDL/parse.js

8d86caa

not using hasImports flag in parse.js anymore

a696ee9

fix eslint

2b0609b

Merge branch 'import_wdl' of https://github.com/epam/pipeline-builder …

951b3eb

…into import_wdl

Updated README.md

71113aa

sidoruka requested a review from daniilsavchuk November 23, 2017 17:02

sidoruka removed the request for review from daniilsavchuk November 24, 2017 12:02

ekoltsova and others added 2 commits November 29, 2017 16:39

display content from sub-workflow

63057b0

SubWorkflow detail and imports resolving recursively

a7092c3

ekoltsova added 2 commits November 30, 2017 19:09

fix link sub-workflow

77f4a52

parseCall working recursively in WDLWorkflow; alias support for detai…

fc1bdbd

…led SubWorkflow; name conflicts resolved in visualisation

paulsmirnov requested changes Dec 1, 2017

View reviewed changes

daniilsavchuk requested changes Dec 1, 2017

View reviewed changes

TimSPb89 and others added 9 commits December 1, 2017 15:41

initial name in visual workflow

599a44a

non-editable links in sub-workflow

5fc4bd7

fix comments on the pull request (WDL imports #43)

832b246

code refactoring and recursive imports resolving

7435035

Merge remote-tracking branch 'origin/import_wdl_sub-workflow_visualiz…

0ff75fa

…ation_detailing' into import_wdl_sub-workflow_visualization_detailing # Conflicts: # src/parser/WDL/parse.js # src/parser/parse.js

tests

8eb0128

tests + demo

3800c38

deleted SubWorkflow actions

9374956

WDL\parse tests and refactoring

9ab68fe

ekoltsova added 2 commits December 8, 2017 12:10

minor fix

8d0468c

fixed WDLWorkflowTest

076c3d9

sidoruka merged commit baef7b2 into dev Dec 28, 2017

sidoruka deleted the import_wdl branch December 28, 2017 14:38

		@@ -0,0 +1,22 @@
		export default function $http(method, url, data) {

WDL imports #43

WDL imports #43

Conversation

ekoltsova commented Nov 22, 2017 • edited by TimSPb89

General idea

Changes

Acceptance criteria

coveralls commented Nov 22, 2017

sidoruka commented Nov 23, 2017 • edited

coveralls commented Nov 23, 2017

sidoruka commented Nov 23, 2017

daniilsavchuk commented Nov 23, 2017 • edited by sidoruka

sidoruka commented Nov 24, 2017 • edited

daniilsavchuk commented Nov 30, 2017

paulsmirnov left a comment

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coveralls commented Dec 7, 2017

ekoltsova commented Dec 7, 2017

coveralls commented Dec 8, 2017

ekoltsova commented Nov 22, 2017 •

edited by TimSPb89

sidoruka commented Nov 23, 2017 •

edited

daniilsavchuk commented Nov 23, 2017 •

edited by sidoruka

sidoruka commented Nov 24, 2017 •

edited