Relabel for collection is not working

dataset-collection
relabel-collection

#1

Hi,
I’m trying to use the ‘Relabel list identifiers from contents of a file’ function on a collection of paired-end reads.

However when I try to do this I get the following error message:

The server could not complete the request. Please contact the Galaxy Team if this error persists. Error executing tool: Invalid new colleciton identifier [“Erthyrocytic stages (3/3) Yeoh”]

{
“tool_id”: “RELABEL_FROM_FILE”,
“tool_version”: “1.0.0”,
“inputs”: {
“input”: {
“values”: [
{
“src”: “hdca”,
“tags”: [],
“hid”: 149,
“id”: “3bcdb03089092049”,
“name”: “Yeoh_pairedenddatalist”
}
],
“batch”: false
},
“how|how_select”: “txt”,
“how|labels”: {
“values”: [
{
“src”: “hda”,
“name”: “yeoh_relabel”,
“tags”: [],
“keep”: false,
“hid”: 259,
“id”: “bbd44e69cb8906b5b8d1bfcf6de3b443”
}
],
“batch”: false
},
“how|strict”: “false”
}
}

My relabelling text file is simply:

“Erthyrocytic stages (3/3) Yeoh”
“Erthyrocytic stages (2/3) Yeoh”
“Erthyrocytic stages (1/3) Yeoh”
“Male gametocytes (3/3) Yeoh”
“Male gametocytes (2/3) Yeoh”
“Male gametocytes (1/3) Yeoh”
“Female gametocytes (3/3) Yeoh”
“Female gametocytes (2/3) Yeoh”
“Female gametocytes (1/3) Yeoh”

and I’m using it on a list of paired data collections (length = 9). I don’t understand from the error message what isn’t working, why is the identifier illegal?

Hope that this is enough information to debug.

Many thanks,
Tim.


#2

These characters are causing problems: ( ) /

Also, avoid whitespace (tabs, spaces).

Try using only these characters in your new identifier:

  • Alphanumeric: A-Z a-z 0-9
  • Underscores: _
  • Dashes: -

If you are familiar with regular expressions, this is the test that is raising the error:

From lines 2781-2783 in https://github.com/galaxyproject/galaxy/blob/10c2f9cbc286477550e708d65bcd1381857dca15/lib/galaxy/tools/__init__.py

for key in new_elements.keys():
        if not re.match(r"^[\w\-_]+$", key):
            raise Exception("Invalid new colleciton identifier [%s]" % key)