Closed claudiologiudice closed 8 months ago
Have you tested first if everything was up and running? ...and connected?
Can you please connect to the inbox container, manually, with
$ docker-compose exec inbox bash
and try a command like
$ id john # you look for the user "john" (used by the testsuite and from the fake CentralEGA)
If the user is not found, you won't be able to connect and even less to run the testsuite.
id john uid=25000(john) gid=1000(lega) groups=1000(lega)
It seems the user is found, but the testsuite keeps giving me that error...
I add more information about the problem I'm facing with the fega toolkit:
docker ps -a
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
47d547fb26e6 egarchive/lega-inbox:latest "entrypoint.sh" 3 seconds ago Up 3 seconds 0.0.0.0:2222->9000/tcp, :::2222->9000/tcp inbox
3bd76b952351 egarchive/lega-mq:latest "/usr/local/bin/ega-…" 5 seconds ago Up 3 seconds 4369/tcp, 5671-5672/tcp, 15671/tcp, 15691-15692/tcp, 25672/tcp, 0.0.0.0:15672->15672/tcp, :::15672->15672/tcp mq
c7e7e7cab165 rabbitmq:3.9.11-management-alpine "/usr/local/bin/cega…" 5 seconds ago Up 4 seconds 4369/tcp, 5672/tcp, 15671/tcp, 15691-15692/tcp, 25672/tcp, 0.0.0.0:5670->5671/tcp, :::5670->5671/tcp, 0.0.0.0:15670->15672/tcp, :::15670->15672/tcp cega-mq
1599741d8a85 egarchive/lega-db:latest "/usr/local/bin/entr…" 5 seconds ago Up 4 seconds 0.0.0.0:15432->5432/tcp, :::15432->5432/tcp archive-db
8000a7b38440 egarchive/lega-base:latest "lega-entrypoint.sh …" 5 seconds ago Up 3 seconds ingest
d687ad586df9 egarchive/lega-base:latest "lega-entrypoint.sh …" 5 seconds ago Up 3 seconds save2db
61714d6a0724 egarchive/lega-base:latest "lega-entrypoint.sh …" 5 seconds ago Up 4 seconds backup2
ddeee1ca02e1 egarchive/cega-users:latest "python /cega/server…" 5 seconds ago Exited (1) 4 seconds ago cega-users
157f2550ded1 egarchive/lega-db:latest "/usr/local/bin/entr…" 5 seconds ago Up 4 seconds 5432/tcp db
7b89fff20eb3 egarchive/lega-base:latest "lega-entrypoint.sh …" 5 seconds ago Up 3 seconds backup1
5f0bb7d00cc8 egarchive/lega-base:latest "lega-entrypoint.sh …" 5 seconds ago Up 4 seconds cleanup
9aafa91ee6dd egarchive/lega-base:latest "lega-entrypoint.sh …" 5 seconds ago Up 4 seconds dispatcher
9dedc43edcf6 egarchive/lega-base:latest "python accession.py" 5 seconds ago Up 4 seconds cega-accession
feganode@fega-ba:/mnt/data/LocalEGA/deploy$ docker logs ddeee1ca02e1
unhandled exception during asyncio.run() shutdown
task: <Task finished name='Task-1' coro=<_run_app() done, defined at /usr/local/lib/python3.9/site-packages/aiohttp/web.py:303> exception=TypeError('The port is required to be int.')>
Traceback (most recent call last):
File "/usr/local/lib/python3.9/site-packages/aiohttp/web.py", line 544, in run_app
loop.run_until_complete(main_task)
File "/usr/local/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
return future.result()
File "/usr/local/lib/python3.9/site-packages/aiohttp/web.py", line 451, in _run_app
names = sorted(str(s.name) for s in runner.sites)
File "/usr/local/lib/python3.9/site-packages/aiohttp/web.py", line 451, in
@claudiologiudice : it makes more sense to try to install the branch "v2" that we will merge into master soon enough. The version you are installing is a very old one, and we don't have the resources to help you out with that one (We will deprecate it in the coming weeks anyway: ping @sdelatorrep ;-) )
Expected Behavior
I'm using the LocalEGA testsuite
Current Behavior
It shoud accomplish all the selected tasks, according to a fake central ega node.
Steps to Reproduce
bats tests/integration ✓ Ingest a file for a user that does not exist in CentralEGA ✓ Ingest a file using the wrong user password ✓ Ingest a file using the wrong user sshkey ✗ Upload a batch of files (from function
load_into_ssh_agent' in file tests/integration/../_common/helpers.bash, line 85, from function
setup' in test file tests/integration/inbox.bats, line 24)load_into_ssh_agent ${TESTUSER}' failed ✗ Ingestion of ghost file goes to error (from function
load_into_ssh_agent' in file tests/integration/../_common/helpers.bash, line 85, from functionsetup' in test file tests/integration/inbox.bats, line 24)
load_into_ssh_agent ${TESTUSER}' failed ✗ File not found goes to error (from functionload_into_ssh_agent' in file tests/integration/../_common/helpers.bash, line 85, from function
setup' in test file tests/integration/inbox.bats, line 24)load_into_ssh_agent ${TESTUSER}' failed ✗ Ingest properly a 10MB file (from function
load_into_ssh_agent' in file tests/integration/../_common/helpers.bash, line 85, from functionsetup' in test file tests/integration/ingestion.bats, line 27)
load_into_ssh_agent ${TESTUSER}' failed ✗ Ingest properly a 1GB file (from functionload_into_ssh_agent' in file tests/integration/../_common/helpers.bash, line 85, from function
setup' in test file tests/integration/ingestion.bats, line 27)load_into_ssh_agent ${TESTUSER}' failed ✗ Do not ingest the same file twice (from function
load_into_ssh_agent' in file tests/integration/../_common/helpers.bash, line 85, from functionsetup' in test file tests/integration/ingestion.bats, line 27)
load_into_ssh_agent ${TESTUSER}' failed ✗ Do not ingest a file not in Crypt4GH format (from functionload_into_ssh_agent' in file tests/integration/../_common/helpers.bash, line 85, from function
setup' in test file tests/integration/ingestion.bats, line 27)load_into_ssh_agent ${TESTUSER}' failed ✗ Ingest a file from a subdirectory (from function
load_into_ssh_agent' in file tests/integration/../_common/helpers.bash, line 85, from functionsetup' in test file tests/integration/ingestion.bats, line 27)
load_into_ssh_agent ${TESTUSER}' failed ✗ Do not ingest file destined for another LocalEGA (from functionload_into_ssh_agent' in file tests/integration/../_common/helpers.bash, line 85, from function
setup' in test file tests/integration/ingestion.bats, line 27)load_into_ssh_agent ${TESTUSER}' failed ✗ Ingest properly a test file, with a dataset mapping (from function
load_into_ssh_agent' in file tests/integration/../_common/helpers.bash, line 85, from functionsetup' in test file tests/integration/mapping.bats, line 27)
load_into_ssh_agent ${TESTUSER}' failed13 tests, 10 failures