Error uploading Galaxy file via HTTP

Question: Error uploading Galaxy file via HTTP

5 months ago by

Inquirer • 80 wrote:

Hi,

In our facility we have a web server that uploads files to Galaxy libraries via HTTP requests in PHP. It has been working for a while, but following an update to the latest version of Galaxy it started returning this error:

Fatal error: Exit code 1 ()
Traceback (most recent call last):
  File "/home/galaxy/galaxy/tools/data_source/upload.py", line 270, in <module>
    __main__()
  File "/home/galaxy/galaxy/tools/data_source/upload.py", line 263, in __main__
    metadata.append(add_file(dataset, registry, output_path))
  File "/home/galaxy/galaxy/tools/data_source/upload.py", line 136, in add_file
    if datatype.dataset_content_needs_grooming(dataset.path):
AttributeError: 'NoneType' object has no attribute 'dataset_content_needs_grooming'

If I comment out this section of the upload.py script, everything proceeds well and the files are usable by Galaxy, but it is not an ideal solution. Besides, those files do not have a known format.

This is the chunk of code that executes the POST request:

$params = array(
    'create_type' => 'file',
    'file_type' => 'auto',
    'dbkey' => '?',
    'folder_id' => $folder_id,
    'filesystem_paths' => $pathToFile,
    'link_data_only' => "link_to_files",
    'upload_option' => "upload_paths",
 );
 $URL = $baseURL . '/api/libraries/' . $library_id . '/contents/?key=' . $adminAPI;
$responseLibrary = httpPOST($URL, $params); // Send POST request

Interestingly, everything works as intended if I use bioblend. Any ideas on what might be wrong? At first I thought that 'file_type' might be necessary and I added it, to no avail...

Thanks!

api upload galaxy http • 238 views

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modified 5 months ago • written 5 months ago by Inquirer • 80

What is the bioblend analog you're using? I haven't had to work with PHP in some time, I'll look and see what might be happening with the payload on post.

ADD REPLY • link written 5 months ago by Dannon Baker ♦ 3.7k

Hi, thanks for the reply. I am using the following in bioblend:

gi = GalaxyInstance(url = GALAXY_URL, key=key_admin)
gi.libraries.upload_from_galaxy_filesystem(library_id=library_id,filesystem_paths=filepath,link_data_only='link_to_files')

As I said, this works fine. In PHP, the file is sent to the library (the POST request is successful), but the upload process fails at the lines mentioned above. As a result, it's shown with the state "error" and it has no data type.

ADD REPLY • link modified 5 months ago • written 5 months ago by Inquirer • 80

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