Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Argo decoder tool #105

Open
wants to merge 10 commits into
base: master
Choose a base branch
from
Open

Argo decoder tool #105

Show file tree
Hide file tree
Changes from 1 commit
Commits
Show all changes
10 commits
Select commit Hold shift + click to select a range
3c9da93
add argo decoder tool
Marie59 Mar 22, 2024
b537511
Update tools/ocean/argo_decoder.xml
Marie59 Mar 25, 2024
71370f4
change type
Marie59 Mar 25, 2024
65e5553
fix outputs folder
Marie59 Apr 3, 2024
6689ada
adapt environment var
Marie59 Apr 8, 2024
557ec95
ameliorate help
Marie59 Apr 9, 2024
7dc2bc8
Update help
Marie59 Apr 9, 2024
64abc25
Update tools/ocean/argo_decoder.xml
Marie59 Apr 11, 2024
a5f1a85
Update tools/ocean/argo_decoder.xml
Marie59 Apr 11, 2024
c164892
Merge branch 'master' into argo
bgruening Jul 13, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
63 changes: 63 additions & 0 deletions tools/ocean/argo_decoder.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,63 @@
<tool id="coriolis_data_processing_chain_for_argo_floats" name="coriolis data processing" version="@VERSION@">
Marie59 marked this conversation as resolved.
Show resolved Hide resolved
<description>chain for argo floats</description>
<macros>
<token name="@VERSION@">061a</token>
<token name="@VERSION_DOCKER@">@VERSION@-galaxy</token>
</macros>
<requirements>
<container type="docker">ghcr.io/euroargodev/coriolis-data-processing-chain-for-argo-floats:@VERSION_DOCKER@</container>
</requirements>
<command detect_errors="exit_code"><![CDATA[

## prepare outputs directory
mkdir -p /mnt/data/output/log &&
Marie59 marked this conversation as resolved.
Show resolved Hide resolved
chmod -R 770 /mnt/data/output &&

## load inputs into data directory
cp '$raw_data' '/tmp/raw_data.zip' &&
unzip /tmp/raw_data.zip -d /mnt/data &&

## execute decoder script
##$APP_HOME/$APP_RUN_FILE /mnt/runtime 'rsynclog' 'all' 'configfile' '/app/config/_argo_decoder_conf_ir_sbd.json' 'xmlreport' 'argo-decoder-report.xml' 'floatwmo' '$float_wmo' 'PROCESS_REMAINING_BUFFERS' '1' &&
/app/run_decode_argo_2_nc_rt.sh /mnt/runtime 'rsynclog' 'all' 'configfile' '/app/config/_argo_decoder_conf_ir_sbd.json' 'xmlreport' 'argo-decoder-report.xml' 'floatwmo' '$float_wmo' 'PROCESS_REMAINING_BUFFERS' '1' &&

## copy (because we need to be in working directory) and create output archive
cp -R /mnt/data/output/* . &&
Marie59 marked this conversation as resolved.
Show resolved Hide resolved
zip -r argo-decoder-outputs.zip .

]]>
</command>
<environment_variables>
Marie59 marked this conversation as resolved.
Show resolved Hide resolved
<environment_variable name="APP_HOME">/app</environment_variable>
<environment_variable name="APP_RUN_FILE">run_decode_argo_2_nc_rt.sh</environment_variable>
</environment_variables>
<inputs>
<param name="raw_data" type="data" format="zip" label="Archived input argo raw data"/>
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

The label is a bit confusing to me. Where is this data coming from? Why is it archived?

<param name="float_wmo" type="text" label="Input WMO number" help="Input float WMO numer (example : 6903014)"/>
Marie59 marked this conversation as resolved.
Show resolved Hide resolved
</inputs>
<outputs>
<data name="outputs_data" format="zip" from_work_dir="argo-decoder-outputs.zip" label="argo decoder netcdf outputs"/>
Marie59 marked this conversation as resolved.
Show resolved Hide resolved
</outputs>
<tests>
<test expect_num_outputs="1">
<param name="raw_data" value="data_input_20240319.zip"/>
<param name="float_wmo" value="6903014"/>
<output name="outputs_data" value="argo-decoder-outputs.zip"/>
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

what do you think about using https://docs.galaxyproject.org/en/latest/dev/schema.html#assertions-for-archives-zip-tar

To assert certain files in this archive, this would also enable us to remove this file.

</test>
</tests>
<help><![CDATA[
Input a zip folder of your Archived Argo data.
Run the tool.
Retrieve a zip folder with your your Argo data decoded and reday to be analysed
]]>
</help>
<citations>
<citation type="bibtex">
@Manual{,
title = {Coriolis data processing chain for Argo floats},
author = {Ifremer},
year = {2024},
note = {https://github.com/euroargodev/Coriolis-data-processing-chain-for-Argo-floats}
</citation>
Comment on lines +67 to +73
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Suggested change
<citation type="bibtex">
@Manual{,
title = {Coriolis data processing chain for Argo floats},
author = {Ifremer},
year = {2024},
note = {https://github.com/euroargodev/Coriolis-data-processing-chain-for-Argo-floats}
</citation>

The DOI is maybe enough?

</citations>
</tool>
Binary file added tools/ocean/test-data/argo_decoder_netcdf_outputs.zip
View file
Open in desktop
Binary file not shown.
Binary file added tools/ocean/test-data/data_input_20240319.zip
View file
Open in desktop
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

can we make this smaller?

Binary file not shown.
Loading