usegalaxy-eu / galaxy Goto Github PK

Describe the bug

I encountered an issue today while attempting to log in to my Galaxy account. My usual password wasn't working, so I tried using the LSLOGIN with the email address associated with my Galaxy server account. However, instead of logging into my existing Galaxy account, a new account was created using the same email address.

Galaxy Version and/or server at which you observed the bug
Galaxy Version: {"version_major":"24.0","version_minor":"rc1"}

To Reproduce
Steps to reproduce the behavior:

1. Go to 'https://usegalaxy.eu/login/start?redirect=None'
2. Click on 'LSLOGIN'
3. follow the subsequent steps with an email address registered on the Galaxy server
4. A new account is created with the existing email address

Expected behavior
Using the LSLOGIN command with my registered email address should have logged me into my existing Galaxy account.

Describe the bug
Dear developers, i just tried the studio interactive tool on the galaxy.eu instance. While the opening and the general rstudion session is active, the access to the galaxy workflow seem not to work at all

Galaxy Version and/or server at which you observed the bug
Galaxy Version: {"version_major":"23.0","version_minor":"1.dev0"}

To Reproduce
Steps to reproduce the behavior:

1. Run studio
2. Type in command line:

data <- read.csv(gx_get(4), sep="\t")
DEBUG:root:Host IP determined to be b'172.17.0.1\n'
DEBUG:root:TestURL url=https://usegalaxy.eu obj=False
/opt/miniconda/lib/python3.9/site-packages/bioblend/galaxy/histories/__init__.py:120: FutureWarning: The history_id parameter is deprecated, use the show_history() method to view details of a history for which you know the ID.
  warnings.warn(
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): usegalaxy.eu:443
DEBUG:urllib3.connectionpool:https://usegalaxy.eu:443 "GET /api/histories HTTP/1.1" 401 61
DEBUG:root:TestURL url=https://usegalaxy.eu state=failure
DEBUG:root:TestURL url=http://b'172.17.0.1':8080 obj=False
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): b'172.17.0.1':8080
DEBUG:root:TestURL url=http://b'172.17.0.1':8080 state=failure
Traceback (most recent call last):
  File "/usr/local/bin/get", line 19, in <module>
    results = get( args.id, args.identifier_type, args.history_id )
  File "/opt/miniconda/lib/python3.9/site-packages/galaxy_ie_helpers/__init__.py", line 167, in get
    gi = get_galaxy_connection(history_id=history_id, obj=False)
  File "/opt/miniconda/lib/python3.9/site-packages/galaxy_ie_helpers/__init__.py", line 100, in get_galaxy_connection
    raise Exception(msg)
Exception: Could not connect to a galaxy instance. Please contact your SysAdmin for help with this error
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
  cannot open file '/import/4': No such file or directory
> put('./my_file.tsv', file_type="tabular")
Error in put("./my_file.tsv", file_type = "tabular") : 
  could not find function "put"
> gx_put('./my_file.tsv', file_type="tabular")
DEBUG:root:Host IP determined to be b'172.17.0.1\n'
DEBUG:root:TestURL url=https://usegalaxy.eu obj=True
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): usegalaxy.eu:443
DEBUG:urllib3.connectionpool:https://usegalaxy.eu:443 "GET /api/histories/cb19bec6de47c5f8 HTTP/1.1" 401 61
DEBUG:root:TestURL url=https://usegalaxy.eu state=failure
DEBUG:root:TestURL url=http://b'172.17.0.1':8080 obj=True
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): b'172.17.0.1':8080
DEBUG:root:TestURL url=http://b'172.17.0.1':8080 state=failure
Traceback (most recent call last):
  File "/usr/local/bin/put", line 17, in <module>
    put( args.filepath, file_type=args.filetype, history_id=args.history_id )
  File "/opt/miniconda/lib/python3.9/site-packages/galaxy_ie_helpers/__init__.py", line 113, in put
    gi = get_galaxy_connection(history_id=history_id)
  File "/opt/miniconda/lib/python3.9/site-packages/galaxy_ie_helpers/__init__.py", line 100, in get_galaxy_connection
    raise Exception(msg)
Exception: Could not connect to a galaxy instance. Please contact your SysAdmin for help with this error```

Describe the bug
Not really a bug BUT using interactive_tool_jupyter_notebook tool, we see that R kernel (and others I guess) are using old version:

You are using R version:    	 4.0.3 (2020-10-10)
And the latest R version is:	 4.4.1 (2024-06-15)

It is thus difficult or impossible to install recent packages

Galaxy Version and/or server at which you observed the bug
usegalaxy.eu

Expected behavior
it seems to me important to update regularly this tool and thus related docker image so 1/ we can use recent packages/libraries 2/ we allow, using previous versions of the tool, to still use jupitool on worklows using nobooks as input datasets

Additional context
need to take care to keep possibilities to use old versions for jupytool use in workflows

Problem:
Visualizing molecule structures directly from SDF format in NGL viewer would enhance convenience.

Specific Use Cases:
The QCXMS tool, used for mass spectrometry prediction, processes SDF files to generate conformers. Directly visualizing from SDF files would simplify the workflow, particularly when dealing with multiple molecules.

Alternatives:
Though converters exist to convert SDF files to PDB format, integrating direct SDF support in NGL plugin would avoid unnecessary conversions.

Copied this over from #131.
Once the beacon integration goes live and sees some use, the limitations described here should be revisited.

The import method uses the following info fields

• AN will map to callCount in the beacon DB. Has 2 * num_called as a fallback (num_called is calculated from VCF)
• AF will map to frequency in the beacon DB. Has AC / AN as a fallback
• VT will map to varianttype in the beacon DB. Database field is nullable, so it still imports fine without this
• AC will map to alleleCount in the beacon DB. Will break the import when missing (for this dataset) - I added a line that AC is required.

There is an option min_ac for filtering out variants that were seen less than a minimal amount (1 by default). I currently set this to 0 - setting this to anything higher than 0 will also break the import for anything that does not contain VT (and maybe others too)

The import is a bit "python-esc" 😅

It has an _unpack method, that reads the INFO fields into nested lists.
While inserting variants list entries are just accessed by indices, leading to "index out of bounds" exceptions whenever something is not set.
There is a try/catch block around the whole for each variant in variants loop that catches these exceptions, cancelling 1000 variant imports a pop.

There is also a whole other block that is calling for SVTYPE and MATEID info field. I just never had any data with variant.is_sv == true

On another note, the same variant is never added twice duo to ON CONFLICT (datasetId, chromosome, start, reference, alternate) DO NOTHING.
In an ideal world we would increment sample and allele counts and recalculate the allele frequency.

But I´d argue that its not that big of a deal, since the datasets uploaded by users are arbitrary and therefore allele frequency across this data has not much meaning anyway.

TL;DR;

Had to add AC info field as a requirement.

The import routine that comes with beacon-python was written for a specific kind of dataset. It does the job for now, but if the feature sees some use we will write our own importer to handle all kinds of data (as suggested in the docs).

Hi @bgruening ! Sorry to bother you.

I tested ODV(https://github.com/usegalaxy-eu/galaxy/blob/release_23.0_europe/tools/interactive/interactivetool_odv.xml) and DIVAnd(https://github.com/usegalaxy-eu/galaxy/blob/release_23.0_europe/tools/interactive/interactivetool_divand.xml) individually everything seems be working fine !

However I started to chain them up and I am an able to get the outputs of neither of the 2 tools in the galaxy history.
I tested the climate notebook tool (https://github.com/usegalaxy-eu/galaxy/blob/release_23.0_europe/tools/interactive/interactivetool_climate_notebook.xml) with the command put and it works just fine. But I was enable to make it work with divand.
With Yvan we found that in the xml the only difference between climate and divand is profile="22.05" and <command detect_errors="aggressive">.

Could it be coming from there or is it a docker issue ?
Same issue with ODV.
Am I doing something wrong ? can you help me ?
Thanks

Problem:
The NGL Viewer Plugin lacks the ability to read multiple molecule files, increasing inconvenience when working with distinct molecular dataset

Specific Use Cases:
Users struggle when trying to check groups of molecules from files with multiple entities, particularly before running batch jobs with tools like QCXMS.

Alternatives:
Enabling the plugin to read multiple files would simplify the process, streamline workflow, and enhance the user experience compared to visualizing molecules individually

Describe the bug
The NGL viewer plugin in Galaxy is visualizing hydrogen atoms instead of chlorine atoms.

Galaxy Version and/or server at which you observed the bug
Galaxy Version: 23.1.5.dev0

To Reproduce
Steps to reproduce the behavior:

1. Load the molecule in pdb format from the attached zip file (mirex.zip).
2. Go to the "Visualize" section and select the NGL viewer plugin.

Expected behavior
The tool should display the chlorine atoms instead of hydrogen atoms (white) as shown in the screenshots.

Screenshots

1. [Correct visualization with NGL viewer]

2. [Incorrect visualization with NGL tool]

Additional context

• The molecule visualization works correctly with the NGL viewer at nglviewer.org.

Hi, I'm not sure if this is the right place to report a bug about the usegalaxy.eu galaxy instance, please tell me where to report issues if it is not

Describe the bug
When trying to use the FITS visualization plugin in galaxy.eu with a .fits file the fits viewer is not loaded because of missing js files (aladin-lite js file https://aladin.cds.unistra.fr/).

Those files are supposed to be located in the "dist" folder of the plugin (copied during plugin build) and are loaded from an npm package (https://www.npmjs.com/package/aladin-lite-galaxy)

Galaxy Version and/or server at which you observed the bug
Galaxy Version: usegalaxy.eu current version

To Reproduce
Steps to reproduce the behavior:

1. Download a fits file to the galaxy instance (one is available in the test-data folder of galaxy) and go to "Visualize" to
   select the FITS viewer plugin
2. Use your browser dev tools console to see the error about the missing js files

Expected behavior
User should be presented with an aladin-lite instance displaying a space view and the selected fits file

Additional context
We have been able to build the plugin locally by forcing a plugin rebuild and we have also been able to install the aladin-lite-galaxy package through npm so everything looks fine on our end

I'm trying to download a dataset (not a collection) from usegalaxy.eu using command line. I'm using WSL2 with Ubuntu. I get this error with wget.

Resolving usegalaxy.eu (usegalaxy.eu)... 132.230.223.239
Connecting to usegalaxy.eu (usegalaxy.eu)|132.230.223.239|:443... connected.
HTTP request sent, awaiting response... 403 Forbidden
2024-05-13 23:26:29 ERROR 403: Forbidden.

I get this with curl.

{"err_msg":"HistoryDatasetAssociation is not accessible by user","err_code":403002}

Just in case, I tried downloading with API key generated for my account, as described here, but it gave the same errors again.

Galaxy Server: European Galaxy Server
{"version_major":"24.0","version_minor":"1.dev0"}

I checked the dataset, and I have access. I followed the commands given in the link, and they don't work.