error message printed unescaped into html stream - cant figure out what the error message is

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error message printed unescaped into html stream - cant figure out what the error message is

Michael Pheasant
Hi

I'm using yesterday's latest galaxy-dist (rev 4cdf4cca0f31) and trying
to 'Upload directory of files' to a library, as admin user (see the
section in http://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles)

When this job runs, I get the success message:

  "Added 47 datasets to the library 'New data library test' (each is
selected). Click the Go button at the bottom of this page to edit the
permissions on these datasets if necessary."

But all the 47 files listed have an error message in the "Information" column:
  "Job error (click name for more info)"

When I click on the name and select "Edit Information" i get to a page
about the dataset which has a partial error message in the "Info" text
box:

  "uploaded fastq fileTraceback (most recent call last):   File "

Then a bit more of the message outside the text box in the frame html,
the rest is lost:

 "   __main__() File
"/mnt/array/home/galaxy/galaxy-dist/tools/data_source/upload.py", line
345, in __mai" size="40"/>"


*) I view the source for the frame and see that the error message from
python has been injected directly into the value field of the "info"
text element without any html escaping (see below).


*) I cant see the error in the log, I'm running the server in the
foreground using run.sh


*) Line 345 of upload.py is marked below:
         ...
        if dataset.type == 'composite':
            files_path = output_paths[int( dataset.dataset_id )][1]
            add_composite_file( dataset, json_file, output_path, files_path )
        else:
            add_file( dataset, json_file, output_path )  /* LINE 345 */


*) I cant see the message in the log either


*) Source of frame with injected error msg:


    <div class="toolForm">

        <div class="toolFormTitle">Edit attributes of s_8_1_sequence.txt</div>
        <div class="toolFormBody">
            <form name="edit_attributes"
action="/library_common/ldda_edit_info?library_id=adb5f5c93f827949&show_deleted=False&cntrller=library_admin&folder_id=adb5f5c93f827949&use_panels=False"
method="post">
                <input type="hidden" name="id" value="b351d620879d6814"/>
                <div class="form-row">
                    <label>Name:</label>
                    <input type="text" name="name"
value="s_8_1_sequence.txt" size="40"/>
                    <div style="clear: both"></div>

                </div>
                <div class="form-row">
                    <label>Info:</label>
                    <input type="text" name="info" value="uploaded
fastq fileTraceback (most recent call last):
  File "/mnt/array/home/galaxy/galaxy-dist/tools/data_source/upload.py",
line 353, in <module>
    __main__()
  File "/mnt/array/home/galaxy/galaxy-dist/tools/data_source/upload.py",
line 345, in __mai" size="40"/>
                    <div style="clear: both"></div>
                </div>



Cheers
Mike

--
Dr Michael Pheasant
Software Engineer
Queensland Facility for Advanced Bioinformatics
Level 6, QBP
University of Queensland, QLD 4072
T: +61 (0)7 3346 2070
F: +61 (0)7 3346 2101
www.qfab.org
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Re: error message printed unescaped into html stream - cant figure out what the error message is

Nate Coraor (nate@bx.psu.edu)
Hi Michael,

Unfortunately we don't have a simple interface for this, but the
following SQL query in your database should show the full error message,
which will help us determine exactly what the problem is.

select stderr from job where stderr != '' order by id desc;

If you have the job ID or dataset ID(s) I can make a more specific query.

--nate

Michael Pheasant wrote:

> Hi
>
> I'm using yesterday's latest galaxy-dist (rev 4cdf4cca0f31) and trying
> to 'Upload directory of files' to a library, as admin user (see the
> section in http://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles)
>
> When this job runs, I get the success message:
>
>   "Added 47 datasets to the library 'New data library test' (each is
> selected). Click the Go button at the bottom of this page to edit the
> permissions on these datasets if necessary."
>
> But all the 47 files listed have an error message in the "Information" column:
>   "Job error (click name for more info)"
>
> When I click on the name and select "Edit Information" i get to a page
> about the dataset which has a partial error message in the "Info" text
> box:
>
>   "uploaded fastq fileTraceback (most recent call last):   File "
>
> Then a bit more of the message outside the text box in the frame html,
> the rest is lost:
>
>  "   __main__() File
> "/mnt/array/home/galaxy/galaxy-dist/tools/data_source/upload.py", line
> 345, in __mai" size="40"/>"
>
>
> *) I view the source for the frame and see that the error message from
> python has been injected directly into the value field of the "info"
> text element without any html escaping (see below).
>
>
> *) I cant see the error in the log, I'm running the server in the
> foreground using run.sh
>
>
> *) Line 345 of upload.py is marked below:
>          ...
>         if dataset.type == 'composite':
>             files_path = output_paths[int( dataset.dataset_id )][1]
>             add_composite_file( dataset, json_file, output_path, files_path )
>         else:
>             add_file( dataset, json_file, output_path )  /* LINE 345 */
>
>
> *) I cant see the message in the log either
>
>
> *) Source of frame with injected error msg:
>
>
>     <div class="toolForm">
>
>         <div class="toolFormTitle">Edit attributes of s_8_1_sequence.txt</div>
>         <div class="toolFormBody">
>             <form name="edit_attributes"
> action="/library_common/ldda_edit_info?library_id=adb5f5c93f827949&show_deleted=False&cntrller=library_admin&folder_id=adb5f5c93f827949&use_panels=False"
> method="post">
>                 <input type="hidden" name="id" value="b351d620879d6814"/>
>                 <div class="form-row">
>                     <label>Name:</label>
>                     <input type="text" name="name"
> value="s_8_1_sequence.txt" size="40"/>
>                     <div style="clear: both"></div>
>
>                 </div>
>                 <div class="form-row">
>                     <label>Info:</label>
>                     <input type="text" name="info" value="uploaded
> fastq fileTraceback (most recent call last):
>   File "/mnt/array/home/galaxy/galaxy-dist/tools/data_source/upload.py",
> line 353, in <module>
>     __main__()
>   File "/mnt/array/home/galaxy/galaxy-dist/tools/data_source/upload.py",
> line 345, in __mai" size="40"/>
>                     <div style="clear: both"></div>
>                 </div>
>
>
>
> Cheers
> Mike
>
> --
> Dr Michael Pheasant
> Software Engineer
> Queensland Facility for Advanced Bioinformatics
> Level 6, QBP
> University of Queensland, QLD 4072
> T: +61 (0)7 3346 2070
> F: +61 (0)7 3346 2101
> www.qfab.org
> _______________________________________________
> galaxy-dev mailing list
> [hidden email]
> http://lists.bx.psu.edu/listinfo/galaxy-dev

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