Simone Leo

CWLProv: cannot reproduce workflow runs with Directory input

2

**cwltool version: 3.1.20220628170238** Ran [this workflow](https://github.com/RenskeW/cwlprov-provenance/tree/f5dd87a950eeaf7f96bd39dc218164832ff3cbea/prov_data_annotations/example2) by @RenskeW with: ```console $ cwltool --provenance ro wf.cwl wf_job.yml ``` Then I tried reproducing the run and I got this error: ```console $...

add_on_binder_for_namespace: place custom code after generated one

4

Currently `add_on_binder_for_namespace` places the call to the function containing the custom manual bindings *before* binder-generated code. This means that the custom code cannot do several things, including: * Bind a...

I ran [this workflow](https://github.com/ResearchObject/workflow-run-crate/tree/eab5f652670299b0a5493c3ab4fbf80a891d227d/tools/cwlprov_to_crate/revsortlcase) with `--provenance`, creating [this RO](https://github.com/ResearchObject/workflow-run-crate/tree/eab5f652670299b0a5493c3ab4fbf80a891d227d/tools/cwlprov_to_crate/test/data/revsortlcase-run-1).  There are two problems with the provenance: 1. There is no trace of the `revsort_in` parameter. 2. The `reverse_sort` parameter...

See [grepsort-run-1](https://github.com/ResearchObject/runcrate/tree/64397c770c565ce7ce747a427a98a267828c61a4/tests/data/grepsort-run-1) (generated with an older cwltool version, but I've verified the problem is still present in version **3.1.20230624081518**). The problem is that a `cwlprov:SecondaryFile` record is generated only for...

CWLProv: secondary files missing from RO

3

cwltool version: 3.1.20221018083734 Workflow: [predictions.cwl](https://github.com/simleo/deephealth-pipelines/tree/3037aa6e2e1795268cf52f4170850bab8c3e4b54/cwl). Job file: ```yaml slide: class: File path: data/Mirax2-Fluorescence-2.mrxs tissue-low-level: 9 tissue-low-label: tissue_low tissue-high-level: 4 tissue-high-label: tissue_high tissue-high-filter: tissue_low>0.9 gpu: null tumor-level: 1 tumor-label: tumor tumor-filter:...

Handle duplicates in property values

2

```python from rocrate.rocrate import ROCrate from rocrate.model.person import Person crate = ROCrate() john = crate.add(Person(crate, "#johndoe")) jane = crate.add(Person(crate, "#janedoe")) crate.root_dataset["author"] = [john, jane, john] crate.root_dataset.properties() ``` ```python {'@id': './',...

Add optional minimal validation

4

Tough RO-Crate's philosophy is to impose few strict requirements, and rely on examples and best practices for details, a certain degree of validation can be performed. We could add an...

[An error message in pick_type](https://github.com/ResearchObject/ro-crate-py/blob/1a45d86711ad67e1b8751c98e2341c20fde091dd/rocrate/rocrate.py#L55) assumes that the entity has an `@id`, but [we pop it before calling the function](https://github.com/ResearchObject/ro-crate-py/blob/1a45d86711ad67e1b8751c98e2341c20fde091dd/rocrate/rocrate.py#L158). If possible, we should probably change callers so they don't...

#53 added initial support for [context extensions](https://simleo.github.io/ro-crate/1.1/appendix/jsonld.html#extending-ro-crate), but this is currently limited to updating the context with [testing namespace terms](https://github.com/ResearchObject/ro-terms/tree/master/test) when a testing-related entity is added to a crate via...

Use gxformat2 to convert .ga to .cwl?

2

Came up at the 2020 Elixir biohackathon. Experimented with this in https://github.com/ResearchObject/ro-crate-py/tree/gxformat2_cwl_conv. [Here are the changes](https://github.com/ResearchObject/ro-crate-py/commit/9c2c74506226f4508985e86df7b1fa72f657f8b2). I checked the output from converting `test/test-data/test_galaxy_wf.ga` and [the one output by gxformat2](https://pastebin.com/TH9VCkrD) is...