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Provenance capture

It is possible to capture the full provenance of a workflow execution to a folder, including intermediate values:

cwltool --provenance revsort-run-1/ tests/wf/revsort.cwl tests/wf/revsort-job.json

Who executed the workflow?

Optional parameters are available to capture information about who executed the workflow where:

cwltool --orcid https://orcid.org/0000-0002-1825-0097
--full-name "Alice W Land" --enable-user-provenance --enable-host-provenance --provenance revsort-run-1/ tests/wf/revsort.cwl tests/wf/revsort-job.json

These parameters are opt-in as they track person-identifiable information. The options --enable-user-provenance and --enable-host-provenance will pick up account/machine info from where cwltool is executed (e.g. UNIX username). This may get the full name of the user wrong, in which case --full-name can be supplied.

For consistent tracking it is recommended to apply for an ORCID identifier and provide it as above, since --enable-user-provenance --enable-host-provenance are only able to identify the local machine account.

It is possible to set the shell environment variables ORCID and CWL_FULL_NAME to avoid supplying --orcid or --full-name for every workflow run, for instance by augmenting the ~/.bashrc or equivalent:

export ORCID=https://orcid.org/0000-0002-1825-0097 export CWL_FULL_NAME="Stian Soiland-Reyes"

Care should be taken to preserve spaces when setting --full-name or CWL_FULL_NAME.

CWLProv folder structure

The CWLProv folder structure under revsort-run-1 is a Research Object that conforms to the RO BagIt profile and contains PROV traces detailing the execution of the workflow and its steps.

A rough overview of the CWLProv folder structure:

  • bagit.txt - bag marker for BagIt.
  • bag-info.txt - minimal bag metadata. The External-Identifier key shows which arcp can be used as base URI within the folder bag.
  • manifest-*.txt - checksums of files under data/ (algorithms subject to change)
  • tagmanifest-*.txt - checksums of the remaining files (algorithms subject to change)
  • metadata/manifest.json - Research Object manifest as JSON-LD. Types and relates files within bag.
  • metadata/provenance/primary.cwlprov* - PROV trace of main workflow execution in alternative PROV and RDF formats
  • data/ - bag payload, workflow/step input/output data files (content-addressable)
  • data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 - a data item with checksum 327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 (checksum algorithm is subject to change)
  • workflow/packed.cwl - The cwltool --pack standalone version of the executed workflow
  • workflow/primary-job.json - Job input for use with packed.cwl (references data/*)
  • snapshot/ - Direct copies of original files used for execution, but may have broken relative/absolute paths

See the CWLProv paper for more details.

Research Object manifest

The file metadata/manifest.json follows the structure defined for Research Object Bundles <https://w3id.org/bundle/#manifest> - but note that .ro/ is instead called metadata/ as this conforms to the RO BagIt profile.

Some of the keys of the CWLProv manifest are explained below:

"@context": [
    {
        "@base": "arcp://uuid,67f38794-d24a-435f-bd4a-0242a56a581b/metadata/"
    },
    "https://w3id.org/bundle/context"
]

This JSON-LD context enables consumers to alternatively consume the JSON file as Linked Data with absolute identifiers. The key for that is the @base which means URIs within this JSON file are relative to the metadata/ folder within this Research Object bag, and the external JSON-LD .

Output from cwltool should follow the JSON structure shown beyond; however interested consumer may alternatively parse it as JSON-LD with a RDF triple store like Apache Jena for further querying.

The manifest lists which software version created the Research Object - we will hear more from this UUID later:

"createdBy": {
    "uri": "urn:uuid:7c9d9e88-666b-4977-85f4-c02da08a942d",
    "name": "cwltool 1.0.20180416145054"
}

Secondly the manifest lists the person who "authored the run" - that is put the workflow and inputs together with cwltool:

"authoredBy": {
    "orcid": "https://orcid.org/0000-0002-1825-0097",
    "name": "Stian Soiland-Reyes"
}

Note that the author of the workflow run may differ from the author of the workflow definition.

The list of aggregates are the main resources that this Research Object transports:

"aggregates": [
    {
        "uri": "urn:hash::sha1:53870991af88a6d678cbeed3255bb65993c52925",
        ...
    },
    { "provenance/primary.cwlprov.xml",
       ...
    },
    {
        "uri": "../workflow/packed.cwl",
        "createdBy": {
            "uri": "urn:uuid:7c9d9e88-666b-4977-85f4-c02da08a942d",
            "name": "cwltool 1.0.20180416145054"
        },
        "conformsTo": "https://w3id.org/cwl/",
        "mediatype": "text/x+yaml; charset=\"UTF-8\"",
        "createdOn": "2018-04-16T18:27:09.513824"
    },
    {
        "uri": "../snapshot/hello-workflow.cwl",
        "conformsTo": "https://w3id.org/cwl/",
        "mediatype": "text/x+yaml; charset=\"UTF-8\"",
        "createdOn": "2018-04-04T13:29:55.717707"
    }

Beyond being a listing of file names and identifiers, this also lists formats and light-weight provenance. We note that the CWL file is marked to conform to the https://w3id.org/cwl/ CWL specification.

Some of the files like packed.cwl have been created by cwltool as part of the run, while others have been created before the run "outside". Note that cwltool is currently unable to extract the original authors and contributors of the original files, this is planned for future versions.

Under annotations we see that the main point of this whole research object (/ aka arcp://uuid,67f38794-d24a-435f-bd4a-0242a56a581b/) is to describe something called urn:uuid:67f38794-d24a-435f-bd4a-0242a56a581b:

"annotations": [
    {
        "about": "urn:uuid:67f38794-d24a-435f-bd4a-0242a56a581b",
        "content": "/",
        "oa:motivatedBy": {
            "@id": "oa:describing"
        }
    },

We will later see that this is the UUID for the workflow run. A workflow run is an activity, something that happens - it can't be directly saved to a file. However it can be described in different ways, in this case as CWLProv provenance:

{
 "about": "urn:uuid:67f38794-d24a-435f-bd4a-0242a56a581b",
 "content": [
     "provenance/primary.cwlprov.xml",
     "provenance/primary.cwlprov.nt",
     "provenance/primary.cwlprov.ttl",
     "provenance/primary.cwlprov.provn",
     "provenance/primary.cwlprov.jsonld",
     "provenance/primary.cwlprov.json"
 ],
 "oa:motivatedBy": {
     "@id": "http://www.w3.org/ns/prov#has_provenance"
 }

Finally the research object wants to highlight the workflow file:

{
    "about": "workflow/packed.cwl",
    "oa:motivatedBy": {
        "@id": "oa:highlighting"
    }
},

And links the run ID 67f38794.. to the `primary-job.json and packed.cwl:

{
    "about": "urn:uuid:67f38794-d24a-435f-bd4a-0242a56a581b",
    "content": [
        "workflow/packed.cwl",
        "workflow/primary-job.json"
    ],
    "oa:motivatedBy": {
        "@id": "oa:linking"
    }
}

Note: oa:motivatedBy in CWLProv are subject to change.

PROV profile

The underlying model and information of the PROV files under metadata/provenance is the same, but is made available in multiple serialization formats:

The below extracts use the PROV-N syntax for brevity.

CWLPROV namespaces

Note that the identifiers must be expanded with the defined prefix-es when comparing across serializations. These set which vocabularies ("namespaces") are used by the CWLProv statements:

prefix data <urn:hash::sha1:>
prefix input <arcp://uuid,0e6cb79e-fe70-4807-888c-3a61b9bf232a/workflow/primary-job.json#>
prefix cwlprov <https://w3id.org/cwl/prov#>
prefix wfprov <http://purl.org/wf4ever/wfprov#>
prefix sha256 <nih:sha-256;>
prefix schema <http://schema.org/>
prefix wfdesc <http://purl.org/wf4ever/wfdesc#>
prefix orcid <https://orcid.org/>
prefix researchobject <arcp://uuid,0e6cb79e-fe70-4807-888c-3a61b9bf232a/>
prefix id <urn:uuid:>
prefix wf <arcp://uuid,0e6cb79e-fe70-4807-888c-3a61b9bf232a/workflow/packed.cwl#>
prefix foaf <http://xmlns.com/foaf/0.1/>

Note that the arcp base URI will correspond to the UUID of each master workflow run.

Account who launched cwltool

If --enable-user-provenance was used, the local machine acccount (e.g. Windows or UNIX user name) who started cwltool is tracked:

agent(id:855c6823-bbe7-48a5-be37-b0f07f20c495, [foaf:accountName="stain", prov:type='foaf:OnlineAccount', prov:label="stain"])

It is assumed that the account was under the control of the named person (in PROV terms "actedOnBehalfOf"):

agent(id:433df002-2584-462a-80b0-cf90b97e6e07, [prov:label="Stian Soiland-Reyes",
      prov:type='prov:Person', foaf:account='id:8815e39c-9711-4105-bf52-dbc016c8028f'])
actedOnBehalfOf(id:8815e39c-9711-4105-bf52-dbc016c8028f, id:433df002-2584-462a-80b0-cf90b97e6e07, -)

However we do not have an identifier for neither the account or the person, so every cwltool run will yield new UUIDs.

With --enable-user-provenance it is possible to associate the account with a hostname:

agent(id:855c6823-bbe7-48a5-be37-b0f07f20c495, [cwlprov:hostname="biggie", prov:type='foaf:OnlineAccount', prov:location="biggie"])

Note that the hostname is often non-global or variable (e.g. on cloud instances or virtual machines), and thus may be unreliable when considering cwltool executions on multiple hosts.

If the --orcid parameter or ORCID shell variable is included, then the person associated with the local machine account is uniquely identified, no matter where the workflow was executed:

agent(orcid:0000-0002-1825-0097, [prov:type='prov:Person', prov:label="Stian Soiland-Reyes",
   foaf:account='id:855c6823-bbe7-48a5-be37-b0f07f20c495'])

actedOnBehalfOf(id:855c6823-bbe7-48a5-be37-b0f07f20c495', orcid:0000-0002-1825-0097, -)

The running of cwltool itself makes it the workflow engine. It is the machine account who launched the cwltool (not necessarily the person behind it):

agent(id:7c9d9e88-666b-4977-85f4-c02da08a942d, [prov:type='prov:SoftwareAgent', prov:type='wfprov:WorkflowEngine', prov:label="cwltool 1.0.20180416145054"])
wasStartedBy(id:855c6823-bbe7-48a5-be37-b0f07f20c495, -, id:9c3d4d1f-473d-468f-a6f2-1ef4de571a7f, 2018-04-16T18:27:09.428090)

Starting a workflow

The main job of the cwltool execution is to run a workflow, here the activity for workflow/packed.cwl#main:

activity(id:67f38794-d24a-435f-bd4a-0242a56a581b, 2018-04-16T18:27:09.428165, -, [prov:type='wfprov:WorkflowRun', prov:label="Run of workflow/packed.cwl#main"])
wasStartedBy(id:67f38794-d24a-435f-bd4a-0242a56a581b, -, id:7c9d9e88-666b-4977-85f4-c02da08a942d, 2018-04-16T18:27:09.428285)

Now what is that workflow again? Well a tiny bit of prospective provenance is included:

entity(wf:main, [prov:type='prov:Plan', prov:type='wfdesc:Workflow', prov:label="Prospective provenance"])
entity(wf:main, [prov:label="Prospective provenance", wfdesc:hasSubProcess='wf:main/step0'])
entity(wf:main/step0, [prov:type='wfdesc:Process', prov:type='prov:Plan'])

But we can also expand the wf identifiers to find that we are talking about arcp://uuid,0e6cb79e-fe70-4807-888c-3a61b9bf232a/workflow/packed.cwl# - that is the main workflow in the file workflow/packed.cwl of the Research Object.

Running workflow steps

A workflow will contain some steps, each execution of these are again nested activities:

activity(id:6c7c04ea-dcc8-40d2-92a4-7705f7286756, -, -, [prov:type='wfprov:ProcessRun', prov:label="Run of workflow/packed.cwl#main"])
wasStartedBy(id:6c7c04ea-dcc8-40d2-92a4-7705f7286756, -, id:67f38794-d24a-435f-bd4a-0242a56a581b, 2018-04-16T18:27:09.430883)
activity(id:a583b025-9a16-49ce-8515-f3249eb2aacf, -, -, [prov:type='wfprov:ProcessRun', prov:label="Run of workflow/packed.cwl#main/step0"])
wasAssociatedWith(id:a583b025-9a16-49ce-8515-f3249eb2aacf, -, wf:main/step0)

Again we see the link back to the workflow plan, the workflow execution of #main/step0 in this case. Note that depending on scattering etc there might be multiple activities for a single step in the workflow definition.

Data inputs (usage)

This activities uses some data at the input message:

activity(id:a583b025-9a16-49ce-8515-f3249eb2aacf, -, -, [prov:type='wfprov:ProcessRun', prov:label="Run of workflow/packed.cwl#main/step0"])
used(id:a583b025-9a16-49ce-8515-f3249eb2aacf, data:53870991af88a6d678cbeed3255bb65993c52925, 2018-04-16T18:27:09.433743, [prov:role='wf:main/step0/message'])

Data files within a workflow execution are identified using urn:hash::sha1: URIs derived from their sha1 checksum (checksum algorithm and prefix subject to change):

entity(data:53870991af88a6d678cbeed3255bb65993c52925, [prov:type='wfprov:Artifact', prov:value="Hei7"])

Small values (typically those provided on the command line may be present as prov:value. The corresponding data/ file within the Research Object has a content-addressable filename based on the checksum; but it is also possible to look up this independent from the corresponding metadata/manifest.json aggregation:

"aggregates": [
    {
        "uri": "urn:hash::sha1:53870991af88a6d678cbeed3255bb65993c52925",
        "bundledAs": {
            "uri": "arcp://uuid,0e6cb79e-fe70-4807-888c-3a61b9bf232a/data/53/53870991af88a6d678cbeed3255bb65993c52925",
            "folder": "/data/53/",
            "filename": "53870991af88a6d678cbeed3255bb65993c52925"
        }
    },

Data outputs (generation)

Similarly a step typically generates some data, here response:

activity(id:a583b025-9a16-49ce-8515-f3249eb2aacf, -, -, [prov:type='wfprov:ProcessRun', prov:label="Run of workflow/packed.cwl#main/step0"])
wasGeneratedBy(data:53870991af88a6d678cbeed3255bb65993c52925, id:a583b025-9a16-49ce-8515-f3249eb2aacf, 2018-04-16T18:27:09.438236, [prov:role='wf:main/step0/response'])

In the hello world example this is interesting because it is the same data output as-is, but typically the outputs will each have different checksums (and thus different identifiers).

The step is ended:

wasEndedBy(id:a583b025-9a16-49ce-8515-f3249eb2aacf, -, id:67f38794-d24a-435f-bd4a-0242a56a581b, 2018-04-16T18:27:09.438482)

In this case the step output is also a workflow output response, so the data is also generated by the workflow activity:

activity(id:67f38794-d24a-435f-bd4a-0242a56a581b, 2018-04-16T18:27:09.428165, -, [prov:type='wfprov:WorkflowRun', prov:label="Run of workflow/packed.cwl#main"])
wasGeneratedBy(data:53870991af88a6d678cbeed3255bb65993c52925, id:67f38794-d24a-435f-bd4a-0242a56a581b, 2018-04-16T18:27:09.439323, [prov:role='wf:main/response'])

Ending the workflow

Finally the overall workflow #main also ends:

activity(id:67f38794-d24a-435f-bd4a-0242a56a581b, 2018-04-16T18:27:09.428165, -, [prov:type='wfprov:WorkflowRun', prov:label="Run of workflow/packed.cwl#main"])
agent(id:7c9d9e88-666b-4977-85f4-c02da08a942d, [prov:type='prov:SoftwareAgent', prov:type='wfprov:WorkflowEngine', prov:label="cwltool 1.0.20180416145054"])
wasEndedBy(id:67f38794-d24a-435f-bd4a-0242a56a581b, -, id:7c9d9e88-666b-4977-85f4-c02da08a942d, 2018-04-16T18:27:09.445785)

Note that the end of the outer cwltool activity is not recorded, as cwltool is still running at the point of writing out this provenance.

Currently the provenance trace do not distinguish executions within nested workflows; it is planned that these will be tracked in separate files under metadata/provenance/.