Add --keyField parameter #13
Open
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
We have a similar need for features, and we use the p3-find-features script, so I added p3-find-genomes. This has been pushed to GitHub and will be absorbed in the currently-outstanding pull request. The advantage is that I can restrict the key fields to those that are indexed, and turn the batching on and off on a key-by-key basis. (So, for example, if we added "genus" as a key, we'd put it in slow mode instead of batch mode.) We already have this logic for features. |
|
Very cool. I thought we had such a find but didn't twig that it was just for features. Thanks much. Now the tedious process of recreating all the CLI packages...
…________________________________
From: Bruce Parrello ***@***.***>
Sent: Tuesday, April 1, 2025 9:11 AM
To: BV-BRC/p3_cli ***@***.***>
Cc: Olson, Robert D. ***@***.***>; Author ***@***.***>
Subject: Re: [BV-BRC/p3_cli] Add --keyField parameter (PR #13)
We have a similar need for features, and we use the p3-find-features script, so I added p3-find-genomes. This has been pushed to GitHub and will be absorbed in the currently-outstanding pull request. The advantage is that I can restrict the
ZjQcmQRYFpfptBannerStart
This Message Is From an External Sender
This message came from outside your organization.
ZjQcmQRYFpfptBannerEnd
We have a similar need for features, and we use the p3-find-features script, so I added p3-find-genomes. This has been pushed to GitHub and will be absorbed in the currently-outstanding pull request.
The advantage is that I can restrict the key fields to those that are indexed, and turn the batching on and off on a key-by-key basis. (So, for example, if we added "genus" as a key, we'd put it in slow mode instead of batch mode.) We already have this logic for features.
—
Reply to this email directly, view it on GitHub<https://urldefense.us/v3/__https://github.com/BV-BRC/p3_cli/pull/13*issuecomment-2769502910__;Iw!!G_uCfscf7eWS!fkyEJephq6gt5YvYcFnFoPsmRkRlHF0S-ovdGy7pVkc1I327MvHGXsCm__j2gpv-HKdVUoOqaTm5nmqW-Pj7W_2gdA$>, or unsubscribe<https://urldefense.us/v3/__https://github.com/notifications/unsubscribe-auth/AAQNOIXD3FODGDVEIYD7QRL2XKNB7AVCNFSM6AAAAAB2EZIRZ2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDONRZGUYDEOJRGA__;!!G_uCfscf7eWS!fkyEJephq6gt5YvYcFnFoPsmRkRlHF0S-ovdGy7pVkc1I327MvHGXsCm__j2gpv-HKdVUoOqaTm5nmqW-PhWQnyNRQ$>.
You are receiving this because you authored the thread.Message ID: ***@***.***>
[bparrello]bparrello left a comment (BV-BRC/p3_cli#13)<https://urldefense.us/v3/__https://github.com/BV-BRC/p3_cli/pull/13*issuecomment-2769502910__;Iw!!G_uCfscf7eWS!fkyEJephq6gt5YvYcFnFoPsmRkRlHF0S-ovdGy7pVkc1I327MvHGXsCm__j2gpv-HKdVUoOqaTm5nmqW-Pj7W_2gdA$>
We have a similar need for features, and we use the p3-find-features script, so I added p3-find-genomes. This has been pushed to GitHub and will be absorbed in the currently-outstanding pull request.
The advantage is that I can restrict the key fields to those that are indexed, and turn the batching on and off on a key-by-key basis. (So, for example, if we added "genus" as a key, we'd put it in slow mode instead of batch mode.) We already have this logic for features.
—
Reply to this email directly, view it on GitHub<https://urldefense.us/v3/__https://github.com/BV-BRC/p3_cli/pull/13*issuecomment-2769502910__;Iw!!G_uCfscf7eWS!fkyEJephq6gt5YvYcFnFoPsmRkRlHF0S-ovdGy7pVkc1I327MvHGXsCm__j2gpv-HKdVUoOqaTm5nmqW-Pj7W_2gdA$>, or unsubscribe<https://urldefense.us/v3/__https://github.com/notifications/unsubscribe-auth/AAQNOIXD3FODGDVEIYD7QRL2XKNB7AVCNFSM6AAAAAB2EZIRZ2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDONRZGUYDEOJRGA__;!!G_uCfscf7eWS!fkyEJephq6gt5YvYcFnFoPsmRkRlHF0S-ovdGy7pVkc1I327MvHGXsCm__j2gpv-HKdVUoOqaTm5nmqW-PhWQnyNRQ$>.
You are receiving this because you authored the thread.Message ID: ***@***.***>
|
|
Is there a PR somewhere for this? I'm not finding it |
|
I implemented it using a new script, p3-find-genome, to parallel p3-find-feature. It’s part of the umpteen changes pending with pull request 12.
From: olsonanl ***@***.***>
Sent: Thursday, April 24, 2025 1:20 PM
To: BV-BRC/p3_cli ***@***.***>
Cc: Bruce Parrello ***@***.***>; Assign ***@***.***>
Subject: Re: [BV-BRC/p3_cli] Add --keyField parameter (PR #13)
<https://avatars.githubusercontent.com/u/2152226?s=20&v=4> olsonanl left a comment (BV-BRC/p3_cli#13) <#13 (comment)>
Is there a PR somewhere for this? I'm not finding it
—
Reply to this email directly, view it on GitHub <#13 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB652NH3GR2O3HBBGP2DJNT23ETMXAVCNFSM6AAAAAB2EZIRZ2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDQMRYGUYDKOBUHE> .
You are receiving this because you were assigned. <https://github.com/notifications/beacon/AB652NDNS3NEL5IG53U4QZ323ETMXA5CNFSM6AAAAAB2EZIRZ2WGG33NNVSW45C7OR4XAZNMJFZXG5LFINXW23LFNZ2KUY3PNVWWK3TUL5UWJTVIS6JPS.gif> Message ID: ***@***.*** ***@***.***> >
|
|
Got it - I saw that one but saw Comparative Systems and was thinking it was something else. Thanks. That's all ready to merge? |
|
Yes, absolutely.
From: olsonanl ***@***.***>
Sent: Friday, April 25, 2025 8:38 AM
To: BV-BRC/p3_cli ***@***.***>
Cc: Bruce Parrello ***@***.***>; Assign ***@***.***>
Subject: Re: [BV-BRC/p3_cli] Add --keyField parameter (PR #13)
<https://avatars.githubusercontent.com/u/2152226?s=20&v=4> olsonanl left a comment (BV-BRC/p3_cli#13) <#13 (comment)>
Got it - I saw that one but saw Comparative Systems and was thinking it was something else. Thanks.
That's all ready to merge?
—
Reply to this email directly, view it on GitHub <#13 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB652NHBBCA67QQ4FH64HNL23I3FFAVCNFSM6AAAAAB2EZIRZ2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDQMZQGQ3DEOBXG4> .
You are receiving this because you were assigned. <https://github.com/notifications/beacon/AB652NDKFPH4YVIUPR6HTJ323I3FFA5CNFSM6AAAAAB2EZIRZ2WGG33NNVSW45C7OR4XAZNMJFZXG5LFINXW23LFNZ2KUY3PNVWWK3TUL5UWJTVIWVXZ2.gif> Message ID: ***@***.*** ***@***.***> >
|
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Hi Bruce - what do you think of this change? I used it to map a file of NCBI genome accessions to BV-BRC data. I don't know if there's an existing mechanism to do this, but changing the key field like this seems pretty clean.
Thanks,
Bob