Tests

[chinchliff]

Changing tests as requested in #79, and general cleanup of installation/testing scripts.

[jar398]

./test.sh: line 8: nosetests: command not found

[chinchliff]

@jar398, here's the line in question

[chinchliff]

I'm not sure how you got that using the latest version of tests.sh, nosetests used to be called on line 8, but now it isn't called until inside run_service_tests.sh, and on line 19 of tests.sh it is checked for and installed by virtualenv if it is missing...

[jar398]

I just updated taxomachine to the tests branch, and ran the top level test.sh. It still says
./test.sh: line 8: nosetests: command not found
as of course it should since it's not making any effort to make sure that nosetests is defined. It's test.sh that needs to be fixed.

[chinchliff]

I am confused. test.sh should not be doing anything related to nosetests on line 8, and it does indeed make an effort to check make sure that nosetests is defined, on line 19, which is also the first occurrence of the string 'nose' in the file. Am I overlooking something? As I indicated earlier in this comment thread, line 8 in the current version of test.sh in this branch should be accessing the count of failed unit tests, not doing anything related to nosetests. E.g.

Meconopsis:taxomachine cody$ pwd
/Users/cody/phylo/taxomachine
Meconopsis:taxomachine cody$ git status
On branch tests
nothing to commit, working directory clean
Meconopsis:taxomachine cody$ git pull origin tests
From github.com:opentreeoflife/taxomachine
 * branch            tests      -> FETCH_HEAD
Already up-to-date.
Meconopsis:taxomachine cody$ head -n 8 test.sh 
## java unit tests
echo "Running Java unit tests"

type mvn >/dev/null 2>&1 || { echo >&2 "maven is required for testing but could not be found. Aborting."; exit 1; }

tests/run_unit_tests.sh

count=$?
Meconopsis:taxomachine cody$ grep -n nose test.sh 
19:type nosetests >/dev/null 2>&1 || { echo "installing test dependencies"; ./install_dependencies_for_tests.sh; }
Meconopsis:taxomachine cody$ 

[jar398]

Did you push your tests branch to github? Here's what I see:

bash-3.2$ ot17
Linux ip-10-17-6-84 3.2.0-4-amd64 #1 SMP Debian 3.2.57-3 x86_64

The programs included with the Debian GNU/Linux system are free software;
the exact distribution terms for each program are described in the
individual files in /usr/share/doc/*/copyright.

Debian GNU/Linux comes with ABSOLUTELY NO WARRANTY, to the extent
permitted by applicable law.
Last login: Thu Oct 9 21:05:43 2014 from 128.30.16.206
opentree@ip-10-17-6-84:$ cd repo/taxomachine
opentree@ip-10-17-6-84:/repo/taxomachine$ ./test.sh
./test.sh: line 8: nosetests: command not found
opentree@ip-10-17-6-84:/repo/taxomachine$ git pull
Already up-to-date.
opentree@ip-10-17-6-84:/repo/taxomachine$ cat test.sh

set the TAXOMACHINE_SERVER environment variable in your shell to point

the script at the right location, e.g.:

TAXOMACHINE_SERVER=devapi.opentreeoflife.org/taxomachine # to run

remotely against devapi

TAXOMACHINE_SERVER=localhost:7476/db/data # to run locally on devapi

[ -z "$TAXOMACHINE_SERVER" ] && TAXOMACHINE_SERVER='localhost:7474/db/data'
&& export TAXOMACHINE_SERVER
cd tests && nosetests -vs curl_tests.pyopentree@ip-10-17-6-84
:~/repo/taxomachine$

On Thu, Oct 16, 2014 at 2:40 PM, Cody Hinchliff notifications@github.com
wrote:

I am confused. test.sh should not be doing anything related to nosetests
on line 8, and it does indeed make an effort to check make sure that
nosetests is defined, on line 19, which is also the first occurrence of the
string 'nose' in the file. Am I overlooking something? As I indicated
earlier in this comment thread, line 8 in the current version of test.sh in
this branch should be accessing the count of failed unit tests, not doing
anything related to nosetests. E.g.

Meconopsis:taxomachine cody$ pwd
/Users/cody/phylo/taxomachine
Meconopsis:taxomachine cody$ git status
On branch tests
nothing to commit, working directory clean
Meconopsis:taxomachine cody$ git pull origin tests
From github.com:opentreeoflife/taxomachine

• branch tests -> FETCH_HEAD
  Already up-to-date.
  Meconopsis:taxomachine cody$ head -n 8 test.sh ## java unit testsecho "Running Java unit tests"
  type mvn >/dev/null 2>&1 || { echo >&2 "maven is required for testing but could not be found. Aborting."; exit 1; }

tests/run_unit_tests.sh
count=$?
Meconopsis:taxomachine cody$ grep -n nose test.sh
19:type nosetests >/dev/null 2>&1 || { echo "installing test dependencies"; ./install_dependencies_for_tests.sh; }
Meconopsis:taxomachine cody$

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Reply to this email directly or view it on GitHub
#80 (comment)
.

[chinchliff]

Yes, it has been pushed to github. That comment is attached to the test.sh
file in github. Perhaps your git is not set up to pull changes to that
branch using the generic pull command? What happens if you try 'git pull
origin tests'?

On Thu, Oct 16, 2014 at 2:54 PM, Jonathan A Rees notifications@github.com
wrote:

Did you push your tests branch to github? Here's what I see:

bash-3.2$ ot17
Linux ip-10-17-6-84 3.2.0-4-amd64 #1 SMP Debian 3.2.57-3 x86_64

The programs included with the Debian GNU/Linux system are free software;
the exact distribution terms for each program are described in the
individual files in /usr/share/doc/*/copyright.

Debian GNU/Linux comes with ABSOLUTELY NO WARRANTY, to the extent
permitted by applicable law.
Last login: Thu Oct 9 21:05:43 2014 from 128.30.16.206
opentree@ip-10-17-6-84:$ cd repo/taxomachine
opentree@ip-10-17-6-84:/repo/taxomachine$ ./test.sh
./test.sh: line 8: nosetests: command not found
opentree@ip-10-17-6-84:/repo/taxomachine$ git pull
Already up-to-date.
opentree@ip-10-17-6-84:/repo/taxomachine$ cat test.sh

set the TAXOMACHINE_SERVER environment variable in your shell to point

the script at the right location, e.g.:

TAXOMACHINE_SERVER=devapi.opentreeoflife.org/taxomachine # to run

remotely against devapi

TAXOMACHINE_SERVER=localhost:7476/db/data # to run locally on devapi

[ -z "$TAXOMACHINE_SERVER" ] &&
TAXOMACHINE_SERVER='localhost:7474/db/data'
&& export TAXOMACHINE_SERVER
cd tests && nosetests -vs curl_tests.pyopentree@ip-10-17-6-84
:~/repo/taxomachine$

On Thu, Oct 16, 2014 at 2:40 PM, Cody Hinchliff notifications@github.com

wrote:

I am confused. test.sh should not be doing anything related to nosetests
on line 8, and it does indeed make an effort to check make sure that
nosetests is defined, on line 19, which is also the first occurrence of
the
string 'nose' in the file. Am I overlooking something? As I indicated
earlier in this comment thread, line 8 in the current version of test.sh
in
this branch should be accessing the count of failed unit tests, not
doing
anything related to nosetests. E.g.

Meconopsis:taxomachine cody$ pwd
/Users/cody/phylo/taxomachine
Meconopsis:taxomachine cody$ git status
On branch tests
nothing to commit, working directory clean
Meconopsis:taxomachine cody$ git pull origin tests
From github.com:opentreeoflife/taxomachine

• branch tests -> FETCH_HEAD
  Already up-to-date.
  Meconopsis:taxomachine cody$ head -n 8 test.sh ## java unit testsecho
  "Running Java unit tests"
  type mvn >/dev/null 2>&1 || { echo >&2 "maven is required for testing
  but could not be found. Aborting."; exit 1; }

tests/run_unit_tests.sh
count=$?
Meconopsis:taxomachine cody$ grep -n nose test.sh
19:type nosetests >/dev/null 2>&1 || { echo "installing test
dependencies"; ./install_dependencies_for_tests.sh; }
Meconopsis:taxomachine cody$

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<
https://github.com/OpenTreeOfLife/taxomachine/pull/80#issuecomment-59409299>

.

—
Reply to this email directly or view it on GitHub
#80 (comment)
.

[jar398]

That was the problem, thanks. I've modified the git_refresh function in the
deployment system per your advice.

I don't fully understand how 'git pull' works. Or 'git fetch' for that
matter.