Merge pull request #1506 from phac-nml/fix_early_file_processor #6200
deepsidhu85ci-test.yml
on: push
docs-build
5m 7s
Matrix: gradle-build
Annotations
18 errors and 16 warnings
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SequencingRunServiceImplIT.testAddSequenceFileToMiseqRunAsSequencer():
src/test/java/ca/corefacility/bioinformatics/irida/service/impl/integration/SequencingRunServiceImplIT.java#L65
org.opentest4j.AssertionFailedError: Saved miseq run should have seqence file ==> expected: <true> but was: <false>
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SequencingRunServiceImplIT.testAddSequenceFileToMiseqRunAsAdmin():
src/test/java/ca/corefacility/bioinformatics/irida/service/impl/integration/SequencingRunServiceImplIT.java#L71
org.opentest4j.AssertionFailedError: Saved miseq run should have seqence file ==> expected: <true> but was: <false>
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gradle-build (galaxy_testing)
Singleton bean creation not allowed while singletons of this factory are in destruction (Do not request a bean from a BeanFactory in a destroy method implementation!)
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gradle-build (galaxy_testing)
Singleton bean creation not allowed while singletons of this factory are in destruction (Do not request a bean from a BeanFactory in a destroy method implementation!)
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AnalysisExecutionServiceGalaxyIT.testTransferAnalysisResultsFailInvalidRemoteAnalysisId():
src/test/java/ca/corefacility/bioinformatics/irida/service/analysis/execution/galaxy/impl/integration/AnalysisExecutionServiceGalaxyIT.java#L1414
java.util.concurrent.ExecutionException: java.lang.IllegalStateException: path 19/1/testReference11858897988626250026.fasta does not exist
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AnalysisExecutionServiceGalaxyIT.testTransferAnalysisResultsSuccessPhylogenomics():
src/test/java/ca/corefacility/bioinformatics/irida/service/analysis/execution/galaxy/impl/integration/AnalysisExecutionServiceGalaxyIT.java#L505
java.util.concurrent.ExecutionException: java.lang.IllegalStateException: path 23/1/testReference683397383522895101.fasta does not exist
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AnalysisExecutionServiceGalaxyIT.testCleanupCompletedAnalysisFailGalaxy():
src/test/java/ca/corefacility/bioinformatics/irida/service/analysis/execution/galaxy/impl/integration/AnalysisExecutionServiceGalaxyIT.java#L1558
java.util.concurrent.ExecutionException: java.lang.IllegalStateException: path 25/1/testReference3265569884956618730.fasta does not exist
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AnalysisExecutionScheduledTaskImplIT.testFullAnalysisRunCleanupFailInvalidRemoteAnalysisId():
src/test/java/ca/corefacility/bioinformatics/irida/service/impl/integration/AnalysisExecutionScheduledTaskImplIT.java#L348
java.util.concurrent.ExecutionException: java.lang.IllegalStateException: path 29/1/testReference14094341890804531665.fasta does not exist
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LoginPageLdapNoServerIT.testLoginNoLdapServer():
src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/LoginPageLdapNoServerIT.java#L41
org.opentest4j.AssertionFailedError: expected: <http://127.0.0.1:45341/irida/login?ldap-error=6> but was: <http://127.0.0.1:45341/irida/login?error=true>
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AnalysisDetailsPageIT.testUnknownPipelineOutput():
src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/analysis/AnalysisDetailsPageIT.java#L450
org.opentest4j.AssertionFailedError: There should be one output file ==> expected: <1> but was: <0>
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AnalysisDetailsPageIT.testOutputFiles():
src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/analysis/AnalysisDetailsPageIT.java#L139
org.openqa.selenium.TimeoutException: Expected condition failed: waiting for visibility of element located by By.cssSelector: span[title='Output File Preview'] (tried for 10 second(s) with 500 milliseconds interval)
Build info: version: '4.1.4', revision: '535d840ee2'
System info: host: 'fv-az656-322', ip: '10.1.0.4', os.name: 'Linux', os.arch: 'amd64', os.version: '5.15.0-1053-azure', java.version: '11.0.21'
Driver info: org.openqa.selenium.chrome.ChromeDriver
Capabilities {acceptInsecureCerts: false, browserName: chrome-headless-shell, browserVersion: 120.0.6099.71, chrome: {chromedriverVersion: 120.0.6099.71 (9729082fe617..., userDataDir: /tmp/.org.chromium.Chromium...}, fedcm:accounts: true, goog:chromeOptions: {debuggerAddress: localhost:46511}, javascriptEnabled: true, networkConnectionEnabled: false, pageLoadStrategy: normal, platform: LINUX, platformName: LINUX, proxy: Proxy(), se:cdp: ws://localhost:46511/devtoo..., se:cdpVersion: 120.0.6099.71, setWindowRect: true, strictFileInteractability: false, timeouts: {implicit: 0, pageLoad: 300000, script: 30000}, unhandledPromptBehavior: dismiss and notify, webauthn:extension:credBlob: true, webauthn:extension:largeBlob: true, webauthn:extension:minPinLength: true, webauthn:extension:prf: true, webauthn:virtualAuthenticators: true}
Session ID: b40af3a75ce0d4ae6dd0d8037fed0bec
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AnalysisDetailsPageIT.testSistrOutput():
src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/analysis/AnalysisDetailsPageIT.java#L285
org.openqa.selenium.TimeoutException: Expected condition failed: waiting for number of elements found by By.className: ant-page-header-heading-title to be "2". Current number: "1" (tried for 2 second(s) with 500 milliseconds interval)
Build info: version: '4.1.4', revision: '535d840ee2'
System info: host: 'fv-az656-322', ip: '10.1.0.4', os.name: 'Linux', os.arch: 'amd64', os.version: '5.15.0-1053-azure', java.version: '11.0.21'
Driver info: org.openqa.selenium.chrome.ChromeDriver
Capabilities {acceptInsecureCerts: false, browserName: chrome-headless-shell, browserVersion: 120.0.6099.71, chrome: {chromedriverVersion: 120.0.6099.71 (9729082fe617..., userDataDir: /tmp/.org.chromium.Chromium...}, fedcm:accounts: true, goog:chromeOptions: {debuggerAddress: localhost:46511}, javascriptEnabled: true, networkConnectionEnabled: false, pageLoadStrategy: normal, platform: LINUX, platformName: LINUX, proxy: Proxy(), se:cdp: ws://localhost:46511/devtoo..., se:cdpVersion: 120.0.6099.71, setWindowRect: true, strictFileInteractability: false, timeouts: {implicit: 0, pageLoad: 300000, script: 30000}, unhandledPromptBehavior: dismiss and notify, webauthn:extension:credBlob: true, webauthn:extension:largeBlob: true, webauthn:extension:minPinLength: true, webauthn:extension:prf: true, webauthn:virtualAuthenticators: true}
Session ID: b40af3a75ce0d4ae6dd0d8037fed0bec
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AnalysisDetailsPageIT.testProvenance():
src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/analysis/AnalysisDetailsPageIT.java#L206
org.openqa.selenium.TimeoutException: Expected condition failed: waiting for visibility of element located by By.cssSelector: span[title='Provenance'] (tried for 10 second(s) with 500 milliseconds interval)
Build info: version: '4.1.4', revision: '535d840ee2'
System info: host: 'fv-az656-322', ip: '10.1.0.4', os.name: 'Linux', os.arch: 'amd64', os.version: '5.15.0-1053-azure', java.version: '11.0.21'
Driver info: org.openqa.selenium.chrome.ChromeDriver
Capabilities {acceptInsecureCerts: false, browserName: chrome-headless-shell, browserVersion: 120.0.6099.71, chrome: {chromedriverVersion: 120.0.6099.71 (9729082fe617..., userDataDir: /tmp/.org.chromium.Chromium...}, fedcm:accounts: true, goog:chromeOptions: {debuggerAddress: localhost:46511}, javascriptEnabled: true, networkConnectionEnabled: false, pageLoadStrategy: normal, platform: LINUX, platformName: LINUX, proxy: Proxy(), se:cdp: ws://localhost:46511/devtoo..., se:cdpVersion: 120.0.6099.71, setWindowRect: true, strictFileInteractability: false, timeouts: {implicit: 0, pageLoad: 300000, script: 30000}, unhandledPromptBehavior: dismiss and notify, webauthn:extension:credBlob: true, webauthn:extension:largeBlob: true, webauthn:extension:minPinLength: true, webauthn:extension:prf: true, webauthn:virtualAuthenticators: true}
Session ID: b40af3a75ce0d4ae6dd0d8037fed0bec
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AnalysisDetailsPageIT.testSamplesPage():
src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/analysis/AnalysisDetailsPageIT.java#L236
org.openqa.selenium.TimeoutException: Expected condition failed: waiting for visibility of element located by By.cssSelector: span[title='Samples'] (tried for 10 second(s) with 500 milliseconds interval)
Build info: version: '4.1.4', revision: '535d840ee2'
System info: host: 'fv-az656-322', ip: '10.1.0.4', os.name: 'Linux', os.arch: 'amd64', os.version: '5.15.0-1053-azure', java.version: '11.0.21'
Driver info: org.openqa.selenium.chrome.ChromeDriver
Capabilities {acceptInsecureCerts: false, browserName: chrome-headless-shell, browserVersion: 120.0.6099.71, chrome: {chromedriverVersion: 120.0.6099.71 (9729082fe617..., userDataDir: /tmp/.org.chromium.Chromium...}, fedcm:accounts: true, goog:chromeOptions: {debuggerAddress: localhost:46511}, javascriptEnabled: true, networkConnectionEnabled: false, pageLoadStrategy: normal, platform: LINUX, platformName: LINUX, proxy: Proxy(), se:cdp: ws://localhost:46511/devtoo..., se:cdpVersion: 120.0.6099.71, setWindowRect: true, strictFileInteractability: false, timeouts: {implicit: 0, pageLoad: 300000, script: 30000}, unhandledPromptBehavior: dismiss and notify, webauthn:extension:credBlob: true, webauthn:extension:largeBlob: true, webauthn:extension:minPinLength: true, webauthn:extension:prf: true, webauthn:virtualAuthenticators: true}
Session ID: b40af3a75ce0d4ae6dd0d8037fed0bec
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AnalysisDetailsPageIT.testPipelineResultsWithoutSpecialTab():
src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/analysis/AnalysisDetailsPageIT.java#L193
org.opentest4j.AssertionFailedError: There should be one output file ==> expected: <1> but was: <0>
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AnalysisDetailsPageIT.testTabRoutingAnalysisCompleted():
src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/analysis/AnalysisDetailsPageIT.java#L316
org.openqa.selenium.TimeoutException: Expected condition failed: waiting for number of elements found by By.className: ant-page-header-heading-title to be "2". Current number: "0" (tried for 2 second(s) with 500 milliseconds interval)
Build info: version: '4.1.4', revision: '535d840ee2'
System info: host: 'fv-az656-322', ip: '10.1.0.4', os.name: 'Linux', os.arch: 'amd64', os.version: '5.15.0-1053-azure', java.version: '11.0.21'
Driver info: org.openqa.selenium.chrome.ChromeDriver
Capabilities {acceptInsecureCerts: false, browserName: chrome-headless-shell, browserVersion: 120.0.6099.71, chrome: {chromedriverVersion: 120.0.6099.71 (9729082fe617..., userDataDir: /tmp/.org.chromium.Chromium...}, fedcm:accounts: true, goog:chromeOptions: {debuggerAddress: localhost:46511}, javascriptEnabled: true, networkConnectionEnabled: false, pageLoadStrategy: normal, platform: LINUX, platformName: LINUX, proxy: Proxy(), se:cdp: ws://localhost:46511/devtoo..., se:cdpVersion: 120.0.6099.71, setWindowRect: true, strictFileInteractability: false, timeouts: {implicit: 0, pageLoad: 300000, script: 30000}, unhandledPromptBehavior: dismiss and notify, webauthn:extension:credBlob: true, webauthn:extension:largeBlob: true, webauthn:extension:minPinLength: true, webauthn:extension:prf: true, webauthn:virtualAuthenticators: true}
Session ID: b40af3a75ce0d4ae6dd0d8037fed0bec
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AnalysisDetailsPageIT.testTreeOutput():
src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/analysis/AnalysisDetailsPageIT.java#L379
org.openqa.selenium.TimeoutException: Expected condition failed: waiting for number of elements found by By.className: ant-page-header-heading-title to be "2". Current number: "0" (tried for 2 second(s) with 500 milliseconds interval)
Build info: version: '4.1.4', revision: '535d840ee2'
System info: host: 'fv-az656-322', ip: '10.1.0.4', os.name: 'Linux', os.arch: 'amd64', os.version: '5.15.0-1053-azure', java.version: '11.0.21'
Driver info: org.openqa.selenium.chrome.ChromeDriver
Capabilities {acceptInsecureCerts: false, browserName: chrome-headless-shell, browserVersion: 120.0.6099.71, chrome: {chromedriverVersion: 120.0.6099.71 (9729082fe617..., userDataDir: /tmp/.org.chromium.Chromium...}, fedcm:accounts: true, goog:chromeOptions: {debuggerAddress: localhost:46511}, javascriptEnabled: true, networkConnectionEnabled: false, pageLoadStrategy: normal, platform: LINUX, platformName: LINUX, proxy: Proxy(), se:cdp: ws://localhost:46511/devtoo..., se:cdpVersion: 120.0.6099.71, setWindowRect: true, strictFileInteractability: false, timeouts: {implicit: 0, pageLoad: 300000, script: 30000}, unhandledPromptBehavior: dismiss and notify, webauthn:extension:credBlob: true, webauthn:extension:largeBlob: true, webauthn:extension:minPinLength: true, webauthn:extension:prf: true, webauthn:virtualAuthenticators: true}
Session ID: b40af3a75ce0d4ae6dd0d8037fed0bec
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AnalysisDetailsPageIT.testAnalysisDetails():
src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/analysis/AnalysisDetailsPageIT.java#L73
org.opentest4j.AssertionFailedError: The correct details are displayed for the analysis ==> expected: <true> but was: <false>
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gradle-build (open_api_testing)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-java@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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gradle-build (open_api_testing)
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
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docs-build
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-ruby@v1, actions/setup-java@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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docs-build
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
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gradle-build (file_system_testing)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-java@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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gradle-build (file_system_testing)
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
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gradle-build (rest_testing)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-java@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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gradle-build (rest_testing)
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
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gradle-build (service_testing)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-java@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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gradle-build (service_testing)
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
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gradle-build (galaxy_testing)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-java@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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gradle-build (galaxy_testing)
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
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gradle-build (galaxy_pipeline_testing)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-java@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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gradle-build (galaxy_pipeline_testing)
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
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gradle-build (ui_testing)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-java@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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gradle-build (ui_testing)
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
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