Create interactive_pampa.xml #168

yvanlebras · 2023-06-10T14:13:01Z

(Please replace this header with a description of your pull request. Please include BOTH what you did and why you made the changes. The "why" may simply be citing a relevant Galaxy issue.)
(If fixing a bug, please add any relevant error or traceback)
(For UI components, it is recommended to include screenshots or screencasts)

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.

Used for training

) EU: Add scool format (galaxyproject#56)

Until the release notes are out.

…ning with Pangeo software stack

[EU] recommendation system

* Add info * Add changes * Increase version

* Add DIVAnd interactive tool * Update interactivetool_divand.xml --------- Co-authored-by: Björn Grüning <[email protected]>

… into two parts: the visualization plugin and backend changes. The client code integrates the h5web visualizer into Galaxy (https://h5web.panosc.eu). The backend changes add the ability to access the contents of a dataset without needing to read the whole dataset, which is essential for large files. It is based on the h5grove API (https://github.com/silx-kit/h5grove).

Add hdf4 support to hdfview tool

* EU: add ODV

bgruening · 2023-06-10T14:29:47Z

tools/interactive/interactive_pampa.xml

+<tool id="interactive_tool_pampa" tool_type="interactive" name="pampa" version="0.0.1" profile="22.01">
+    <description>Performance Indicators of Marine Protected Areas for the management of coastal ecosystems, resources and their uses</description>
+    <requirements>
+        <container type="docker">ylebras/pampa:latest</container>


Always remember to version those images when you bring them in production, ideally in sync with the tool version.

tools/interactive/interactive_pampa.xml

yvanlebras · 2023-06-10T14:57:50Z

Ok, I tested it on a local Galaxy instance. It seems to work well!!!

yvanlebras · 2023-06-10T15:11:12Z

Ok, tested, and it seems ok on my side now! The app is launched and work. Need to look at it more deeply to see if there is app dedicated errors using it with real data AND look to ameliorate data format (tabular instead csv) and links with inputs and outputs

yvanlebras · 2023-06-10T15:13:07Z

hmmm .Stooping the GxIT, just see that ouput datasets, are not synchronized with Galaxy... duno why

yvanlebras · 2023-06-10T15:28:46Z

the same with last version. But output datasets are now on the good PATH, '{Galaxy working dir}/Results' as seen here :

root@87a0b7f9057e:/home/ylebras/GxIT/galaxy/database/jobs_directory/000/164/working# ls
Results
root@87a0b7f9057e:/home/ylebras/GxIT/galaxy/database/jobs_directory/000/164/working# ls Results
MoyenneAnneeVisiteSite.csv       TableEspeces.csv                        UnitobsMetriques.csv
NombreSiteAnnee.csv              UnitobsEspeceClassetailleMetriques.csv
PlanEchantillonnage_basique.csv  UnitobsEspeceMetriques.csv
root@87a0b7f9057e:/home/ylebras/GxIT/galaxy/database/jobs_directory/000/164/working#

Any idea ?

For information, here is the Galaxy xml outputs tag:

    <outputs>
        <data name="moy" from_work_dir="Results/MoyenneAnneeVisiteSite.csv" format="csv" />
		<data name="nbre" from_work_dir="Results/NombreSiteAnnee.csv" format="csv" />
		<data name="plan" from_work_dir="Results/PlanEchantillonnage_basique.csv" format="csv" />
		<data name="table" from_work_dir="Results/TableEspeces.csv" format="csv" />
		<data name="mettaille" from_work_dir="Results/UnitobsEspeceClassetailleMetriques.csv" format="csv" />
		<data name="metsp" from_work_dir="Results/UnitobsEspeceMetriques.csv" format="csv" />
		<data name="metunitobs" from_work_dir="Results/UnitobsMetriques.csv" format="csv" />
    </outputs>

bgruening · 2023-06-10T16:10:08Z

tools/interactive/interactivetool_pampa.xml

@@ -0,0 +1,55 @@
+<tool id="interactive_tool_pampa" tool_type="interactive" name="pampa" version="0.0.1" profile="22.01">
+    <description>Performance Indicators of Marine Protected Areas for the management of coastal ecosystems, resources and their uses</description>


too long for my taste

bgruening · 2023-06-10T21:14:02Z

tools/interactive/interactivetool_pampa.xml

-        ln -s /srv/shiny-server/sample-apps/PAMPA/Results . &&
+        mkdir Results &&
+        mkdir /srv/shiny-server/sample-apps/PAMPA/Results/ &&
+        ln -s Results  /srv/shiny-server/sample-apps/PAMPA/Results/ &&


is this working? folder "Results" exist already as you do mkdir before

bgruening · 2024-03-23T10:40:56Z

This needs a rebase and retarget to the release_24.0_europe branch.

yvanlebras · 2024-03-24T07:40:59Z

Thank you Björn! Will look at it!

gmauro and others added 30 commits May 20, 2023 16:05

EU: LOCALONLY Fix FTP URL in UI

94fe574

EU: Favico

78faa2a

EU: Expand velvet kmer values

e38f7c6

Used for training

EU: LOCALONLY fix loading of tools

c2325a9

EU: Add local phinch site in lieu of GIE

e8335f5

EU: add SEEK data source

d954c79

EU: Adding support for juicer hic and test data for it (galaxyproject#49

97422ca

) EU: Add scool format (galaxyproject#56)

add OMICS-DI

9ab22f5

Update recommendations.py

88c5b6b

EU: Add ARC Gitlab File Source Plugin

1380505

Temporary disable Release Notes icon

ca13546

Until the release notes are out.

backport new cellxgene tool

18c90ba

add interactive_blobtoolkit.xml

6011cff

change name of the interactive blobtool

9790105

add interactive_blobtoolkit.xml

5225c34

change name of the interactive blobtool

2128b21

updaged pangeo notebook and added pangeo ml-notebook for machine lear…

db58507

…ning with Pangeo software stack

Update MetaShARK for 1.7.3 version ok on 22.05

6139a7a

Create interactivetool_audiolabeler.xml

3fe5b53

Fix issue with d3 js tree for tool recommendations (galaxyproject#153)

4925da4

[EU] recommendation system

Update interactive Blobtoolkit folder structure (galaxyproject#158)

1d7c2e4

* Add info * Add changes * Increase version

Add DIVAnd interactive tool (galaxyproject#160)

046dc6b

* Add DIVAnd interactive tool * Update interactivetool_divand.xml --------- Co-authored-by: Björn Grüning <[email protected]>

Try fixing ITs callback

c150228

Fix lint warnings

b3ef2ae

Fix data api test. Ran make format.

c673130

Fix OpenAPI linting. Remove unused dependencies.

7d9d53d

Add dependency to data package.

38b0d7f

Fix failing tests.

e721757

Fix mypy errors

73f5ec1

bgruening and others added 9 commits May 20, 2023 16:05

small edits

2f22e41

Update interactivetool_hdfview.xml

1e8bef3

don't start application after the server

c5a6b61

few more fixes to hdfview

a374ca8

Add hdf4 support to hdfview tool

13748f7

Merge pull request galaxyproject#164 from TheoMathurin/add-hdf4-support

71e867c

Add hdf4 support to hdfview tool

Odv (galaxyproject#166)

8fffd56

* EU: add ODV

Create interactivetool_metashrimps.xml (galaxyproject#167)

587db02

Create interactive_pampa.xml

11e2a48

bgruening reviewed Jun 10, 2023

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yvanlebras added 2 commits June 10, 2023 16:38

Update interactive_pampa.xml

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add &&

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bgruening reviewed Jun 10, 2023

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yvanlebras added 2 commits June 10, 2023 17:03

Finalize a first operational version of the app

956f97f

Update interactive_pampa.xml

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Update interactive_pampa.xml

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bgruening added 2 commits June 10, 2023 17:50

Update and rename interactive_pampa.xml to interactivetool_pampa.xml

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Update interactivetool_pampa.xml

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bgruening reviewed Jun 10, 2023

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Update interactivetool_pampa.xml

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bgruening reviewed Jun 10, 2023

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bgruening force-pushed the release_23.0_europe branch from e19ba2e to 01e4d19 Compare June 28, 2023 19:54

bgruening force-pushed the release_23.0_europe branch from 613623e to 7eab9d9 Compare July 26, 2023 08:40

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Create interactive_pampa.xml #168

Create interactive_pampa.xml #168

yvanlebras commented Jun 10, 2023

bgruening Jun 10, 2023

yvanlebras commented Jun 10, 2023

yvanlebras commented Jun 10, 2023

yvanlebras commented Jun 10, 2023

yvanlebras commented Jun 10, 2023 •

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bgruening commented Mar 23, 2024

yvanlebras commented Mar 24, 2024

		@@ -0,0 +1,55 @@
		<tool id="interactive_tool_pampa" tool_type="interactive" name="pampa" version="0.0.1" profile="22.01">
		<description>Performance Indicators of Marine Protected Areas for the management of coastal ecosystems, resources and their uses</description>

Create interactive_pampa.xml #168

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Create interactive_pampa.xml #168

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yvanlebras commented Jun 10, 2023

How to test the changes?

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