Updates to requirements packages and Elasticsearch connections #309
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This reverts commit e4caab3.
| @@ -3,7 +3,7 @@ | |||
| # A container for the core semantic-search capability. | |||
| # | |||
| ###################################################### | |||
| FROM python:3.9.6-slim | |||
| FROM python:3.10.10-slim | |||
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Could we get this updated to 3.11?
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I attempted to use 3.11 it caused additional breaking packages.
I will try again now that you are using fastAPI instead of flask though if I remember right that was the issue however it may also cause issues with Roger.
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@braswent if it takes more than minor updates, i think it will be enough to create a task for this and handle it separately.
| app.logger.error (f"ERROR: {str(error)}") | ||
| traceback.print_exc (error) | ||
| abort(Response(str(error), 400)) | ||
| # if not self.specs: |
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why is it commented out?
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This is all due to issues with the JSON from elasticsearch not playing with the old flask api conversion to a dictionary. This is apparently a issue that is known but as of yet not solved however we do not need to worry about it since we have moved to FastAPI anyways
| description = Digging up data | ||
| long_description = file: README.md | ||
| long_description_content_type = text/markdown | ||
| url = https://github.com/helxplatform/dug | ||
| url = https://github.com/RTIInternational/dug |
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do we want to revert this back to this repo ?
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since we have converted to fastapi , i don't think we should include api.py in the codebase anymore, maybe the elastic search query object needs these changes in the fastapi (server.py ) ?
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Yeah the server.py has to change. I can work on that since I did that already in the Dug-API repo I created
src/dug/config.py
Outdated
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do we need the scheme ? is this for support for HTTPS?
Wondering if we need this to be in roger config too ? maybe we can specify it on the host itself ?
| node_type = [self._snake_case(x.replace('biolink:', '')) for x in node_details.get("category", [])] | ||
| category = node_details.get("category", []) | ||
| if type(category) == list: | ||
| node_type = [self._snake_case(x.replace('biolink.', '')) for x in category] |
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can we store the biolink. in the config object somewhere and pass it down ?
I think that way we could use this code with the current graph, and later change the config and would be able to run it on multiple labeled graph aswell ?
| @@ -1,4 +1,4 @@ | |||
| elasticsearch==7.12.0 | |||
| elasticsearch==8.5.2 | |||
| flake8 | |||
| flasgger | |||
| Flask | |||
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If we are not using Flask anymore, could you delete this entry?
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merged via #322 |
These are basic package updates to Dug. The Dug APIs in our project have been separated into it's own repository.
The biggest updates here are:
biolink.