Hello Hakeem,

Did you ever solve this import problem?

We suddenly started seeing this on our main (old) Galaxy server,
which we have not intentionally changed recently:


$ hg log | head
changeset:   17125:e837a68e8d14
tag:         tip
parent:      17121:7a4e3a661a76
parent:      17124:46a4ef8850b5
user:        Nate Coraor <n...@bx.psu.edu>
date:        Fri May 15 15:21:34 2015 -0400
summary:     Merge stable to default


I suspect either a system update, or an accidental change
where I meant to edit the test instance on the same machine,
or a new Galaxy instance we're working on using a new VM.

Turning on debug level logging, I could deduce the ImportError
happens when the local job runner tries to run the upload1
tool's Python script:


galaxy.jobs.runners DEBUG 2016-03-04 11:14:17,449 (13809) command is:
python /mnt/galaxy/galaxy-dist/tools/data_source/upload.py
/mnt/galaxy/galaxy-dist /mnt/galaxy/galaxy-dist/database/tmp/tmp2qzTWC
/mnt/galaxy/galaxy-dist/database/tmp/tmpC6Tq0J
16915:/mnt/galaxy/galaxy-dist/database/job_working_directory/013/13809/dataset_16915_files:/mnt/galaxy/galaxy-dist/database/files/016/dataset_16915.dat;
return_code=$?; python
/mnt/galaxy/galaxy-dist/database/job_working_directory/013/13809/set_metadata_SP3B7H.py
/mnt/galaxy/galaxy-dist/database/tmp/tmp2qzTWC
/mnt/galaxy/galaxy-dist/database/job_working_directory/013/13809/galaxy.json
/mnt/galaxy/galaxy-dist/database/job_working_directory/013/13809/metadata_in_HistoryDatasetAssociation_16276_0wz2tR,/mnt/galaxy/galaxy-dist/database/job_working_directory/013/13809/metadata_kwds_HistoryDatasetAssociation_16276_1IeKfn,/mnt/galaxy/galaxy-dist/database/job_working_directory/013/13809/metadata_out_HistoryDatasetAssociation_16276_cKjsLG,/mnt/galaxy/galaxy-dist/database/job_working_directory/013/13809/metadata_results_HistoryDatasetAssociation_16276_iyGIDI,/mnt/galaxy/galaxy-dist/database/files/016/dataset_16915.dat,/mnt/galaxy/galaxy-dist/database/job_working_directory/013/13809/metadata_override_HistoryDatasetAssociation_16276_K9ebdM;
sh -c "exit $return_code"


I can reproduce the error at the command line with just:


$ python /mnt/galaxy/galaxy-dist/tools/data_source/upload.py
Traceback (most recent call last):
  File "/mnt/galaxy/galaxy-dist/tools/data_source/upload.py", line 8,
in <module>
    from galaxy import eggs
ImportError: cannot import name eggs


I could hack this script based on how Galaxy adds its libraries to
the Python import path, and now uploads work again:


$ hg diff tools/data_source/upload.py
diff -r c3cef260df88 tools/data_source/upload.py
--- a/tools/data_source/upload.py    Fri May 15 15:20:17 2015 -0400
+++ b/tools/data_source/upload.py    Fri Mar 04 11:12:51 2016 +0000
@@ -5,6 +5,10 @@
 # to be reflected in galaxy.web.controllers.tool_runner and galaxy.tools

 import urllib, sys, os, gzip, tempfile, shutil, re, gzip, zipfile,
codecs, binascii
+
+# Peter hack 2016/03/04 due to unexplained import failure...
+sys.path.insert(1, "/mnt/galaxy/galaxy-dist/lib")
+
 from galaxy import eggs
 # need to import model before sniff to resolve a circular import dependency
 import galaxy.model


However, this is only treating the symptoms rather than the as yet
unexplained root cause of the problem.

Peter

On Thu, Sep 5, 2013 at 8:22 PM, Hakeem Almabrazi <halmabr...@idtdna.com> wrote:
> Hi,
>
>
>
> I started getting the following error whenever I try to load a file into
> Galaxy local.
>
> Traceback (most recent call last):
>
>   File "/usr/local/galaxy/galaxy-dist/tools/data_source/upload.py", line 8,
> in <module>
>
>     from galaxy import eggs
>
> ImportError: cannot import name eggs
>
>
>
>
>
> I will appreciate if someone can tell me what could happen to cause such
> issue and how to resolve it.
>
>
>
> Regards,
>
>
>
>
>
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