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Abort trap: 6 about matchminer-ui HOT 20 CLOSED

cegg avatar cegg commented on September 4, 2024
Abort trap: 6

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Comments (20)

ethansiegl avatar ethansiegl commented on September 4, 2024

Hello,

I just tried to reproduce your issue by pulling and starting the repository and was not able to. Do you have gulp installed globally on your machine?

npm install -g gulp

from matchminer-ui.

cegg avatar cegg commented on September 4, 2024

Hi Ethan,
I forgot to mention I am in a conda environment. Not sure if this affects anything.
Yes, gulp is in place but jut in case I re-ran it, here is the output

(matchminer-ui) ~/matchminer-ui$ $ npm install -g gulp
npm WARN deprecated [email protected]: gulp-util is deprecated - replace it, following the guidelines at https://medium.com/gulpjs/gulp-util-ca3b1f9f9ac5
npm WARN deprecated [email protected]: please upgrade to graceful-fs 4 for compatibility with current and future versions of Node.js
npm WARN deprecated [email protected]: Please update to minimatch 3.0.2 or higher to avoid a RegExp DoS issue
npm WARN deprecated [email protected]: Please update to minimatch 3.0.2 or higher to avoid a RegExp DoS issue
npm WARN deprecated [email protected]: please upgrade to graceful-fs 4 for compatibility with current and future versions of Node.js
/usr/local/bin/gulp -> /usr/local/lib/node_modules/gulp/bin/gulp.js

then:

(matchminer-ui) ~/matchminer-ui$ gulp test
gulp[12593]: ../src/node_contextify.cc:627:static void node::contextify::ContextifyScript::New(const FunctionCallbackInfov8::Value &): Assertion `args[1]->IsString()' failed.
1: 0x100039393 node::Abort() [/usr/local/bin/node]
2: 0x10003849d node::MakeCallback(v8::Isolate*, v8::Localv8::Object, char const*, int, v8::Localv8::Value, node::async_context) [/usr/local/bin/node]
3: 0x10005e5fc node::contextify::ContextifyScript::New(v8::FunctionCallbackInfov8::Value const&) [/usr/local/bin/node]
4: 0x1001fd3e7 v8::internal::FunctionCallbackArguments::Call(v8::internal::CallHandlerInfo) [/usr/local/bin/node]
5: 0x1001fc704 v8::internal::MaybeHandlev8::internal::Object v8::internal::(anonymous namespace)::HandleApiCallHelper(v8::internal::Isolate*, v8::internal::Handlev8::internal::HeapObject, v8::internal::Handlev8::internal::HeapObject, v8::internal::Handlev8::internal::FunctionTemplateInfo, v8::internal::Handlev8::internal::Object, v8::internal::BuiltinArguments) [/usr/local/bin/node]
6: 0x1001fc141 v8::internal::Builtin_Impl_HandleApiCall(v8::internal::BuiltinArguments, v8::internal::Isolate*) [/usr/local/bin/node]
7: 0x929047dc01d
8: 0x9290478d145
9: 0x9290480b900
10: 0x929047918b5
11: 0x929047918b5
Abort trap: 6

from matchminer-ui.

ethansiegl avatar ethansiegl commented on September 4, 2024

Hmmm I'm not sure if being in a conda environment effects any of the gulp processes. Could you try running the commands outside the environment and see if there is any difference?

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cegg avatar cegg commented on September 4, 2024

Tried just in bash with no conda env. Identical error.

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cegg avatar cegg commented on September 4, 2024

Also: tried to build a docker container (there is Dockerfile in the repo even though the docs do not mention dockerization). the build arrived almost to the end and the exited with this really long error trace (I had to cut out the middle section of it due to the comment length limit of 65K chars) ending with "The command '/bin/sh -c gulp test' returned a non-zero code: 1", so it might be the same issue:

[16:14:35] Starting 'test'...
15 10 2018 16:14:36.043:WARN [watcher]: Pattern "/usr/src/app/app//*.module.js" does not match any file.
15 10 2018 16:14:36.369:WARN [watcher]: Pattern "/usr/src/app/app/assets//*" does not match any file.
15 10 2018 16:14:38.313:INFO [karma]: Karma v0.13.22 server started at http://localhost:9876/
15 10 2018 16:14:38.325:INFO [launcher]: Starting browser PhantomJS
15 10 2018 16:14:39.148:INFO [PhantomJS 2.1.1 (Linux 0.0.0)]: Connected on socket od09vXWuPMQSz0IwAAAA with id 71997157
PhantomJS 2.1.1 (Linux 0.0.0) Controller: ClinicalTrialsCtrl should be set the isAuthenticated parameter on init FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/app/clinical-trials/clinical-trials.controller.spec.js:40:9
TypeError: undefined is not an object (evaluating 'ctrl.isAuthenticated') in /usr/src/app/app/scripts/app/clinical-trials/clinical-trials.controller.spec.js (line 57)
/usr/src/app/app/scripts/app/clinical-trials/clinical-trials.controller.spec.js:57:14
PhantomJS 2.1.1 (Linux 0.0.0) Controller: ClinicalTrialsCtrl should be able to detect changes of the searchterm in the elasticsearchservice and update the metadata FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/app/clinical-trials/clinical-trials.controller.spec.js:40:9
TypeError: undefined is not an object (evaluating 'ctrl.searchTerm') in /usr/src/app/app/scripts/app/clinical-trials/clinical-trials.controller.spec.js (line 61)
/usr/src/app/app/scripts/app/clinical-trials/clinical-trials.controller.spec.js:61:14
PhantomJS 2.1.1 (Linux 0.0.0) Controller: ClinicalTrialsCtrl should be able to detect changes of the loading indicator used in the clinicaltrialsservice FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/app/clinical-trials/clinical-trials.controller.spec.js:40:9
TypeError: undefined is not an object (evaluating 'ctrl.isLoading') in /usr/src/app/app/scripts/app/clinical-trials/clinical-trials.controller.spec.js (line 72)
/usr/src/app/app/scripts/app/clinical-trials/clinical-trials.controller.spec.js:72:14
PhantomJS 2.1.1 (Linux 0.0.0) Controller: ClinicalTrialsCtrl should be able to detect changes of the clinical trials list in the service FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/app/clinical-trials/clinical-trials.controller.spec.js:40:9
TypeError: Attempted to assign to readonly property. in /usr/src/app/app/scripts/app/clinical-trials/clinical-trials.controller.spec.js (line 81)
/usr/src/app/app/scripts/app/clinical-trials/clinical-trials.controller.spec.js:81:24
PhantomJS 2.1.1 (Linux 0.0.0) Controller: ClinicalTrialsFiltersCtrl should be able to load a clinical trial FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/app/clinical-trials/details/clinical-trials-details.controller.spec.js:56:9
Error: : could not find an object to spy upon for getTrialCoordinator()
Usage: spyOn(, ) in /usr/src/app/node_modules/jasmine-core/lib/jasmine-core/jasmine.js (line 4927)
/usr/src/app/app/scripts/app/clinical-trials/details/clinical-trials-details.controller.spec.js:97:8
PhantomJS 2.1.1 (Linux 0.0.0) Controller: ClinicalTrialsFiltersCtrl should be able to gracefully fail parsing a clinical trial FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/app/clinical-trials/details/clinical-trials-details.controller.spec.js:56:9
TypeError: undefined is not an object (evaluating 'ctrl.loadClinicalTrial') in /usr/src/app/app/scripts/app/clinical-trials/details/clinical-trials-details.controller.spec.js (line 134)
/usr/src/app/app/scripts/app/clinical-trials/details/clinical-trials-details.controller.spec.js:134:7
PhantomJS 2.1.1 (Linux 0.0.0) Controller: ClinicalTrialsFiltersCtrl should be able to gracefully fail retrieving undefined for a clinical trial FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/app/clinical-trials/details/clinical-trials-details.controller.spec.js:56:9
TypeError: undefined is not an object (evaluating 'ctrl.loadClinicalTrial') in /usr/src/app/app/scripts/app/clinical-trials/details/clinical-trials-details.controller.spec.js (line 154)
/usr/src/app/app/scripts/app/clinical-trials/details/clinical-trials-details.controller.spec.js:154:7
PhantomJS 2.1.1 (Linux 0.0.0) Controller: ClinicalTrialsFiltersCtrl should be able to fetch a study coordinator when there is no Lead Study Coordinator FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/app/clinical-trials/details/clinical-trials-details.controller.spec.js:56:9
TypeError: undefined is not an object (evaluating 'ctrl.getTrialCoordinator') in /usr/src/app/app/scripts/app/clinical-trials/details/clinical-trials-details.controller.spec.js (line 167)
/usr/src/app/app/scripts/app/clinical-trials/details/clinical-trials-details.controller.spec.js:167:7
PhantomJS 2.1.1 (Linux 0.0.0) Controller: ClinicalTrialsFiltersCtrl should be able to open a link to CTgov FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/app/clinical-trials/details/clinical-trials-details.controller.spec.js:56:9
TypeError: undefined is not an object (evaluating 'ENV.resources') in /usr/src/app/app/scripts/app/clinical-trials/details/clinical-trials-details.controller.spec.js (line 175)
/usr/src/app/app/scripts/app/clinical-trials/details/clinical-trials-details.controller.spec.js:175:17
PhantomJS 2.1.1 (Linux 0.0.0) Controller: ClinicalTrialsFiltersCtrl should be able to open a link to OncoPro FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/app/clinical-trials/details/clinical-trials-details.controller.spec.js:56:9
TypeError: undefined is not an object (evaluating 'ENV.resources') in /usr/src/app/app/scripts/app/clinical-trials/details/clinical-trials-details.controller.spec.js (line 185)
/usr/src/app/app/scripts/app/clinical-trials/details/clinical-trials-details.controller.spec.js:185:17
PhantomJS 2.1.1 (Linux 0.0.0) Controller: ClinicalTrialsFiltersCtrl should be able to email an investigator FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/app/clinical-trials/details/clinical-trials-details.controller.spec.js:56:9
TypeError: undefined is not an object (evaluating 'mockTrial.staff_list') in /usr/src/app/app/scripts/app/clinical-trials/details/clinical-trials-details.controller.spec.js (line 193)
/usr/src/app/app/scripts/app/clinical-trials/details/clinical-trials-details.controller.spec.js:193:24
PhantomJS 2.1.1 (Linux 0.0.0) Controller: ClinicalTrialsFiltersCtrl should be able to resolve the correct status CSS for the detail badge FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/app/clinical-trials/details/clinical-trials-details.controller.spec.js:56:9
TypeError: undefined is not an object (evaluating 'ctrl.getStatusCss') in /usr/src/app/app/scripts/app/clinical-trials/details/clinical-trials-details.controller.spec.js (line 201)
/usr/src/app/app/scripts/app/clinical-trials/details/clinical-trials-details.controller.spec.js:201:20
PhantomJS 2.1.1 (Linux 0.0.0) Controller: ClinicalTrialsFiltersCtrl should be able to resolve the correct icon for different trials FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/app/clinical-trials/details/clinical-trials-details.controller.spec.js:56:9
TypeError: undefined is not an object (evaluating 'ctrl.getIconForTrialStatus') in /usr/src/app/app/scripts/app/clinical-trials/details/clinical-trials-details.controller.spec.js (line 209)
/usr/src/app/app/scripts/app/clinical-trials/details/clinical-trials-details.controller.spec.js:209:19
forEach@/usr/src/app/bower_components/underscore/underscore.js:153:17
/usr/src/app/app/scripts/app/clinical-trials/details/clinical-trials-details.controller.spec.js:208:9
PhantomJS 2.1.1 (Linux 0.0.0) Controller: ClinicalTrialsFiltersCtrl should initialize with no trial filters categories loaded FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/app/clinical-trials/filters/clinical-trials-filters.controller.spec.js:33:9
TypeError: undefined is not an object (evaluating 'ctrl.filters') in /usr/src/app/app/scripts/app/clinical-trials/filters/clinical-trials-filters.controller.spec.js (line 55)
/usr/src/app/app/scripts/app/clinical-trials/filters/clinical-trials-filters.controller.spec.js:55:14
PhantomJS 2.1.1 (Linux 0.0.0) Controller: ClinicalTrialsFiltersCtrl should be able to detect changes of the loading indicator used in the clinicaltrialsservice FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/app/clinical-trials/filters/clinical-trials-filters.controller.spec.js:33:9
TypeError: undefined is not an object (evaluating 'ctrl.isLoading') in /usr/src/app/app/scripts/app/clinical-trials/filters/clinical-trials-filters.controller.spec.js (line 59)
/usr/src/app/app/scripts/app/clinical-trials/filters/clinical-trials-filters.controller.spec.js:59:14
PhantomJS 2.1.1 (Linux 0.0.0) Controller: ClinicalTrialsFiltersCtrl should be able to check if a aggregator is active by its value FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/app/clinical-trials/filters/clinical-trials-filters.controller.spec.js:33:9
Error: : could not find an object to spy upon for isActiveFilter()
Usage: spyOn(, ) in /usr/src/app/node_modules/jasmine-core/lib/jasmine-core/jasmine.js (line 4927)
/usr/src/app/app/scripts/app/clinical-trials/filters/clinical-trials-filters.controller.spec.js:67:8
PhantomJS 2.1.1 (Linux 0.0.0) Controller: ClinicalTrialsFiltersCtrl should return false when trying to toggle a filter and the controller is loading. FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/app/clinical-trials/filters/clinical-trials-filters.controller.spec.js:33:9
Error: : could not find an object to spy upon for searchFilter()
Usage: spyOn(, ) in /usr/src/app/node_modules/jasmine-core/lib/jasmine-core/jasmine.js (line 4927)
/usr/src/app/app/scripts/app/clinical-trials/filters/clinical-trials-filters.controller.spec.js:76:8
PhantomJS 2.1.1 (Linux 0.0.0) Controller: ClinicalTrialsFiltersCtrl should be able to toggle a filter by aggregator and value FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/app/clinical-trials/filters/clinical-trials-filters.controller.spec.js:33:9
Error: : could not find an object to spy upon for searchFilter()
Usage: spyOn(, ) in /usr/src/app/node_modules/jasmine-core/lib/jasmine-core/jasmine.js (line 4927)
/usr/src/app/app/scripts/app/clinical-trials/filters/clinical-trials-filters.controller.spec.js:86:8
PhantomJS 2.1.1 (Linux 0.0.0) Controller: ClinicalTrialsFiltersCtrl should be able to toggle all facets for a single filter FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/app/clinical-trials/filters/clinical-trials-filters.controller.spec.js:33:9
Error: : could not find an object to spy upon for setFacetOptionsState()
Usage: spyOn(, ) in /usr/src/app/node_modules/jasmine-core/lib/jasmine-core/jasmine.js (line 4927)
/usr/src/app/app/scripts/app/clinical-trials/filters/clinical-trials-filters.controller.spec.js:97:8
PhantomJS 2.1.1 (Linux 0.0.0) Controller: ClinicalTrialsResultsCtrl should initialize without any trial search results FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/app/clinical-trials/results/clinical-trials-results.controller.spec.js:34:9
TypeError: undefined is not an object (evaluating 'ctrl.trials') in /usr/src/app/app/scripts/app/clinical-trials/results/clinical-trials-results.controller.spec.js (line 58)
/usr/src/app/app/scripts/app/clinical-trials/results/clinical-trials-results.controller.spec.js:58:14
.
.
.
.
.

/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
TypeError: undefined is not an object (evaluating 'MatchesService.setFilterStatus') in /usr/src/app/app/scripts/components/matches/matches.service.spec.js (line 262)
/usr/src/app/app/scripts/components/matches/matches.service.spec.js:262:18

PhantomJS 2.1.1 (Linux 0.0.0) Matches Service Unit Tests Public methods should be able to get the match counts FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
Error: : could not find an object to spy upon for countMatches()
Usage: spyOn(, ) in /usr/src/app/node_modules/jasmine-core/lib/jasmine-core/jasmine.js (line 4927)
/usr/src/app/app/scripts/components/matches/matches.service.spec.js:283:9
PhantomJS 2.1.1 (Linux 0.0.0) Matches Service Unit Tests Public methods should be able to generate the matchmap FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
TypeError: undefined is not an object (evaluating 'MatchesMocks.mockMatchesResponse') in /usr/src/app/app/scripts/components/matches/matches.service.spec.js (line 289)
/usr/src/app/app/scripts/components/matches/matches.service.spec.js:289:34
PhantomJS 2.1.1 (Linux 0.0.0) Matches Service Unit Tests Public methods should be able to generate reduced count map FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
TypeError: undefined is not an object (evaluating 'MatchesService.setTableFilters') in /usr/src/app/app/scripts/components/matches/matches.service.spec.js (line 319)
/usr/src/app/app/scripts/components/matches/matches.service.spec.js:319:18
PhantomJS 2.1.1 (Linux 0.0.0) Matches Service Unit Tests Public methods should return false when trying to updateStatus without any selected matches FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
TypeError: undefined is not an object (evaluating 'MatchesService.updateStatus') in /usr/src/app/app/scripts/components/matches/matches.service.spec.js (line 334)
/usr/src/app/app/scripts/components/matches/matches.service.spec.js:334:28
PhantomJS 2.1.1 (Linux 0.0.0) Matches Service Unit Tests Public methods should be able to update the status of several matches FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
Error: : could not find an object to spy upon for _promiseToUpdateMatch()
Usage: spyOn(, ) in /usr/src/app/node_modules/jasmine-core/lib/jasmine-core/jasmine.js (line 4927)
/usr/src/app/app/scripts/components/matches/matches.service.spec.js:339:9
PhantomJS 2.1.1 (Linux 0.0.0) Timeout Controller should listen to IdleStart event FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/components/session/timeout.controller.spec.js:26:9
Error: : could not find an object to spy upon for show()
Usage: spyOn(, ) in /usr/src/app/node_modules/jasmine-core/lib/jasmine-core/jasmine.js (line 4927)
/usr/src/app/app/scripts/components/session/timeout.controller.spec.js:37:8
PhantomJS 2.1.1 (Linux 0.0.0) Timeout Controller should listen to IdleTimeout event FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/components/session/timeout.controller.spec.js:26:9
Error: : could not find an object to spy upon for hide()
Usage: spyOn(, ) in /usr/src/app/node_modules/jasmine-core/lib/jasmine-core/jasmine.js (line 4927)
/usr/src/app/app/scripts/components/session/timeout.controller.spec.js:50:8
PhantomJS 2.1.1 (Linux 0.0.0) Timeout Controller should listen to the IdleEnd event FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/components/session/timeout.controller.spec.js:26:9
Error: : could not find an object to spy upon for hide()
Usage: spyOn(, ) in /usr/src/app/node_modules/jasmine-core/lib/jasmine-core/jasmine.js (line 4927)
/usr/src/app/app/scripts/components/session/timeout.controller.spec.js:59:8
PhantomJS 2.1.1 (Linux 0.0.0) Trial Match Service Unit Tests should able to fetch trial matches by MRN, vital status, trial accrual status and sample id FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
Error: : could not find an object to spy upon for query()
Usage: spyOn(, ) in /usr/src/app/node_modules/jasmine-core/lib/jasmine-core/jasmine.js (line 4927)
/usr/src/app/app/scripts/components/trial-match/trial-match.service.spec.js:63:8
PhantomJS 2.1.1 (Linux 0.0.0) Trial Match Service Unit Tests should able to fetch trial matches by MRN, vital status and trial accrual status FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
Error: : could not find an object to spy upon for query()
Usage: spyOn(, ) in /usr/src/app/node_modules/jasmine-core/lib/jasmine-core/jasmine.js (line 4927)
/usr/src/app/app/scripts/components/trial-match/trial-match.service.spec.js:80:8
PhantomJS 2.1.1 (Linux 0.0.0) Trial Match Service Unit Tests should able to fetch trial matches by MRN and vital status FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
Error: : could not find an object to spy upon for query()
Usage: spyOn(, ) in /usr/src/app/node_modules/jasmine-core/lib/jasmine-core/jasmine.js (line 4927)
/usr/src/app/app/scripts/components/trial-match/trial-match.service.spec.js:96:8
PhantomJS 2.1.1 (Linux 0.0.0) Trial Match Service Unit Tests should able to fetch trial matches by MRN FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
Error: : could not find an object to spy upon for query()
Usage: spyOn(, ) in /usr/src/app/node_modules/jasmine-core/lib/jasmine-core/jasmine.js (line 4927)
/usr/src/app/app/scripts/components/trial-match/trial-match.service.spec.js:111:8
PhantomJS 2.1.1 (Linux 0.0.0) Various utilities function and filters should be able to capitalize a string FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/components/utilities/utilities.filters.spec.js:24:9
TypeError: undefined is not a function (evaluating 'filter('capitalize')') in /usr/src/app/app/scripts/components/utilities/utilities.filters.spec.js (line 31)
/usr/src/app/app/scripts/components/utilities/utilities.filters.spec.js:31:32
PhantomJS 2.1.1 (Linux 0.0.0) Various utilities function and filters should return an empty string when input is null FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/components/utilities/utilities.filters.spec.js:24:9
TypeError: undefined is not a function (evaluating 'filter('capitalize')') in /usr/src/app/app/scripts/components/utilities/utilities.filters.spec.js (line 39)
/usr/src/app/app/scripts/components/utilities/utilities.filters.spec.js:39:32
PhantomJS 2.1.1 (Linux 0.0.0) Various utilities function and filters should be able to parse a date FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/components/utilities/utilities.filters.spec.js:24:9
TypeError: undefined is not a function (evaluating 'filter('parsedate')') in /usr/src/app/app/scripts/components/utilities/utilities.filters.spec.js (line 46)
/usr/src/app/app/scripts/components/utilities/utilities.filters.spec.js:46:31
PhantomJS 2.1.1 (Linux 0.0.0) Various utilities function and filters should return an empty string when parsing a null date FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/components/utilities/utilities.filters.spec.js:24:9
TypeError: undefined is not a function (evaluating 'filter('parsedate')') in /usr/src/app/app/scripts/components/utilities/utilities.filters.spec.js (line 53)
/usr/src/app/app/scripts/components/utilities/utilities.filters.spec.js:53:31
PhantomJS 2.1.1 (Linux 0.0.0) Various utilities function and filters should be able to format an underscore formatted string FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/components/utilities/utilities.filters.spec.js:24:9
TypeError: undefined is not a function (evaluating 'filter('formatUnderscoreString')') in /usr/src/app/app/scripts/components/utilities/utilities.filters.spec.js (line 60)
/usr/src/app/app/scripts/components/utilities/utilities.filters.spec.js:60:24
PhantomJS 2.1.1 (Linux 0.0.0) Various utilities function and filters should return an empty string when formatting null underscore formatted string FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/components/utilities/utilities.filters.spec.js:24:9
TypeError: undefined is not a function (evaluating 'filter('formatUnderscoreString')') in /usr/src/app/app/scripts/components/utilities/utilities.filters.spec.js (line 67)
/usr/src/app/app/scripts/components/utilities/utilities.filters.spec.js:67:24
PhantomJS 2.1.1 (Linux 0.0.0) Various utilities function and filters should be able to transform a negating field FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/components/utilities/utilities.filters.spec.js:24:9
TypeError: undefined is not a function (evaluating 'filter('transformNegation')') in /usr/src/app/app/scripts/components/utilities/utilities.filters.spec.js (line 74)
/usr/src/app/app/scripts/components/utilities/utilities.filters.spec.js:74:33
PhantomJS 2.1.1 (Linux 0.0.0) Various utilities function and filters should return an empty string when formatting null negating field FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/components/utilities/utilities.filters.spec.js:24:9
TypeError: undefined is not a function (evaluating 'filter('transformNegation')') in /usr/src/app/app/scripts/components/utilities/utilities.filters.spec.js (line 81)
/usr/src/app/app/scripts/components/utilities/utilities.filters.spec.js:81:33
PhantomJS 2.1.1 (Linux 0.0.0) Various utilities function and filters should return the normal string when value is non negating FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/components/utilities/utilities.filters.spec.js:24:9
TypeError: undefined is not a function (evaluating 'filter('transformNegation')') in /usr/src/app/app/scripts/components/utilities/utilities.filters.spec.js (line 88)
/usr/src/app/app/scripts/components/utilities/utilities.filters.spec.js:88:33
PhantomJS 2.1.1 (Linux 0.0.0) Various utilities function and filters should be able to parse and transform comments FAILED
/usr/src/app/bower_components/angular/angular.js:4588:53
forEach@/usr/src/app/bower_components/angular/angular.js:322:24
loadModules@/usr/src/app/bower_components/angular/angular.js:4548:12
createInjector@/usr/src/app/bower_components/angular/angular.js:4470:30
workFn@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2954:60
inject@/usr/src/app/bower_components/angular-mocks/angular-mocks.js:2934:46
/usr/src/app/app/scripts/components/utilities/utilities.filters.spec.js:24:9
TypeError: undefined is not a function (evaluating 'filter('parsecomments')') in /usr/src/app/app/scripts/components/utilities/utilities.filters.spec.js (line 95)
/usr/src/app/app/scripts/components/utilities/utilities.filters.spec.js:95:29
PhantomJS 2.1.1 (Linux 0.0.0): Executed 325 of 325 (325 FAILED) ERROR (2.402 secs / 0 secs)
[16:14:42] 'test' errored after 6.99 s
[16:14:42] Error: Failed 1 tests.
at /usr/src/app/gulp/unit-tests.js:54:20
at removeAllListeners (/usr/src/app/node_modules/karma/lib/server.js:336:7)
at Server. (/usr/src/app/node_modules/karma/lib/server.js:347:9)
at Object.onceWrapper (events.js:293:19)
at emitNone (events.js:91:20)
at Server.emit (events.js:188:7)
at emitCloseNT (net.js:1577:8)
at _combinedTickCallback (internal/process/next_tick.js:77:11)
at process._tickCallback (internal/process/next_tick.js:104:9)
The command '/bin/sh -c gulp test' returned a non-zero code: 1

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ethansiegl avatar ethansiegl commented on September 4, 2024

what version of node/npm are you using? on my machine I have node 9.10.1 and npm 5.6.0

also from the logs you posted it looks like all the tests are failing. just as a test, if you comment out line 22 in the dockerfile RUN gulp test what happens?

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cegg avatar cegg commented on September 4, 2024

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cegg avatar cegg commented on September 4, 2024

I commented out line 22 in the dockerfile RUN gulp test
The same error about Abort Trap:

matchminer-ui$ gulp test
gulp[50350]: ../src/node_contextify.cc:627:static void node::contextify::ContextifyScript::New(const FunctionCallbackInfo<v8::Value> &): Assertion `args[1]->IsString()' failed.
 1: 0x100039393 node::Abort() [/usr/local/bin/node]
 2: 0x10003849d node::MakeCallback(v8::Isolate*, v8::Local<v8::Object>, char const*, int, v8::Local<v8::Value>*, node::async_context) [/usr/local/bin/node]
 3: 0x10005e5fc node::contextify::ContextifyScript::New(v8::FunctionCallbackInfo<v8::Value> const&) [/usr/local/bin/node]
 4: 0x1001fd3e7 v8::internal::FunctionCallbackArguments::Call(v8::internal::CallHandlerInfo*) [/usr/local/bin/node]
 5: 0x1001fc704 v8::internal::MaybeHandle<v8::internal::Object> v8::internal::(anonymous namespace)::HandleApiCallHelper<true>(v8::internal::Isolate*, v8::internal::Handle<v8::internal::HeapObject>, v8::internal::Handle<v8::internal::HeapObject>, v8::internal::Handle<v8::internal::FunctionTemplateInfo>, v8::internal::Handle<v8::internal::Object>, v8::internal::BuiltinArguments) [/usr/local/bin/node]
 6: 0x1001fc141 v8::internal::Builtin_Impl_HandleApiCall(v8::internal::BuiltinArguments, v8::internal::Isolate*) [/usr/local/bin/node]
 7: 0x27913c35c01d
 8: 0x27913c30d145
 9: 0x27913c38b900
10: 0x27913c3118b5
11: 0x27913c3118b5
Abort trap: 6

Basically, there is the same failure fromgulp whatever in conda env, in bash and during docker build in two different Mac OS versions - what does this point at?

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ethansiegl avatar ethansiegl commented on September 4, 2024

Ah, I meant after you comment out RUN gulp test and then run docker build . is there any difference? Should have been clearer..

As far as gulp goes, I'm not entirely sure why your version is so unhappy. When I run which gulp I get this: /Users/ethansiegel/.nvm/versions/node/v9.10.1/bin/gulp and my version of gulp is also 3.9.1. Is there anything different on your end?

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cegg avatar cegg commented on September 4, 2024

With RUN gulp test commented out docker build succeeds.

npm WARN [email protected] requires a peer of grunt@~0.4.0 but none was installed.
npm info ok
Removing intermediate container c57342759c75
---> b630bd211343
Step 7/10 : COPY . /data
---> 788cb5ec55b9
Step 8/10 : RUN bower install --config.interactive=false --allow-root
---> Running in 6fb181e10785
Removing intermediate container 6fb181e10785
---> f5b7e1dd43d8
Step 9/10 : WORKDIR /data
---> Running in 30f2aa7f8bbd
Removing intermediate container 30f2aa7f8bbd
---> a6f67c1d80a4
Step 10/10 : COPY dist /var/www/apache-flask/api/static
---> 8e068616d391
Successfully built 8e068616d391

However, docker container ls and docker ps do not find any containers.

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cegg avatar cegg commented on September 4, 2024

As of which gulp, it gives this: ```
$ which gulp
/usr/local/bin/gulp

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ethansiegl avatar ethansiegl commented on September 4, 2024

I see. to start the container you need to run docker start [container_name]. You can list the docker images with docker image ls to find the container you just built with the build command. I think you will still run into some issues with the key and certificate though, since those need to be configured in order to communicate with the API properly

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cegg avatar cegg commented on September 4, 2024

Tried docker build . on El Capitan today.

It ends with:

Removing intermediate container cf6fa35c8dc8
 ---> 1e9f955b7e3e
Step 9/10 : WORKDIR /data
 ---> Running in be4fd4daf202
Removing intermediate container be4fd4daf202
 ---> 0427c21a80f7
Step 10/10 : COPY dist /var/www/apache-flask/api/static
 ---> 08c5f9ef619b
Successfully built 08c5f9ef619b

Then I check docker container ls
Got back empty list:
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES

Just for curiosity checked aforementioned directory (STEP 10):

$ ls /var/www/apache-flask/api/static
ls: /var/www/apache-flask/api/static: No such file or directory

So what is the way to access the newly build container?

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cegg avatar cegg commented on September 4, 2024

Looks like I got image successfully build (with RUN gulp test commented out):

$ docker image ls
REPOSITORY                      TAG                 IMAGE ID            CREATED             SIZE
matchminer-ui                   latest              08c5f9ef619b        23 hours ago        2.12GB

But an atempt to start the container results in this error (both by REPOSITORY and IMAGE ID):

$ docker run 08c5f9ef619b
npm info it worked if it ends with ok
npm info using [email protected]
npm info using [email protected]
npm ERR! Linux 4.9.93-linuxkit-aufs
npm ERR! argv "/usr/local/bin/node" "/usr/local/bin/npm" "start"
npm ERR! node v7.10.1
npm ERR! npm  v4.2.0

npm ERR! missing script: start
npm ERR!
npm ERR! If you need help, you may report this error at:
npm ERR!     <https://github.com/npm/npm/issues>

npm ERR! Please include the following file with any support request:
npm ERR!     /root/.npm/_logs/2018-10-18T08_03_36_934Z-debug.log

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ethansiegl avatar ethansiegl commented on September 4, 2024

alright glad the container is up! So I think the reason the container is not starting is because you are trying to run npm run start or something like that, but the application is usually started with grunt serve. If you swap out the npm command from the grunt, can you let me know what happens?

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cegg avatar cegg commented on September 4, 2024

Sorry I am lost. The container is not up. Only the image is created. I did not get the comment about npm run start and grunt serve . To get that error, I ran $ docker run 08c5f9ef619b (using the id I got from $docker image ls). Could you explain please the connection, I never used npm / node before, it's all new stuff for me.

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ethansiegl avatar ethansiegl commented on September 4, 2024

ah I see. sorry about that. so there are a few things going on let me try to explain as best I can.

Earlier I was talking about adding a CMD command to the docker file to execute once the container is started. To do that you can go to the dockerfile and add CMD ["grunt", "serve"] at the very end. So then once you rundocker run [image_id], the image will start and (hopefully) start up the UI.

If it is not crucial to dockerize the UI at this time, I would suggest trying to get the app up and running with the API and db outside of containers first, and then coming back to containerize them afterwards since that will probably be easier

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cegg avatar cegg commented on September 4, 2024

Thanks. OK, I tried adding CMD ["grunt", "serve"] to the Dockerfile. Before running another docker build, I install grunt globally and locally in my project (below, I hope it's the right way to do it).
brew install grunt
npm install -g grunt-cli
npm install grunt --save-dev

After docker build, when I run docker run <imageid> I get this:

$ docker run 059ddd317ad4
docker: Error response from daemon: OCI runtime create failed: container_linux.go:348: starting container process caused "exec: \"grunt\": executable file not found in $PATH": unknown.

Adding grunt's full path to Dockerfile CMD line ( CMD ["/usr/local/bin/grunt", "serve"] ) and doing another docker build / docker run does not change anything, just the full path is now listed in the error. I suspect it wants grunt or some part of it is not getting installed inside the docker container image.

As of not dockerized way - when I run gulp build, I get that Abort trap 6 th started this thread.

$ gulp --env production build
gulp[7025]: ../src/node_contextify.cc:628:static void node::contextify::ContextifyScript::New(const FunctionCallbackInfo<v8::Value> &): Assertion `args[1]->IsString()' failed.
 1: 0x10003ab5a node::Abort() [/usr/local/bin/node]
 2: 0x100039bc9 node::AddEnvironmentCleanupHook(v8::Isolate*, void (*)(void*), void*) [/usr/local/bin/node]
 3: 0x10005eb02 node::contextify::ContextifyScript::New(v8::FunctionCallbackInfo<v8::Value> const&) [/usr/local/bin/node]
 4: 0x1001f1089 v8::internal::FunctionCallbackArguments::Call(v8::internal::CallHandlerInfo*) [/usr/local/bin/node]
 5: 0x1001f0324 v8::internal::MaybeHandle<v8::internal::Object> v8::internal::(anonymous namespace)::HandleApiCallHelper<true>(v8::internal::Isolate*, v8::internal::Handle<v8::internal::HeapObject>, v8::internal::Handle<v8::internal::HeapObject>, v8::internal::Handle<v8::internal::FunctionTemplateInfo>, v8::internal::Handle<v8::internal::Object>, v8::internal::BuiltinArguments) [/usr/local/bin/node]
 6: 0x1001efd60 v8::internal::Builtin_Impl_HandleApiCall(v8::internal::BuiltinArguments, v8::internal::Isolate*) [/usr/local/bin/node]
 7: 0x19630975be3d
Abort trap: 6

Running $ gulp serve from my project directory gives this:

$ grunt serve
A valid Gruntfile could not be found. Please see the getting started guide for
more information on how to configure grunt: http://gruntjs.com/getting-started

I wonder if all these problems happen to me because I am on MAc or maybe because I am on specific Mac OS (El Capitan)? Are you on Ubuntu ?

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cegg avatar cegg commented on September 4, 2024

Hi Ethan,

Today I tried to docker build again but on Mac OSX 10.13.6 ( High Sierra ) and the behaviour is different.
My $ docker build matchminer-ui . finished successfully.
so I start the container:
$ docker run -it matchminer-ui bash
then I tried $ gulp serve - got this error:
(node:7) UnhandledPromiseRejectionWarning: Unhandled promise rejection (rejection id: 1): Error: Error: angular is not installed. Try running bower install``.
So I ran this:
$ bower install --allow-root (it won't run without --allow-root)
Got one warning, the rest went OK:

Resort to using angular#1.5.5 which resolved to angular#1.5.5
Code incompatibilities may occur.

Now:
ran $ gulp test

Again, all good! (but #RUN gulp test in Dockerfile is commented out)
No, I try $ gulp serve again - it stops at the absence of something called certificates/matchminder.key:

$ gulp serve
[13:09:22] Using gulpfile /data/gulpfile.js
[13:09:22] Starting 'config'...
[13:09:22] Starting 'load-templates'...
[13:09:22] Starting 'scripts'...
[13:09:22] Starting 'styles'...
[13:09:23] Finished 'config' after 818 ms
[13:09:23] Finished 'load-templates' after 804 ms
[13:09:23] gulp-inject 34 files into matchminer.less.
[13:09:24] Finished 'styles' after 1.79 s
[13:09:26] all files 543.3 kB
[13:09:26] Finished 'scripts' after 3.36 s
[13:09:26] Starting 'inject'...
[13:09:26] gulp-inject 1 files into index.html.
[13:09:26] gulp-inject 92 files into index.html.
[13:09:26] Finished 'inject' after 443 ms
[13:09:26] Starting 'watch'...
[13:09:26] Finished 'watch' after 141 ms
[13:09:26] Starting 'serve'...
[13:09:26] 'serve' errored after 879 μs
[13:09:26] Error: ENOENT: no such file or directory, open '../certificates/matchminer.key'
    at Object.fs.openSync (fs.js:584:18)
    at Object.fs.readFileSync (fs.js:491:33)
    at browserSyncInit (/data/gulp/server.js:52:12)
    at Gulp.<anonymous> (/data/gulp/server.js\:100\:2)
    at module.exports (/data/node_modules/orchestrator/lib/runTask.js:34:7)
    at Gulp.Orchestrator._runTask (/data/node_modules/orchestrator/index.js:273:3)
    at Gulp.Orchestrator._runStep (/data/node_modules/orchestrator/index.js:214:10)
    at /data/node_modules/orchestrator/index.js:279:18
    at finish (/data/node_modules/orchestrator/lib/runTask.js:21:8)
    at module.exports (/data/node_modules/orchestrator/lib/runTask.js:60:3)
    at Gulp.Orchestrator._runTask (/data/node_modules/orchestrator/index.js:273:3)
    at Gulp.Orchestrator._runStep (/data/node_modules/orchestrator/index.js:214:10)
    at /data/node_modules/orchestrator/index.js:279:18
    at finish (/data/node_modules/orchestrator/lib/runTask.js:21:8)
    at /data/node_modules/orchestrator/lib/runTask.js:52:4
    at f (/data/node_modules/end-of-stream/node_modules/once/once.js:17:25)

It does not go back to the command line prompt, just hangs there.
And the site is not available at http://localhost:8001, and there's nothing on ports 5555 or 9200 either.

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cegg avatar cegg commented on September 4, 2024

Some update: the error about "Abort trap 6" goes away if I run this : $ npm i natives Just found it in some forum, no idea how it fixes the problem. Maybe this can be closed. I am going to open a new issue for the next failure in a minute. Thanks for your help!

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