Question: ImportError: cannot import name email_mime_text
1
gravatar for yychangsd
2.3 years ago by
yychangsd30
yychangsd30 wrote:

I set up a galaxy server.

I can upload and delete data but can not permanently delete data from disk.

in my config/galaxy.ini

allow_user_dataset_purge = True

Then I'd like to run

python scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d 5 -1 -r

And it shows that

Traceback (most recent call last):

File "scripts/cleanup_datasets/cleanup_datasets.py", line 18, in <module>

import galaxy.config

File "/root/galaxy/lib/galaxy/config.py", line 22, in <module>

from galaxy.util import listify

File "/root/galaxy/lib/galaxy/util/__init__.py", line 31, in <module>

from six.moves import email_mime_text, xrange, zip

ImportError: cannot import name email_mime_text

Any help would be appreciate.

galaxy • 1.4k views
ADD COMMENTlink modified 2.3 years ago by orlando.wong10 • written 2.3 years ago by yychangsd30

Hello,

How many times did you run the command? Is it possible that it was run without "-r" once, then re-run again with that used?

Try running this again but adding in a "-f" and let us know if that solves the problem.

The error is not familiar to me, so if that doesn't work we can bring in some admins to help troubleshoot.

Reference: https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets

Thanks, Jen, Galaxy team

ADD REPLYlink written 2.3 years ago by Jennifer Hillman Jackson25k

Thanks Jen. I tried without "-r" and adding "-f", but neither of them works for me.

And it shows that:

root@master:~/galaxy# python scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d 5 -1 Traceback (most recent call last): File "scripts/cleanup_datasets/cleanup_datasets.py", line 18, in <module> import galaxy.config File "/root/galaxy/lib/galaxy/config.py", line 22, in <module> from galaxy.util import listify File "/root/galaxy/lib/galaxy/util/__init__.py", line 31, in <module> from six.moves import email_mime_text, xrange, zip ImportError: cannot import name email_mime_text root@master:~/galaxy# python scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d 5 -1 -f Traceback (most recent call last): File "scripts/cleanup_datasets/cleanup_datasets.py", line 18, in <module> import galaxy.config File "/root/galaxy/lib/galaxy/config.py", line 22, in <module> from galaxy.util import listify File "/root/galaxy/lib/galaxy/util/__init__.py", line 31, in <module> from six.moves import email_mime_text, xrange, zip ImportError: cannot import name email_mime_text

ADD REPLYlink written 2.3 years ago by yychangsd30

What version of the six module is installed?

ADD REPLYlink written 2.3 years ago by Devon Ryan1.9k

Thanks Ryan. What do you mean, the six module?

ADD REPLYlink written 2.3 years ago by yychangsd30

For example, what does pip freeze | grep six say? The error you're seeing is coming from that module.

ADD REPLYlink written 2.3 years ago by Devon Ryan1.9k
1
gravatar for orlando.wong
2.3 years ago by
orlando.wong10
orlando.wong10 wrote:

Hi,

I had the same import error a few days ago. What worked for me was installing all the missing Python modules. You can try this too.

To check your version of the six module: Open up python:

$python

Import six module:

$import six

Then type this command down to check for version:

$six.__version__.

If you don't have six, you can install it with

$pip install six

Her's the list of all the modules I was missing and had to install (you may already have them) using pip install modulename.

modulename:

paste
webhelpers
pysam
numpy
bxpython
kombu
mako
pycrypto
webob
webhelpers
routes
ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by orlando.wong10

Thanks for your help.

I got a new error now:

Traceback (most recent call last): File "scripts/cleanup_datasets/cleanup_datasets.py", line 22, in <module> import galaxy.model.mapping File "/root/galaxy-dist/lib/galaxy/model/__init__.py", line 26, in <module> import galaxy.datatypes.registry File "/root/galaxy-dist/lib/galaxy/datatypes/registry.py", line 8, in <module> import data File "/root/galaxy-dist/lib/galaxy/datatypes/data.py", line 18, in <module> import dataproviders File "/root/galaxy-dist/lib/galaxy/datatypes/dataproviders/__init__.py", line 29, in <module> import dataset File "/root/galaxy-dist/lib/galaxy/datatypes/dataproviders/dataset.py", line 17, in <module> from bx import seq as bx_seq ImportError: cannot import name seq

Any idea about it?

Thanks...

ADD REPLYlink written 2.3 years ago by yychangsd30
2

You apparently don't have the requirements installed. Ensure that everything in /galaxy-central/lib/galaxy/dependencies/pinned-requirements.txt is installed.

ADD REPLYlink written 2.3 years ago by Devon Ryan1.9k

Thanks for your advice.

I tried it. and got a new error"

error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

Any comments? Thanks...

ADD REPLYlink written 2.3 years ago by yychangsd30
1

You're apparently missing most of the normal Linux tools for compiling things. If you're using a system that uses apt (e.g., ubuntu or debian), try apt-get install build-essential python-dev. Something similar will work on other systems. Personally I would avoid all of this and just use the Docker version, but to each his/her own.

ADD REPLYlink written 2.3 years ago by Devon Ryan1.9k

Hi, I also had that same error. I don't remember what I did exactly.

"from bx import seq as bx_seq ImportError: cannot import name seq"

Looks like you're missing the bx-python possibly? Try to install bx-python:

$pip install bx-python

You might be missing some more so you can just do what I did and

$pip install kombu
$pip install mako
$pip install kombu
$pip install numpy
$pip install paste


..

and so forth for each module listed on the requirements.txt that Devon Ryan mentioned

Here's the requirements.txt and list of all the modules

I opened up the requirements.txt and pasted the contents below:

packages with C extensions

bx-python==0.7.3

MarkupSafe==0.23

PyYAML==3.11

SQLAlchemy==1.0.8

mercurial==3.7.3

numpy==1.9.2

pycrypto==2.6.1

Install python_lzo if you want to support indexed access to lzo-compressed

locally cached maf files via bx-python

python_lzo==1.8

pure Python packages

Paste==2.0.2

PasteDeploy==1.5.2

docutils==0.12

wchartype==0.1

repoze.lru==0.6

Routes==2.2

WebOb==1.4.1

WebHelpers==1.3

Mako==1.0.2

pytz==2015.4

Babel==2.0

Beaker==1.7.0

dictobj==0.3.1

Cheetah and dependencies

Cheetah==2.4.4

Markdown==2.6.3

BioBlend and dependencies

bioblend==0.7.0

boto==2.38.0

requests==2.8.1

requests-toolbelt==0.4.0

kombu and dependencies

kombu==3.0.30

amqp==1.4.8

anyjson==0.3.3

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by orlando.wong10

Thanks for your advice.

I got a new error when pip install pysam

error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

Any comments? Thanks...

ADD REPLYlink written 2.3 years ago by yychangsd30

Do you have the rest of the error message above? Maybe it will mention the specific file or module that caused the error. I am not too sure about this

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by orlando.wong10
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