Feature #38
closedCreate tools for troubleshooting Appion Install
0%
Description
Can we create a script to check that the versions of dependencies are all correct?
Brainstorm other ideas.
Updated by Amber Herold almost 15 years ago
- Project changed from 5 to Appion
- Target version deleted (
2)
Updated by Amber Herold over 14 years ago
- Target version set to Appion/Leginon 2.1.0
Updated by Amber Herold over 14 years ago
appion/test has several test scripts:
createtestsession.py takes a project id and run directory and loads up a session filled with sample images for one to test with.
testsuite.py needs to be completed with error checking, runs through precessing pipeline
teststack.py - reads and writes stacks
Updated by Amber Herold over 14 years ago
- Category set to Installation
- Status changed from New to Assigned
- Assignee set to Amber Herold
Updated by Amber Herold over 14 years ago
- Status changed from Assigned to In Code Review
- Assignee changed from Amber Herold to Eric Hou
Updated by Eric Hou over 14 years ago
- Status changed from In Code Review to In Test
- Assignee changed from Eric Hou to Amber Herold
I don't have time to go over all the code line by line, so let's test this in the test machine and see what's going on.
Please provided testing procedures.
Thanks.
Updated by Amber Herold over 14 years ago
You already reviewed most of it in person, so that should be fine.
To Test:
Open a terminal and cd to myami/install
then: python troubleshooter.py
answer "y" to each question to run most of the tests.
You can also run all the tests with: python checkPackages.py
but this will run every test possible without stopping so it is a bit difficult to see the results flying by the screen.
The tests that are run with this that are not in the other is:
1. a check to see if Leginon is already installed - gives an error if it is
2. Checks for SInedon.cfg and Leginon.cfg to exist, does not give output unless they are missing
to do proper testing, we would need to do positive and negative for each, listed below. I tested all of the code paths with code modifications, but not with the real thing. Doing everything below would take too long, so take a "do what you can" approach.
| Package | function | Description | Tests |
|---|---|---|---|
| PYTHON | checkPythonVersion | looking for min version to be 2.3.4 | test not installed, version less than 2.3.4, version at 2.3.4 |
| PYTHONPATH | printPythonPath | prints the python path | confirm that the path is printed |
| PIL | checkPILVersion | looks for min version of 1.1.4 | test not installed, less than min version, at min version |
| MYSQLDB | checkMySQLdbVersion | checks for min version 1.2 | test not installed, less than min version, at min version |
| NUMPY | checkNumpyVersion | Warns user if version is other then 1.0.2 or 1.0.1 | test not installed, untested version, tested version |
| NUMPYTEST | runNumpyTest | runs numpy unit tests | |
| SCIPY | checkScipyVersion | imports scipy and looks for leastsq function | test not installed, version w/o leastsq, version with leastsq |
| SCIPYTEST | runScipyTest | runs scipy unit tests | |
| PYXML | checkPyXMLVersion | min version 0.8.2 | test not installed, less than min version, at min version |
| WXPYTHON | checkWxPythonVersion | min version 2.5.2.8 | test not installed, less than min version, at min version |
| WXPYTHONAPP | testWxPythonApp | ensure the test app is displayed when wxpython is installed, use close button to close it | |
| LEGINON | leginonInstalled | gives a warning if leginon is installed | test with leginon installed and without |
| SINEDONCFG | checkSinedonConfig | imports sinedon, gives warning if cant find sinedon cfg | test sinedon not installed, sinedon installed but config file not there, sinedon installed with config file present |
| SINEDONCFGPATH | printSinedonCfgPath | same as previous function but prints the path to the config file on the screen | ensure path is displayed |
| LEGINONCFG | checkLeginonConfig | imports sinedon, gives warning if cant find sinedon cfg | test sinedon not installed, sinedon installed but config file not there, sinedon installed with config file present |
| LEGINONCFGPATH | printLeginonCfgPath | same as previous function but prints the path to the config file on the screen | ensure path is displayed |
| EMANTEST | runEmanTest | displays eman help | test eman not installed, eman installed |
| XMIPPTEST | runXmippTest | displays xmipp help | test xmipp not installed, xmipp installed |
| APPION | checkAppion | trys to import all the appion libraries and binaries | test appion installed, appion not installed |
| WEBSERVER | runWebServerCheck | tests many aspects of the web server, php settings, config.php, extensions | |
| test config file with an extra blank line, config file no blank line, | |||
| php version at least 5.0.0 and less than 5.3.0 | |||
| set php.ini settings to something not recommended - should all show up red (run the script to see the recommended values) | |||
| set php.ini values to recommended values - all black | |||
| Check for the following items when installed and not installed: | |||
| GD | |||
| Jpeg library | |||
| ssh2 | |||
| mrc module | |||
| fftw |
Updated by Amber Herold over 14 years ago
- Assignee changed from Amber Herold to Eric Hou
Updated by Eric Hou about 14 years ago
- Assignee changed from Eric Hou to Jim Pulokas
please test this on Fedora....
:)
Eric
Updated by Jim Pulokas about 14 years ago
- Assignee changed from Jim Pulokas to Eric Hou
Tested on Fedora. It runs to the end. Although I did not have web server stuff installed, so not sure if my test is complete enough. Anyway, Fedora web stuff will not work without php-mrc.
One weird thing that shows up in the log is:
"Pick-wei fix this"
Sending it back to you in case there are other things to test.
Updated by Eric Hou about 14 years ago
- Status changed from In Test to Assigned
- Assignee changed from Eric Hou to Amber Herold
Updated by Amber Herold about 14 years ago
- Status changed from Assigned to Closed
The pick-wei refference comes from spiderRecon_PWL.py:
try:
from appionlib.apSpider import backprojectPWL
except ImportError:
print "Pick-wei fix this"