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MOZI-AI / annotation-scheme

Human Gene annotation service backend
GNU General Public License v3.0
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Cache find pathway #156

Closed linas closed 4 years ago

linas commented 4 years ago

Unwrap the GroundedSchema and replace by srfi-1 map. This allows simplification of the overall structure, but avoiding the need to wrap and unwrap boolean arguments as Atoms. This is similar to #149 and together with that, will allow find-rna arguments to just be #t and #f

linas commented 4 years ago

Unit tests pass for me; I can't tell why circle-ci fails; it won't surrender a log.

tanksha commented 4 years ago

Tests passed for me too when I try it locally. @Habush please check the circle-ci.

And also,running the annotation-service docker with this update, tests are failing. Any recent changes you didn't include to the dockerfile?? might be the cause. I tried to change the json repo from yours to https://github.com/aconchillo/guile-json but still tests are failing. Please have a look

Habush commented 4 years ago

The reason the tests fail for this PR is because it is based on a version that doesn't contain other fixes I made for the unit-test failures. So merging it won't cause any test failures.

tanksha commented 4 years ago

@Habush How about in the annotation-service docker? Tests are failing building the docker

Habush commented 4 years ago

I haven't checked which commit the scheme submodule for the annotation-service is at right now. I believe it is out-of sync.

tanksha commented 4 years ago

No, its not synch issue. I tried updating the scheme submodule to the current but tests failed

Habush commented 4 years ago

can you post which tests are failing and their logs?

tanksha commented 4 years ago 
make[1]: Entering directory '/root/mozi_annotation_service/scheme'
make[2]: Entering directory '/root/mozi_annotation_service/scheme'
PASS: tests/parser-tests.scm
PASS: tests/util-tests.scm
PASS: tests/pathway-tests.scm
FAIL: tests/main-tests.scm
============================================================================
Testsuite summary for gene-annotation 0.1
============================================================================
# TOTAL: 17
# PASS:  13
# SKIP:  0
# XFAIL: 0
# FAIL:  4
# XPASS: 0
# ERROR: 0
============================================================================
See ./test-suite.log
============================================================================
Makefile:662: recipe for target 'test-suite.log' failed
make[2]: *** [test-suite.log] Error 1
make[2]: Leaving directory '/root/mozi_annotation_service/scheme'
make[1]: *** [check-TESTS] Error 2
Makefile:768: recipe for target 'check-TESTS' failed
make[1]: Leaving directory '/root/mozi_annotation_service/scheme'
Makefile:960: recipe for target 'check-am' failed
make: *** [check-am] Error 2
ERROR: Service 'backend' failed to build: The command '/bin/sh -c autoreconf -vif &&     ./configure  &&     make &&     make install &&     make check' returned a non-zero code: 2
tanksha commented 4 years ago

Cant access the log, the container exited