Align result format to what is expected from website #269
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KaiWaldrant
previously approved these changes
Oct 20, 2023
KaiWaldrant
dismissed
their stale review
error in ci test due to changes in script
KaiWaldrant
suggested changes
Oct 20, 2023
| @@ -22,7 +24,7 @@ def check_structure(slot_info, adata_slot): | |||
| return missing | |||
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| print('Load data', flush=True) | |||
| adata = ad.read_h5ad(par['input']).copy() | |||
| adata = ad.read_h5ad(par['input'], backed='r') | |||
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Due to this change .X is not available anymore if it is empty/None and causes an error downstream on line 100:
rcannood
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rcannood
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rcannood
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Nov 24, 2023
* wip attempt at storing metadata as part of the pipeline * extract scores as yaml * fix metadata storage * undo extract scores changes * make sure check_dataset_schema also works with np.ndarray and pd.core.series.Series * fix is_atomic * simplify types * require less resources * remove unnecessary changes * collect data in separate steps * revert andata import * add trace collectin for seqera platform * refactor get_results * update get_method info * update metric * refactor task_info * WIP workflow transform inf yamls * fix common workflow * remove local trace * update transform workflow cmd * remove view * WIP fix test * update res test scripts * fix test resource script * fix common tests * fix typo * disable api_info comp * add labelsto common configs * add nf_tower test * convert nan to none * wip add normalize results * add normalize function * update workflow * fix adding resources * fix errors in get_results output * add method info * reformat nextflow wf * ignore different normalization methods in the dataset meta * add missing uns fields * clean up script * use solution to check dataset uns * fix comment in script * flatten method info results --------- Co-authored-by: Kai Waldrant <[email protected]>
rcannood
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Nov 28, 2023
* WIP cellxgene component * update to specific cellxgene version * Add initial cellxgene comp * small update * add source download componnent * update cellcensus query comp * remove cellcensus_source, rename cellxgene to query_cellxgene_census * use formatter * update component * add todo to test * fix test * remove filter function * Ali (#269) * wip attempt at storing metadata as part of the pipeline * extract scores as yaml * fix metadata storage * undo extract scores changes * make sure check_dataset_schema also works with np.ndarray and pd.core.series.Series * fix is_atomic * simplify types * require less resources * remove unnecessary changes * collect data in separate steps * revert andata import * add trace collectin for seqera platform * refactor get_results * update get_method info * update metric * refactor task_info * WIP workflow transform inf yamls * fix common workflow * remove local trace * update transform workflow cmd * remove view * WIP fix test * update res test scripts * fix test resource script * fix common tests * fix typo * disable api_info comp * add labelsto common configs * add nf_tower test * convert nan to none * wip add normalize results * add normalize function * update workflow * fix adding resources * fix errors in get_results output * add method info * reformat nextflow wf * ignore different normalization methods in the dataset meta * add missing uns fields * clean up script * use solution to check dataset uns * fix comment in script * flatten method info results --------- Co-authored-by: Kai Waldrant <[email protected]> * change namespace * update component --------- Co-authored-by: Robrecht Cannoodt <[email protected]>
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