Run tests in travis

[dominikl]

Took over #14 from @joshmoore

[dominikl]

Seems to run fine, until trying to connect to the test server:

omero.gateway.exception.DSOutOfServiceException: Can't connect to OMERO. OMERO info not valid

Might be just an issue with login credentials... what are the login credentials of the omero-test-daemon-c7 server?

What I also don't understand is, is the tests/testthat/init_testserver.sh script actually run after the docker test server is spun up? If not, from where I can launch that? And is omeroserver in tests/testthat/setup.csv really the correct hostname?

[dominikl]

I will merge #21 and rebase this PR, with 5.3.3 there should be more information in the DSOutOfServiceException.

[dominikl]

Argh, can't merge, no permission. Will rebase this PR onto #21 then instead.

[dominikl]

Ok, the exception is Connection refused, so I guess omeroserver as hostname is wrong? Unfortunately I have no idea how this docker, travis thing works...

omero.gateway.exception.DSOutOfServiceException: java.net.ConnectException: Connection refused

[jburel]

There is an issue with the new images that travis uses and docker
you should try to add to the travis file
group: deprecated-2017Q2 since you require sudo
This workaround will have to be removed in few weeks (only available until September)

That's what I had to do in ome/omero-install#158

[dominikl]

I'm giving up on this, can't get the init_testserver.sh script to run on the omeroserver docker thing. Without setting up the testdata devtools::test() will obviously fail.

[joshmoore]

In local tests I'm seeing:

8. Failure: Test Screen getImages (@test-SPW.R#54) -----------------------------
length(imgs) not equal to `plateSize`.
1/1 mismatches
[1] 192 - 64 == 128

which means that some of my changes will need looking into at a semantic level (i.e. handle unexpected data). cc: @dominikl

The travis build is failing with:

Warning messages:
1: replacing previous import ‘rJava::tail’ by ‘utils::tail’ when loading ‘romero.gateway’ 
2: replacing previous import ‘rJava::str’ by ‘utils::str’ when loading ‘romero.gateway’ 
3: replacing previous import ‘rJava::head’ by ‘utils::head’ when loading ‘romero.gateway’ 
> 
> # Retry connecting until server is up and running
> for (i in 1:60) {
+   server <- tryCatch(
+             {
+               server <- OMEROServer(
+                 host='omero',
+                 port=4064,
+                 username='root',
+                 password='omero')
+               server <- connect(server)
+               return(server)
+             },
+             error=function(cond) {
+               Sys.sleep(10)
+               return(NA)
+             },
+             warning=function(cond) {
+             },
+             finally={
+             }
+           )
+   if (!is.na(server))
+     break
+ }
No output has been received in the last 10m0s, this potentially indicates a stalled build or something wrong with the build itself.
Check the details on how to adjust your build configuration on: https://docs.travis-ci.com/user/common-build-problems/#Build-times-out-because-no-output-was-received

which I'll keep looking into.

[dominikl]

Oh wow, you got it working, thanks @joshmoore ! Yes, looks like the expected values of the tests are not correct any longer, I'll update that, which should be simple now.
I check if it's possible that the tests get stuck in a loop somewhere (although I don't think so). Locally the tests run in about 1 - 2 min, definitely not exceeding 10min.

[dominikl]

Everything seems to work now (incl integration tests), but still Done. Your build exited with 1. !?

[joshmoore]

Hmm.... passing locally with:

$ docker cp .omeroci/test-data omero_omero_1:/tmp/data
$ docker exec -ti omero_omero_1 bash /tmp/data
$ docker run --link omero_omero_1:omero --net omero_default --rm test
...
...........................Rows:  150
Columns:  5
          Name Description      Type
1 Sepal.Length               numeric
2  Sepal.Width               numeric
3 Petal.Length               numeric
4  Petal.Width               numeric
5      Species             character
................
DONE ===========================================================================
Warning messages:
1: character(0)
2: character(0)
3: character(0)
>
>
$ echo $?
0

I'll try pushing the current state of test-omero and then re-build to see if we can get it green.

Note: this isn't yet idempotent. If test-data is run more than once, then the test fails.

[dominikl]

Oh, so it's possible that test-data runs multiple times? Have to include a check then and only run if omero db is empty.

[joshmoore]

Can discuss. I guess I'm less worried less about the "test-data has already been run once" than I am "some arbitrary data already exists".

[dominikl]

I see. I'll overhaul the tests in a follow-up PR so that preexisting data doesn't break them.

[dominikl]

Same again, tests pass, build exits with 1 :-/

[joshmoore]

@dominikl : green!

[dominikl]

Awesome, thanks @joshmoore !