cwlprov 0.1.1

cwlprov API for Python

CWLProv Python tool

The cwlprov Python tool is a command line interface to validate and inspect CWLProv Research Objects that capture workflow runs, typically executed in a Common Workflow Language implementation.

Installation

You'll need Python 3.

To install from pip try:

pip3 install cwlprov

If you would rather install from the checkout of this source code:

pip3 install .

If you would like to use the cwltool rerun feature you may also need:

pip3 install cwlref-runner 

Development

To develop cwlprov-py it is recommended to set up a new virtualenv:

virtualenv -p python3 venv

To activate the environment and install your development version of cwlprov:

. venv3/bin/activate
pip3 install .

Usage

Use cwlprov --help to see all options. For instance cwlprov validate will validate the folder is valid according to CWLProv.

$ cwlprov --help
usage: cwlprov [-h] [--version] [--directory DIRECTORY] [--relative]
            [--absolute] [--output OUTPUT] [--verbose] [--quiet] [--hints]
            [--no-hints]
            {validate,info,who,prov,inputs,outputs,run,runs,rerun,derived,runtimes}
            ...

cwlprov explores Research Objects containing provenance of Common Workflow
Language executions. <https://w3id.org/cwl/prov/>

optional arguments:
-h, --help            show this help message and exit
--version             show program's version number and exit
--directory DIRECTORY, -d DIRECTORY
                        Path to CWLProv Research Object (default: .)
--relative            Output paths relative to current directory (default if
                        -d is missing or relative)
--absolute            Output absolute paths (default if -d is absolute)
--output OUTPUT, -o OUTPUT
                        File to write output to (default: stdout)
--verbose, -v         Verbose logging (repeat for more verbose)
--quiet, -q           No logging or hints
--hints               Show hints on cwlprov usage
--no-hints            Do not show hints

commands:
{validate,info,who,prov,inputs,outputs,run,runs,rerun,derived,runtimes}
    validate            validate the CWLProv Research Object
    info                show research object metadata
    who                 show who ran the workflow
    prov                export workflow execution provenance in PROV format
    inputs              list workflow/step input files/values
    outputs             list workflow/step output files/values
    run                 show workflow execution log
    runs                List all workflow executions in RO
    rerun               Rerun a workflow or step
    derived             List what was derived from a data item, based on
                        activity usage/generation
    runtimes            Calculate average step execution runtimes

The test/ folder contains some examples of workflow runs for different CWLProv profiles.

All commands for cwlprov will attempt to detect the CWLProv research object from the current directory, alternatively take the --directory option to specify the root folder.

The --quiet option may be used in scripts for less verbose outputs. The --verbose option has the opposite affect to enable logging. For debug logging, use -vv or --verbose --verbose.

Note that the general arguments listed above must be provided before the command, e.g.

cwlprov --quiet --directory /tmp/1 validate

Many of the commands accept additional arguments, which can be accessed by cwlprov COMMAND --help, e.g.:

$ cwlprov run --help
usage: cwlprov run [-h] [--step STEP] [--steps] [--no-steps] [--start]
                [--no-start] [--end] [--no-end] [--duration]
                [--no-duration] [--labels] [--no-labels] [--inputs]
                [--outputs]
                [id]

positional arguments:
id                    workflow run UUID

optional arguments:
-h, --help            show this help message and exit
--step STEP, -s STEP  Show only step with given UUID
--steps               List steps of workflow
--no-steps            Do not list steps
--start               Show start timestamps (default)
--no-start, -S        Do not show start timestamps
--end, -e             Show end timestamps
--no-end              Do not show end timestamps
--duration            Show step duration (default)
--no-duration, -D     Do not show step duration
--labels              Show activity labels
--no-labels, -L       Do not show activity labels
--inputs, -i          Show inputs

--outputs, -o Show outputs

Validation

Running cwlprov with no commands will return with status 0 if a CWLProv folder structure is detected:

$ cd test/revsort-cwlprov-0.4.0
test/revsort-cwlprov-0.4.0$ cwlprov 
Detected CWLProv Research Object: /home/stain/src/cwlprov-py/test/revsort-cwlprov-0.4.0

$ cd /tmp
/tmp$ cwlprov
ERROR:cwlprov.tool:Could not find bagit.txt, try cwlprov -d mybag/

If a cwlprov is not detected or invalid, an error code is raised.

cwlprov && echo Do cwlprov-stuff
ERROR:cwlprov.tool:Could not find bagit.txt, try cwlprov -d mybag/

Combined with the --quiet option cwlprov can be useful to find the root of a CWLProv folder:

test/revsort-cwlprov-0.4.0/metadata/provenance$ cwlprov -q
/home/stain/src/cwlprov-py/test/revsort-cwlprov-0.4.0

All commands of cwlprov will by default perform a quick validation, which conforms all files are present in the correct file size. For instance, if we remove a file:

test/revsort-cwlprov-0.4.0$ rm data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 

test/revsort-cwlprov-0.4.0$ cwlprov 
ERROR:cwlprov.tool:BagIt validation failed for: /home/stain/src/cwlprov-py/test/revsort-cwlprov-0.4.0: Payload-Oxum validation failed. Expected 3 files and 3333 bytes but found 2 files and 2222 bytes

To perform full validation, use cwlprov validate:

test/revsort-cwlprov-0.4.0$ cwlprov validate 
WARNING:bdbag.bdbagit:data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 exists in manifest but was not found on filesystem
ERROR:cwlprov.tool:BagIt validation failed for: /home/stain/src/cwlprov-py/test/revsort-cwlprov-0.4.0: Bag validation failed: data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 exists in manifest but was not found on filesystem

test/revsort-cwlprov-0.4.0$ git checkout . 

test/revsort-cwlprov-0.4.0$ cwlprov validate
Valid CWLProv RO: .

Unlike the quick validation, cwlprov validate will confirm checksums on all files, and thus detect byte-level changes. For instance, let's pretend I has been replaced with lower case i in a data file:

test/revsort-cwlprov-0.4.0$ sed -i 's/I/i/g' data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376
test/revsort-cwlprov-0.4.0$ cwlprov 
Detected CWLProv Research Object: /home/stain/src/cwlprov-py/test/revsort-cwlprov-0.4.0

test/revsort-cwlprov-0.4.0$ cwlprov validate
WARNING:bdbag.bdbagit:data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 sha1 validation failed: expected="327fc7aedf4f6b69a42a7c8b808dc5a7aff61376" found="60c41d3758bc8b03e78db07bc0f17d1804d2662d"
ERROR:cwlprov.tool:BagIt validation failed for: /home/stain/src/cwlprov-py/test/revsort-cwlprov-0.4.0: Bag validation failed: data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 sha1 validation failed: expected="327fc7aedf4f6b69a42a7c8b808dc5a7aff61376" found="60c41d3758bc8b03e78db07bc0f17d1804d2662d"

Research Object information

The cwlprov info command gives high-level information about the research object and its identifiers.

test/revsort-cwlprov-0.4.0$ cwlprov info
Research Object of CWL workflow run
Research Object ID: arcp://uuid,d47d3d43-4830-44f0-aa32-4cda74849c63/
Profile: https://w3id.org/cwl/prov/0.4.0
Workflow run ID: urn:uuid:d47d3d43-4830-44f0-aa32-4cda74849c63
Packaged: 2018-08-21

The Profile indicates the version of the CWLProv the research object implements, which determine which features of a workflow run is represented.

Note that a warning will be printed if an unknown CWLProv version is detected:

$ cwlprov
WARNING:cwlprov.tool:Unsupported CWLProv version: {'https://w3id.org/cwl/prov/0.8.0'}
Supported profiles:
https://w3id.org/cwl/prov/0.6.0
https://w3id.org/cwl/prov/0.5.0
https://w3id.org/cwl/prov/0.4.0
https://w3id.org/cwl/prov/0.3.0

This typically means that cwlprov-py is outdated, although that is normally harmless. Try pip install --upgrade cwlprov

The cwlprov who command will try to determine the user that ran the workflow.

$ cwlprov who
Packaged By: cwltool 1.0.20180925133620 <urn:uuid:d9c16ea5-c3fd-4c56-b125-f3a5207e6c38>
Executed By: Stian Soiland-Reyes <https://orcid.org/0000-0001-9842-9718>

Note that for privacy concerns, CWL executors like cwltool would not log such user information unless this has been enabled with options like --orcid --full-name or --enable-user-provenance.

Workflow run

To list the step executions of a workflow use cwlprov run:

test/revsort-cwlprov-0.4.0$ cwlprov run
2018-08-21 17:26:24.467844 Flow d47d3d43-4830-44f0-aa32-4cda74849c63 [ Run of workflow/packed.cwl#main 
2018-08-21 17:26:24.530884 Step 6f501717-0c97-492e-b18a-10bc096f1797   Run of workflow/packed.cwl#main/rev  (0:00:01.122498)
2018-08-21 17:26:25.656084 Step e7c8b2c0-dee6-4c61-b674-f0807cb47344   Run of workflow/packed.cwl#main/sorted  (0:00:01.087999)
2018-08-21 17:26:26.752493 Flow d47d3d43-4830-44f0-aa32-4cda74849c63 ] Run of workflow/packed.cwl#main  (0:00:02.284649)
Legend:
[ Workflow start
] Workflow end

The listing can be customized, see cwlprov run --help for details. For example:

test/revsort-cwlprov-0.4.0$ cwlprov --no-hints run --no-labels --start --end --no-duration 
2018-08-21 17:26:24.467844                            Flow d47d3d43-4830-44f0-aa32-4cda74849c63 [
2018-08-21 17:26:24.530884 2018-08-21 17:26:25.653382 Step 6f501717-0c97-492e-b18a-10bc096f1797  
2018-08-21 17:26:25.656084 2018-08-21 17:26:26.744083 Step e7c8b2c0-dee6-4c61-b674-f0807cb47344  
                           2018-08-21 17:26:26.752493 Flow d47d3d43-4830-44f0-aa32-4cda74849c63 ]

Nested workflows

Nested workflows, steps that themselves are workflows, are indicated in cwlprov run with a *:

(venv3) stain@biggie:~/src/cwlprov-py/test/nested-cwlprov-0.3.0$ cwlprov run
2018-08-08 22:44:06.573330 Flow 39408a40-c1c8-4852-9747-87249425be1e [ Run of workflow/packed.cwl#main 
2018-08-08 22:44:06.691722 Step 4f082fb6-3e4d-4a21-82e3-c685ce3deb58   Run of workflow/packed.cwl#main/create-tar  (0:00:00.010133)
2018-08-08 22:44:06.702976 Step 0cceeaf6-4109-4f08-940b-f06ac959944a * Run of workflow/packed.cwl#main/compile  (unknown duration)
2018-08-08 22:44:12.680097 Flow 39408a40-c1c8-4852-9747-87249425be1e ] Run of workflow/packed.cwl#main  (0:00:06.106767)
Legend:
[ Workflow start
* Nested provenance, use UUID to explore: cwlprov run 0cceeaf6-4109-4f08-940b-f06ac959944a
] Workflow end

(venv3) stain@biggie:~/src/cwlprov-py/test/nested-cwlprov-0.3.0$ cwlprov run 0cceeaf6-4109-4f08-940b-f06ac959944a
2018-08-08 22:44:06.607210 Flow 0cceeaf6-4109-4f08-940b-f06ac959944a [ Run of workflow/packed.cwl#main 
2018-08-08 22:44:06.707070 Step 83752ab4-8227-4d4a-8baa-78376df34aed   Run of workflow/packed.cwl#main/untar  (0:00:00.008149)
2018-08-08 22:44:06.718554 Step f56d8478-a190-4251-84d9-7f69fe0f6f8b   Run of workflow/packed.cwl#main/argument  (0:00:00.532052)
2018-08-08 22:44:07.251588 Flow 0cceeaf6-4109-4f08-940b-f06ac959944a ] Run of workflow/packed.cwl#main  (0:00:00.644378)
Legend:
[ Workflow start
] Workflow end

Note that there is a bug in CWLProv 0.3.0 logging shown above; steps of nested workflows are misleadingly labeled under #main

You can list all workflow runs (including nested workflow runs) with cwlprov runs:

test/nested-cwlprov-0.3.0$ cwlprov runs
39408a40-c1c8-4852-9747-87249425be1e * Run of workflow/packed.cwl#main
0cceeaf6-4109-4f08-940b-f06ac959944a   Run of workflow/packed.cwl#main
Legend:
* master workflow

To explore the nested workflow run with other commands you may have to provide the run UUID with --run argument, e.g.

test/nested-cwlprov-0.3.0$ cwlprov outputs --format=files --run 0cceeaf6-4109-4f08-940b-f06ac959944a 83752ab4-8227-4d4a-8baa-78376df34aed
Output example_out:
data/93/93035905e94e150874f5a881d39f3c5c6378dd38

License

This repository is distributed under Apache License, version 2.0

See the file LICENSE.txt for details, and NOTICE for required notices.

SPDX-License-Identifier: Apache-2.0

Contributing

cwlprov.py is maintained at https://github.com/common-workflow-language/cwlprov-py/ by the Common Workflow Language project.

Feel free to raise an issue or a pull request to contribute to CWLProv. Contributions are assumed to be covered by section 5 of the Apache License.

For an informal CWLProv discussion with other developers, join the (relatively quiet) Gitter room common-workflow-language/cwlprov, or the (more busy) common-workflow-language/common-workflow-language.

Code of Conduct

The CWL Project is dedicated to providing a harassment-free experience for everyone, regardless of gender, gender identity and expression, sexual orientation, disability, physical appearance, body size, age, race, or religion. We do not tolerate harassment of participants in any form. This code of conduct applies to all CWL Project spaces, including the Google Group, the Gitter chat room, the Google Hangouts chats, both online and off. Anyone who violates this code of conduct may be sanctioned or expelled from these spaces at the discretion of the leadership team.

For more details, see our Code of Conduct.