dalmatian
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getzlab
dalmatian is a collection of high-level companion functions for Firecloud and FISS.
When installing using pip, a version that is before September 2019 is installed.
when trying to use upload_entities for another entity than participant, sample, sampleset, it never works. df.index.name = [entityname]_id upload_entities(entityname, df) getting ``` APIException: Sample_group import failed.: (400) : { "causes":...
Hi, we have a code to make workflow graphs (with nodes being workflows rather than tasks) within a workspace. You can find it [here](https://github.com/broadinstitute/genepy/pull/7). It's helping us figure out how...
Hi, I have been receiving errors when attempting to retrieve the sample set table from the data model. This function worked for me last week. For clarity this is the...
Hi, is there any option to upload files (e.g. interval lists) to the Workspace Data using this? I wasn't able to find that in the documents. -thanks
Hi, When running e.g. delete_sample_attributes with `dry_run=True`, the current logic within delete_entity_attributes dictates that dry_run mode is active only if `delete_files=True`. I think it would be more intuitive and prevent...
I'm using firecloud-dalmatian==0.0.17 and get an error message when trying to import a public config: `wm.import_config('broadinstitute-gtex/rnaseq_bam_star_rsem_rnaseqc_v1-2_BETA_cfg')` --------------------------------------------------------------------------- UnboundLocalError Traceback (most recent call last) in ----> 1 wm.import_config('broadinstitute-gtex/rnaseq_bam_star_rsem_rnaseqc_v1-2_BETA_cfg') ~/anaconda3/lib/python3.7/site-packages/dalmatian/wmanager.py in import_config(self,...
(Probably related to #32) I recently added a column containing lists of ints to the participant table, and now `get_participants` fails: `-> 1378 df = df.applymap(lambda x: [i['entityName'] if 'entityName'...
List attribute updating was added to FISS in broadinstitute/fiss#175. It would be great for Dalmatian to incorporate it.
