feat(directory): molgenis-emx2-directory-client #3863
Conversation
|
| ONCOLOGY = "oncology" | ||
| PAEDIATRICS = "paediatrics" | ||
| # PAEDIATRIC = "paediatric_only" | ||
| # PAEDIATRIC_INCLUDED = "paediatric_included" |
There was a problem hiding this comment.
Remove commented out code
| schema: str = None, | ||
| as_df: bool = False, | ||
| ) -> list | pd.DataFrame: | ||
| # response_data = super().get(table, query_filter, schema, as_df) |
There was a problem hiding this comment.
Remove commented out code
| rows = self.get( | ||
| schema=self.ONTOLOGY_SCHEMA, | ||
| table=entity_type_id, | ||
| # attributes=f"id,{parent_attr},ontology,{','.join(matching_attrs)}", |
There was a problem hiding this comment.
Remove commented out code
|
|
||
| biobank_qualities = self.get( | ||
| table="QualityInfoBiobanks", | ||
| # attributes="id,biobank,assess_level_bio", |
There was a problem hiding this comment.
Remove commented out code
| ) | ||
| collection_qualities = self.get( | ||
| table="QualityInfoCollections", | ||
| # attributes="id,collection,assess_level_col", |
There was a problem hiding this comment.
Remove commented out code
| :param code: node to get by code | ||
| :return: ExternalServerNode object | ||
| """ | ||
| # Query filter on null is not yet possible therefore this workaround |
There was a problem hiding this comment.
If there is an issue in Github for this, please reference it in the comment
…th latest pyclient version
…/directory-client
There was a problem hiding this comment.
Looks good, as far as I can tell. I tested it on my own testserver, with an external node on the bbmri-testserver, and only with a dummy PID service and it worked well. I did have to do some extra work to get it to run, I don't know to what extent we want to include those in the documentation somewhere:
- create the .env, it would be helpful to have an example .env included
- add rows to the NationalNodes table in the target directory (1 local, CZ, 1 EU and 1 external, NL)
- make sure the staging areas followed the naming conventions of prefix + national node code
- install python-dotenv, which isn't listed as a requirement
- empty the 'studies'-column in the Collections tables of the staging areas
|
* Initial commit: copy of molgenis-py-bbmri-eric * chore: adjust tool setup files * chore: rename some modules and classes and fix imports * chore: rename tool name folder * chore: change import paths * chore: update molgenis-emx2-pyclient * chore: change email and project URLs * feat: EMX2 version of the publish script * chore: fix tests * chore: added additional packages to setup.cfg * chore: working example file to run the package * fix: import pyhandle from forked git repo to solve incompatibility with latest pyclient version * chore(directory): new version of PYHANDLE available * chore: remove commented out code --------- Co-authored-by: Hessel Haagsma <h.haagsma@umcg.nl>
What are the main changes you did:
Created a new tool: molgenis-emx2-directory-client, which is also known as the EMX2 Publish script for BBMRI-ERIC, which combines data from the staging areas, add some extra fields and adds the data to the ERIC tables which are used in the Directory App.
This is initial a copy of molgenis-py-bbmri-eric 1.18.1, which is the EMX1 version of the Publish script.
how to test:
todo:
- [ ] Adjust README=> separate ticket- [ ] updated docs in case of new feature=> separate ticketOptional todo:separate ticket