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Pipeline execution on CONP datasets #63
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I agree with this suggestion. How would you like to proceed? |
This has two aspects:
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I think we should do the CBRAIN execution in two stages:
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@glatard should this issue be closed? |
actually, I will close it. Feel free to reopen it if you think there is still work involved on that issue. |
On the CBRAIN front it would be useful to have a tighter integration than just redirecting to the login page. We should check with the CBRAIN team if point 2. in @shots47s' list above would be doable. |
We should discuss about the new interface in the coming weeks, I will bring the point 2 to this discussion. |
Discussed briefly at the CONP dev call of September 30th, 2020. Will focus and split that issue in smaller tasks at the next CONP dev call (October 7th). @glatard should we invite people from the CBRAIN team to the next CONP dev call to discuss the plan? If so, who should be invited? |
Here are a few possible actions regarding this issue, organized in four Goals summarized below. All goals can be worked on in parallel, except Goal 3 as it depends on 1 and 2. Goal 1: Run CONP pipelines in CBRAINTasks
HowPoint 2 most likely requires storing a CBRAIN tool config id for each pipeline, preferably as a config file also available on GitHub for easier update. This design would also solve point 1, as a pipeline will be assumed to be installed in CBRAIN if and only if it has a valid tool config id. When registering config ids, one should make sure that they match the exact same pipeline (boutiques descriptor) than registered in CONP. WhoCONP developers (@cmadjar, @mandana-mazaheri), liaise with @natacha-beck to get tool config ids. Goal 2: Process CONP datasets in CBRAINTask
HowThe ideal solution would be to use CBRAIN's DataLad data provider. Otherwise, install and download the datasets on a server (suggestion: Beluga, to facilitate processing), and register this location as a regular CBRAIN data provider. Make sure that simple pipelines (Diagnostics) can be run on the files. In any case, new datasets should be created automatically (either create a new data provider or register new files to an existing data provider). The CBRAIN data provider id should be stored using a mechanism similar to the one used to store CBRAIN tool config ids (see previous point). Suggestion: JSON file available in the portal config on GitHub. WhoThis is on the CBRAIN roadmap. Need to make sure that the CBRAIN datalad provider works as expected. NotesSomething specific has to be done for datasets that require authentication. The CBRAIN team will manually configure permissions. Goal 3: Process CONP datasets in CBRAIN using CONP pipelinesTasks
HowNeeds discussion, it might be a bit tricky, as fine-grained file selection in the dataset might be necessary. WhoCONP portal developers: @liamocn, @xlecours Goal 4: Analytics on pipeline executionTask
How
Who@mandana-mazaheri for the provenance dashboard, liaise with @nbeck for provenance upload from CBRAIN. |
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ooooops, closed the wrong issue. |
This issue is stale because it has been open 5 months with no activity. Remove stale label or comment or this will be closed in 3 months. |
This issue was closed because it has been stalled for 3 months with no activity. |
We should streamline the processing of CONP datasets with CONP pipelines, possibly by reviving https://github.com/CONP-PCNO/conp-pipeline
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