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Add new datatype bcsp #19363

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Add new datatype bcsp #19363

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SantaMcCloud
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Hello,

this PR should add the new datatype bcsp. Sadly there is no docomuentation to it but it is used in a tool which i did wrapped and without it the tool can not be used in Galaxy. The only thing i know is that this file format is a binary format and was generate with a Rust program.

How to test the changes?

(Select all options that apply)

  • I've included appropriate automated tests.
  • This is a refactoring of components with existing test coverage.
  • Instructions for manual testing are as follows:
    1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

  • I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

@github-actions github-actions bot added this to the 25.0 milestone Dec 20, 2024
@SantaMcCloud
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Here is the tool which need this datatype for more information: galaxyproject/tools-iuc#6647

@SantaMcCloud
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SantaMcCloud commented Dec 20, 2024 •
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and a question when this will be merged will this datatype be available immediately or do i have to wait till v25?

@SantaMcCloud SantaMcCloud mentioned this pull request Dec 20, 2024
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@bgruening
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@SantaMcCloud you can target the release_24.1 or release_24.2 branch. Then it will be available right a way.

bgruening
bgruening reviewed Dec 20, 2024
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lib/galaxy/datatypes/binary.py Outdated
@@ -4747,3 +4747,8 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
return dataset.peek
except Exception:
return f"Binary numpy file ({nice_size(dataset.get_size())})"

class bcsp(Binary):
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You don't need to do that.

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So i can delete this?

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9ead291

bgruening
bgruening reviewed Dec 20, 2024
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lib/galaxy/config/sample/datatypes_conf.xml.sample Outdated
@@ -1017,6 +1017,7 @@
<datatype extension="fits" type="galaxy.datatypes.binary:FITS" mimetype="application/octet-stream" display_in_upload="true" description="Flexible Image Transport System (FITS) used in Astronomy"/>
<datatype extension="chain" type="galaxy.datatypes.chain:Chain" display_in_upload="true" description_url="https://genome.ucsc.edu/goldenPath/help/chain.html"/>
<datatype extension="ucsc.net" type="galaxy.datatypes.chain:Net" display_in_upload="true" description_url="https://genome.ucsc.edu/goldenPath/help/net.html"/>
<datatype extension="bcsp" type="galaxy.datatypes.binary:bcsp" display_in_upload="true"/>
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You can do it similar to here, just subclass the Binary datatype.

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9ead291

@SantaMcCloud
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@SantaMcCloud you can target the release_24.1 or release_24.2 branch. Then it will be available right a way.

i will have a lookt at this then thank you. If i dont understand it i will ask here again!

bgruening
bgruening reviewed Dec 20, 2024
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lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -1017,6 +1017,7 @@
<datatype extension="fits" type="galaxy.datatypes.binary:FITS" mimetype="application/octet-stream" display_in_upload="true" description="Flexible Image Transport System (FITS) used in Astronomy"/>
<datatype extension="chain" type="galaxy.datatypes.chain:Chain" display_in_upload="true" description_url="https://genome.ucsc.edu/goldenPath/help/chain.html"/>
<datatype extension="ucsc.net" type="galaxy.datatypes.chain:Net" display_in_upload="true" description_url="https://genome.ucsc.edu/goldenPath/help/net.html"/>
<datatype extension="bcsp" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" display_in_upload="true" subclass="true"/>
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Do you have a discription_url or something like that?

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No i didnt found anything about this file extension. I think it is a file extension made by rust but even in the documentary i didnt find anything about it

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@bgruening when i commit to the release_24.1 branch the PR where the PR should be merge and all old commit will be stated there? I want to ask if this is correct befor i open the PR :)

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You go to the release_24.1 branch, you create a new branch from this one, commit your changes and create a new PR.

git checkout release_24.1
git checkout -b my_new_branch
git commit .....
git push ....

@SantaMcCloud SantaMcCloud closed this by deleting the head repository Dec 20, 2024
@SantaMcCloud SantaMcCloud mentioned this pull request Dec 20, 2024
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change it! #19365

Thank @bgruening for helping me!

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