Bacpop-186 v9 db support #48
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…op/beebop_py into bacpop-186-v9-db-support
…op/beebop_py into bacpop-186-v9-db-support
…op/beebop_py into bacpop-186-v9-db-support
…op/beebop_py into bacpop-186-v9-db-support
…op/beebop_py into bacpop-186-v9-db-support
…nhance unit tests for query graph functionality
This reverts commit 465a54f.
…hod in PoppunkFileStore
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This looks good to me, but I'm a bit unsure about what some of the changes are - I expect they're mostly just new requirements of the poppunk version? Maybe we could have a quick call tomorrow to go over them?
Looks good on beebop-dev - network task seems to be working (for strep)..?
| @@ -118,6 +118,13 @@ def output_network(self, p_hash) -> str: | |||
| """ | |||
| return str(PurePath(self.output(p_hash), "network")) | |||
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| def parital_query_graph(self, p_hash) -> str: | |||
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| def parital_query_graph(self, p_hash) -> str: | |
| def partial_query_graph(self, p_hash) -> str: |
| @@ -118,6 +118,13 @@ def output_network(self, p_hash) -> str: | |||
| """ | |||
| return str(PurePath(self.output(p_hash), "network")) | |||
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| def parital_query_graph(self, p_hash) -> str: | |||
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How is this addition related to the new DB?
| recalculate_distances=self.args.visualise.recalculate_distances, | ||
| use_partial_query_graph=self.fs.parital_query_graph(self.p_hash), | ||
| tmp=self.fs.tmp(self.p_hash) |
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These are all new parameters required by latest poppunk version?
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| # try to do in 1 call just add --cytoscape |
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Is this comment obsolete?
| "stable": null, | ||
| "use_full_network": false |
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Are these new properties required by poppunk, or just related to this particular version?
| @@ -31,116 +31,6 @@ def get_args() -> SimpleNamespace: | |||
| NODE_SCHEMA = ".//{http://graphml.graphdrawing.org/xmlns}node/" | |||
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| def generate_mapping( | |||
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Why do we not need this any more?
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DO NOT MERGE UNTIL POPUNK fix for network is up In Poppunk v2.7.3 |
This PR updates poppunk to version 2.7.1, which now supports full v9 database. The updates in beebop_py is to account for these changes.
Testing:
The best way to test this is to use the branch in bacpop/beebop#83 (bacpop-201-stream-microreact) and then run this branch locally (ensure you install poppunk version 2.7.1) and then change
dbnamefield for pnuemo inargs.jsontoGPS_v9. You can now run an analysis from beebop and it should all work..Side note: I will also put this up on https://beebop-dev.dide.ic.ac.uk/ so you can test their if it is easier.