nipype test failed(boto ERROR/SSLError)

[caixixixi]

Hi,after i installed nipype,i tested my system.:python -c "import nipype; nipype.test()". I got the following error:

self = <ssl.SSLSocket object at 0x7f7d66861668>, len = 425, buffer = None

def read(self, len=1024, buffer=None):
    """Read up to LEN bytes and return them.
        Return zero-length string on EOF."""

    self._checkClosed()
    if not self._sslobj:
        raise ValueError("Read on closed or unwrapped SSL socket.")
    try:
        if buffer is not None:
            v = self._sslobj.read(len, buffer)
        else:

          v = self._sslobj.read(len)

E SSLError: (u'The read operation timed out\nInterface S3DataGrabber failed to run. ',)
/home/caixi/anaconda/lib/python2.7/ssl.py:653: SSLError

----------------------------- Captured stdout call -----------------------------
170508-06:24:42,918 boto ERROR:
Caught exception reading instance data
Traceback (most recent call last):
File "/home/caixi/anaconda/lib/python2.7/site-packages/boto/utils.py", line 214, in retry_url
r = opener.open(req)
File "/home/caixi/anaconda/lib/python2.7/urllib2.py", line 429, in open
response = self._open(req, data)
File "/home/caixi/anaconda/lib/python2.7/urllib2.py", line 447, in _open
'_open', req)
File "/home/caixi/anaconda/lib/python2.7/urllib2.py", line 407, in _call_chain
result = func(*args)
File "/home/caixi/anaconda/lib/python2.7/urllib2.py", line 1228, in http_open
return self.do_open(httplib.HTTPConnection, req)
File "/home/caixi/anaconda/lib/python2.7/urllib2.py", line 1198, in do_open
raise URLError(err)
URLError: <urlopen error [Errno 111] Connection refused>
170508-06:24:42,946 boto ERROR:
Unable to read instance data, giving up
!!!!!!!!!!!!!!!!!!!! Interrupted: stopping after 1 failures !!!!!!!!!!!!!!!!!!!!
======== 1 failed, 2326 passed, 32 skipped, 5 xfailed in 357.66 seconds ========

Kind regards.

[djarecka]

can you please write the version of nipype you're using, please try print(nipype.get_info()) and print(nipype.__version__).
What is your operating system?

[caixixixi]

@djarecka Hi, thanks for the reply
@ubuntu:~$ print(nipype.get_info())
bash: syntax error near unexpected token nipype.get_info' @ubuntu:~$ print(nipype.__version__) bash: syntax error near unexpected token nipype.version'

I downloaded 0.10.0 from https://github.com/nipy/nipype/archive/0.13.0-rc1.tar.gz,

[djarecka]

Sorry, I didn't specify that you have to type this commands in the python interpreter after importing nipype. In your terminal you can type python -c "import nipype; print(nipype.__version__)"

Can you also please write the test name that give you this error. If you can't find the name, you can also just paste everything.

[caixixixi]

@djarecka thanks a lot for replay

@ubuntu:~$ python -c "import nipype; print(nipype.__version__)"
0.13.0-dev

=================================== FAILURES ===================================
_______________________ test_s3datagrabber_communication _______________________

tmpdir = local('/tmp/pytest-of-caixi/pytest-0/test_s3datagrabber_communicati0')

    @pytest.mark.skipif(noboto, reason="boto library is not available")
    def test_s3datagrabber_communication(tmpdir):
        dg = nio.S3DataGrabber(
            infields=['subj_id', 'run_num'], outfields=['func', 'struct'])
        dg.inputs.anon = True
        dg.inputs.bucket = 'openfmri'
        dg.inputs.bucket_path = 'ds001/'
        dg.inputs.local_directory = str(tmpdir)
        dg.inputs.sort_filelist = True
        dg.inputs.template = '*'
        dg.inputs.field_template = dict(func='%s/BOLD/task001_%s/bold.nii.gz',
                                        struct='%s/anatomy/highres001_brain.nii.gz')
        dg.inputs.subj_id = ['sub001', 'sub002']
        dg.inputs.run_num = ['run001', 'run003']
        dg.inputs.template_args = dict(
            func=[['subj_id', 'run_num']], struct=[['subj_id']])
>       res = dg.run()

/home/caixi/anaconda/lib/python2.7/site-packages/nipype/interfaces/tests/test_io.py:122: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
/home/caixi/anaconda/lib/python2.7/site-packages/nipype/interfaces/base.py:1082: in run
    outputs = self.aggregate_outputs(runtime)
/home/caixi/anaconda/lib/python2.7/site-packages/nipype/interfaces/base.py:1153: in aggregate_outputs
    predicted_outputs = self._list_outputs()
/home/caixi/anaconda/lib/python2.7/site-packages/nipype/interfaces/io.py:872: in _list_outputs
    bkt_files = list(k.key for k in bkt.list())
/home/caixi/anaconda/lib/python2.7/site-packages/nipype/interfaces/io.py:872: in <genexpr>
    bkt_files = list(k.key for k in bkt.list())
/home/caixi/anaconda/lib/python2.7/site-packages/boto/s3/bucketlistresultset.py:32: in bucket_lister
    encoding_type=encoding_type)
/home/caixi/anaconda/lib/python2.7/site-packages/boto/s3/bucket.py:474: in get_all_keys
    '', headers, **params)
/home/caixi/anaconda/lib/python2.7/site-packages/boto/s3/bucket.py:401: in _get_all
    body = response.read()
/home/caixi/anaconda/lib/python2.7/site-packages/boto/connection.py:409: in read
    self._cached_response = http_client.HTTPResponse.read(self)
/home/caixi/anaconda/lib/python2.7/httplib.py:573: in read
    return self._read_chunked(amt)
/home/caixi/anaconda/lib/python2.7/httplib.py:631: in _read_chunked
    value.append(self._safe_read(chunk_left))
/home/caixi/anaconda/lib/python2.7/httplib.py:688: in _safe_read
    chunk = self.fp.read(min(amt, MAXAMOUNT))
/home/caixi/anaconda/lib/python2.7/socket.py:384: in read
    data = self._sock.recv(left)
/home/caixi/anaconda/lib/python2.7/ssl.py:766: in recv
    return self.read(buflen)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <ssl.SSLSocket object at 0x7fef21953230>, len = 7617, buffer = None

    def read(self, len=1024, buffer=None):
        """Read up to LEN bytes and return them.
            Return zero-length string on EOF."""
    
        self._checkClosed()
        if not self._sslobj:
            raise ValueError("Read on closed or unwrapped SSL socket.")
        try:
            if buffer is not None:
                v = self._sslobj.read(len, buffer)
            else:
>               v = self._sslobj.read(len)
E               SSLError: (u'The read operation timed out\nInterface S3DataGrabber failed to run. ',)

/home/caixi/anaconda/lib/python2.7/ssl.py:653: SSLError
----------------------------- Captured stdout call -----------------------------
170508-23:51:15,443 boto ERROR:
	 Caught exception reading instance data
Traceback (most recent call last):
  File "/home/caixi/anaconda/lib/python2.7/site-packages/boto/utils.py", line 214, in retry_url
    r = opener.open(req)
  File "/home/caixi/anaconda/lib/python2.7/urllib2.py", line 429, in open
    response = self._open(req, data)
  File "/home/caixi/anaconda/lib/python2.7/urllib2.py", line 447, in _open
    '_open', req)
  File "/home/caixi/anaconda/lib/python2.7/urllib2.py", line 407, in _call_chain
    result = func(*args)
  File "/home/caixi/anaconda/lib/python2.7/urllib2.py", line 1228, in http_open
    return self.do_open(httplib.HTTPConnection, req)
  File "/home/caixi/anaconda/lib/python2.7/urllib2.py", line 1198, in do_open
    raise URLError(err)
URLError: <urlopen error [Errno 111] Connection refused>
170508-23:51:15,463 boto ERROR:
	 Unable to read instance data, giving up
!!!!!!!!!!!!!!!!!!!! Interrupted: stopping after 1 failures !!!!!!!!!!!!!!!!!!!!
======== 1 failed, 2326 passed, 32 skipped, 5 xfailed in 372.02 seconds =======

By the way, should i install Camino, MRtrix, Slicer and ConnectomeViewer?

[caixixixi]

FAIL: Doctest: nipype.interfaces.bru2nii.Bru2
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/doctest.py", line 2226, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for nipype.interfaces.bru2nii.Bru2
  File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/bru2nii.py", line 26, in Bru2

----------------------------------------------------------------------
File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/bru2nii.py", line 34, in nipype.interfaces.bru2nii.Bru2
Failed example:
    converter.inputs.input_dir = "brukerdir"
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest nipype.interfaces.bru2nii.Bru2[2]>", line 1, in <module>
        converter.inputs.input_dir = "brukerdir"
      File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/traits_extension.py", line 169, in validate
        self.error(object, name, value)
      File "/usr/local/lib/python2.7/dist-packages/traits/trait_handlers.py", line 172, in error
        value )
    TraitError: The 'input_dir' trait of a Bru2InputSpec instance must be an existing directory name, but a value of 'brukerdir' <type 'str'> was specified.
----------------------------------------------------------------------
File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/bru2nii.py", line 35, in nipype.interfaces.bru2nii.Bru2
Failed example:
    converter.cmdline  # doctest: +ELLIPSIS
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest nipype.interfaces.bru2nii.Bru2[3]>", line 1, in <module>
        converter.cmdline  # doctest: +ELLIPSIS
      File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.py", line 1608, in cmdline
        self._check_mandatory_inputs()
      File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.py", line 940, in _check_mandatory_inputs
        raise ValueError(msg)
    ValueError: Bru2 requires a value for input 'input_dir'. For a list of required inputs, see Bru2.help()


----------------------------------------------------------------------
Ran 17309 tests in 221.245s

FAILED (SKIP=23, failures=1)
Out[5]: <nose.result.TextTestResult run=17309 errors=0 failures=1>

In [6]: 

[djarecka]

It looks to me that you send me 2 different errors from running 2 different version of nipype. Am I right? The bru2nii error it seems to come from running old nipype. I'm not saying that you can't see it now, but don't want to mix 2 different versions of nipype and 2 independent errors. Let's start from the first issue - test_s3datagrabber_communication.

This test is usually being skipped, since the boto3 library is often not present (it's an interface to work with AWS). It looks like you have the library, so I also installed it, but couldn't reproduce the error on Ubuntu:16.04. The test runs for quite long, but it works. Just noticed that you use Python from Anaconda, so will try to rerun the tests with Anaconda, but can you please type python --version, so I can be sure which version of Python you're using.
And also to check the boto3 version you can type python -c "import boto3; print(boto3.__version__)"

[caixixixi]

@djarecka thanks for the reply
Firstly, i installed nipype with:conda install nipype.beacause of some errors,i changed to version10.0.beacase of the error no module named aniso2iso,pip uninstall nipype; pip install https://github.com/nipy/nipype/archive/master.zip.So i think my nipype version is 13?Actually,i am new in nipype,i am not sure i am right.
And the two different error was the result of
python -c "import nipype; nipype.test()"————the first fialure

import nipype
nipype.config.set('logging', 'workflow_level', 'CRITICAL')
nipype.config.set('logging', 'interface_level', 'CRITICAL')
nipype.logging.update_logging(nipype.config)
nipype.test(verbose=0) ————the second failure

Python 2.7.13

Traceback (most recent call last):
File "", line 1, in
ImportError: No module named boto3
So i pip install boto3
now the version is 1.4.4
I test again, still have the same failure

[djarecka]

I was asking, because I could see that some tests were run by pytest and some tests were run by nose that was a testing interface some months ago, but I understand your confusion. What I would suggest now is that you might want to wait just a few days, because the new version will be released and it will be available form conda install. It might be better just to focus on the new version and, in case of any errors, concentrate on them.
In the meantime, you can of course try to use the version you have, I'm guessing that you're not using AWS, so the boto3 related error will not affect you.

btw. have you considered moving to Python3? The coming release still supports both Python2 and Python3, but some future versions will be available for Python3 users only. If you're just starting working with nipype, you might want to consider using Python3 from the very beginning.

[caixixixi]

thanks

[caixixixi]

@djarecka hi
when i open up an IPython environment and run the following code:

# Import the nipype module
import nipype

# Optional: Use the following lines to increase verbosity of output
nipype.config.set('logging', 'workflow_level',  'CRITICAL')
nipype.config.set('logging', 'interface_level', 'CRITICAL')
nipype.logging.update_logging(nipype.config)

# Run the test: Increase verbosity parameter for more info
nipype.test(verbose=0)

TypeError                                 Traceback (most recent call last)
<ipython-input-1-61095b6edbda> in <module>()
      8 
      9 # Run the test: Increase verbosity parameter for more info
---> 10 nipype.test(verbose=0)

TypeError: __call__() got an unexpected keyword argument 'verbose'


————————————————————————————————————————
i open up an IPython environment and run the following code:run  tutorial_3_first_steps.py

In [3]: run  tutorial_3_first_steps.py
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
/home/caixi/tutorial_3_first_steps.py in <module>()
     34 
     35 # Slicetiming - correct for slice wise acquisition
---> 36 interleaved_order = range(1,number_of_slices+1,2) + range(2,number_of_slices+1,2)
     37 sliceTiming = Node(SliceTiming(num_slices=number_of_slices,
     38                                time_repetition=TR,

TypeError: unsupported operand type(s) for +: 'range' and 'range'

what should i do to fix this error?

[satra]

this is due to python 3, in which range is a generator. you will need something like:
list(range(1,number_of_slices+1,2)) + list(range(2,number_of_slices+1,2))

[caixixixi]

@djarecka @satra hi，I tried to build a pipeline for a first level fMRI analysis and run example_fMRI_1_first_level.py.

RuntimeError                              Traceback (most recent call last)
/home/caixi/nipype_tutorial/example_fMRI_1_first_level.py in <module>()
    348 # Run Workflow
    349 metaflow.write_graph(graph2use='colored')
--> 350 metaflow.run('MultiProc', plugin_args={'n_procs': 8})

/home/caixi/anaconda3/envs/py27/lib/python2.7/site-packages/nipype/pipeline/engine/workflows.pyc in run(self, plugin, plugin_args, updatehash)
    588         if str2bool(self.config['execution']['create_report']):
    589             self._write_report_info(self.base_dir, self.name, execgraph)
--> 590         runner.run(execgraph, updatehash=updatehash, config=self.config)
    591         datestr = datetime.utcnow().strftime('%Y%m%dT%H%M%S')
    592         if str2bool(self.config['execution']['write_provenance']):

/home/caixi/anaconda3/envs/py27/lib/python2.7/site-packages/nipype/pipeline/plugins/base.pyc in run(self, graph, config, updatehash)
    277 
    278         self._remove_node_dirs()
--> 279         report_nodes_not_run(notrun)
    280 
    281         # close any open resources

/home/caixi/anaconda3/envs/py27/lib/python2.7/site-packages/nipype/pipeline/plugins/base.pyc in report_nodes_not_run(notrun)
     99                 logger.debug(subnode._id)
    100         logger.info("***********************************")
--> 101         raise RuntimeError(('Workflow did not execute cleanly. '
    102                             'Check log for details'))
    103 

RuntimeError: Workflow did not execute cleanly. Check log for details



In [2]: !nipype_display_crash /home/caixi/nipype_tutorial/crash-20170517-003326-
   ...: caixi-level1estimate.a0-9b4c9420-768e-4363-a4ee-941cc5f48e70.pklz


File: /home/caixi/nipype_tutorial/crash-20170517-003326-caixi-level1estimate.a0-9b4c9420-768e-4363-a4ee-941cc5f48e70.pklz
Node: metaflow.l1analysis.level1estimate.a0
Working directory: /home/caixi/nipype_tutorial/workingdir_fMRI_example_1st/metaflow/l1analysis/_subject_id_sub001/level1estimate


Node inputs:

estimation_method = {'Classical': 1}
flags = <undefined>
ignore_exception = False
matlab_cmd = <undefined>
mfile = True
paths = <undefined>
spm_mat_file = /home/caixi/nipype_tutorial/workingdir_fMRI_example_1st/metaflow/l1analysis/_subject_id_sub001/level1design/SPM.mat
use_mcr = <undefined>
use_v8struct = True



Traceback: 
Traceback (most recent call last):
  File "/home/caixi/anaconda3/envs/py27/lib/python2.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 52, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/home/caixi/anaconda3/envs/py27/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 372, in run
    self._run_interface()
  File "/home/caixi/anaconda3/envs/py27/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 482, in _run_interface
    self._result = self._run_command(execute)
  File "/home/caixi/anaconda3/envs/py27/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 613, in _run_command
    result = self._interface.run()
  File "/home/caixi/anaconda3/envs/py27/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1081, in run
    runtime = self._run_wrapper(runtime)
  File "/home/caixi/anaconda3/envs/py27/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1029, in _run_wrapper
    runtime = self._run_interface(runtime)
  File "/home/caixi/anaconda3/envs/py27/lib/python2.7/site-packages/nipype/interfaces/spm/base.py", line 323, in _run_interface
    results = self.mlab.run()
  File "/home/caixi/anaconda3/envs/py27/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1081, in run
    runtime = self._run_wrapper(runtime)
  File "/home/caixi/anaconda3/envs/py27/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1724, in _run_wrapper
    runtime = self._run_interface(runtime)
  File "/home/caixi/anaconda3/envs/py27/lib/python2.7/site-packages/nipype/interfaces/matlab.py", line 152, in _run_interface
    self.raise_exception(runtime)
  File "/home/caixi/anaconda3/envs/py27/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1682, in raise_exception
    **runtime.dictcopy()))
RuntimeError: Command:
matlab -nodesktop -nosplash -nodesktop -nosplash -singleCompThread -r "addpath('/home/caixi/nipype_tutorial/workingdir_fMRI_example_1st/metaflow/l1analysis/_subject_id_sub001/level1estimate');pyscript_estimatemodel;exit"
Standard output:

                            < M A T L A B (R) >
                  Copyright 1984-2014 The MathWorks, Inc.
                    R2014a (8.3.0.532) 64-bit (glnxa64)
                             February 11, 2014

 
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
 
Executing pyscript_estimatemodel at 17-May-2017 00:32:58:
----------------------------------------------------------------------------------------------------
MATLAB Version: 8.3.0.532 (R2014a)
MATLAB License Number: 405329
Operating System: Linux 3.19.0-80-generic #88~14.04.1-Ubuntu SMP Fri Jan 13 14:54:07 UTC 2017 x86_64
Java Version: Java 1.7.0_11-b21 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
----------------------------------------------------------------------------------------------------
MATLAB                                                Version 8.3        (R2014a)
Simulink                                              Version 8.3        (R2014a)
Aerospace Blockset                                    Version 3.13       (R2014a)
Aerospace Toolbox                                     Version 2.13       (R2014a)
Bioinformatics Toolbox                                Version 4.4        (R2014a)
Communications System Toolbox                         Version 5.6        (R2014a)
Computer Vision System Toolbox                        Version 6.0        (R2014a)
Control System Toolbox                                Version 9.7        (R2014a)
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Datafeed Toolbox                                      Version 4.7        (R2014a)
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Embedded Coder                                        Version 6.6        (R2014a)
Filter Design HDL Coder                               Version 2.9.5      (R2014a)
Financial Instruments Toolbox                         Version 1.3        (R2014a)
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Simulink Report Generator                             Version 3.16       (R2014a)
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System Identification Toolbox                         Version 9.0        (R2014a)
SystemTest                                            Version 2.6.7      (R2014a)
Wavelet Toolbox                                       Version 4.13       (R2014a)
SPM version: SPM12 Release: 6906
SPM path: /usr/local/MATLAB/R2014a/toolbox/spm12/spm.m


------------------------------------------------------------------------
Running job #1
------------------------------------------------------------------------
Running 'Model estimation'

SPM12: spm_spm (v6842)                             00:33:19 - 17/05/2017
========================================================================

SPM12: spm_est_non_sphericity (v6827)              00:33:21 - 17/05/2017
========================================================================
Failed  'Model estimation'
Reference to non-existent field 'xVol'.
In file "/usr/local/MATLAB/R2014a/toolbox/spm12/spm_est_non_sphericity.m" (v6827), function "spm_est_non_sphericity" at line 105.
In file "/usr/local/MATLAB/R2014a/toolbox/spm12/spm_spm.m" (v6842), function "spm_spm" at line 431.
In file "/usr/local/MATLAB/R2014a/toolbox/spm12/config/spm_run_fmri_est.m" (v5809), function "spm_run_fmri_est" at line 33.

The following modules did not run:
Failed: Model estimation


Standard error:
MATLAB code threw an exception:
Job execution failed. The full log of this run can be found in MATLAB command window, starting with the lines (look for the line showing the exact #job as displayed in this error message)
------------------ 
Running job #1
------------------

File:
Name:MATLABbatch system
Line:0

Return code: 0
Interface MatlabCommand failed to run. 
Interface EstimateModel failed to run.