Fix file processor running on files that are on unfinished upload runs. #6193
Triggered via pull request
December 13, 2023 23:43
JeffreyThiessen
Status
Success
Total duration
45m 47s
Artifacts
–
ci-test.yml
on: pull_request
docs-build
5m 25s
Matrix: gradle-build
Annotations
15 errors and 16 warnings
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SequencingRunServiceImplIT.testDeleteFilesOnFilesystem():
src/test/java/ca/corefacility/bioinformatics/irida/service/impl/integration/SequencingRunServiceImplIT.java#L293
org.opentest4j.AssertionFailedError: Sequence file should exist on the file system ==> expected: <true> but was: <false>
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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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AnalysisExecutionServiceGalaxyIT.testTransferAnalysisResultsFailTestAnalysisMissingOutput():
src/test/java/ca/corefacility/bioinformatics/irida/service/analysis/execution/galaxy/impl/integration/AnalysisExecutionServiceGalaxyIT.java#L1335
java.util.concurrent.ExecutionException: java.lang.IllegalStateException: path 20/1/testReference18317515262451817074.fasta does not exist
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AnalysisExecutionScheduledTaskImplIT.testFullAnalysisRunSuccessWithSampleUpdates():
src/test/java/ca/corefacility/bioinformatics/irida/service/impl/integration/AnalysisExecutionScheduledTaskImplIT.java#L172
java.util.concurrent.ExecutionException: java.lang.IllegalStateException: path 40/1/testReference17328897594948858242.fasta does not exist
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CartPageIT.testCartPageAsAdmin():
src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/CartPageIT.java#L241
org.opentest4j.AssertionFailedError: The add cart to sample button should be displayed ==> expected: <true> but was: <false>
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LoginPageLdapNoServerIT.testLoginNoLdapServer():
src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/LoginPageLdapNoServerIT.java#L41
org.opentest4j.AssertionFailedError: expected: <http://127.0.0.1:44127/irida/login?ldap-error=6> but was: <http://127.0.0.1:44127/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-az1394-568', ip: '10.1.0.19', os.name: 'Linux', os.arch: 'amd64', os.version: '5.15.0-1052-azure', java.version: '11.0.21'
Driver info: org.openqa.selenium.chrome.ChromeDriver
Capabilities {acceptInsecureCerts: false, browserName: chrome, browserVersion: 119.0.6045.199, chrome: {chromedriverVersion: 119.0.6045.105 (38c72552c5e..., userDataDir: /tmp/.org.chromium.Chromium...}, fedcm:accounts: true, goog:chromeOptions: {debuggerAddress: localhost:42393}, javascriptEnabled: true, networkConnectionEnabled: false, pageLoadStrategy: normal, platform: LINUX, platformName: LINUX, proxy: Proxy(), se:cdp: ws://localhost:42393/devtoo..., se:cdpVersion: 119.0.6045.199, 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: 372c7a54be5e17e4ac3b67477588ea4f
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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-az1394-568', ip: '10.1.0.19', os.name: 'Linux', os.arch: 'amd64', os.version: '5.15.0-1052-azure', java.version: '11.0.21'
Driver info: org.openqa.selenium.chrome.ChromeDriver
Capabilities {acceptInsecureCerts: false, browserName: chrome, browserVersion: 119.0.6045.199, chrome: {chromedriverVersion: 119.0.6045.105 (38c72552c5e..., userDataDir: /tmp/.org.chromium.Chromium...}, fedcm:accounts: true, goog:chromeOptions: {debuggerAddress: localhost:42393}, javascriptEnabled: true, networkConnectionEnabled: false, pageLoadStrategy: normal, platform: LINUX, platformName: LINUX, proxy: Proxy(), se:cdp: ws://localhost:42393/devtoo..., se:cdpVersion: 119.0.6045.199, 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: 372c7a54be5e17e4ac3b67477588ea4f
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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-az1394-568', ip: '10.1.0.19', os.name: 'Linux', os.arch: 'amd64', os.version: '5.15.0-1052-azure', java.version: '11.0.21'
Driver info: org.openqa.selenium.chrome.ChromeDriver
Capabilities {acceptInsecureCerts: false, browserName: chrome, browserVersion: 119.0.6045.199, chrome: {chromedriverVersion: 119.0.6045.105 (38c72552c5e..., userDataDir: /tmp/.org.chromium.Chromium...}, fedcm:accounts: true, goog:chromeOptions: {debuggerAddress: localhost:42393}, javascriptEnabled: true, networkConnectionEnabled: false, pageLoadStrategy: normal, platform: LINUX, platformName: LINUX, proxy: Proxy(), se:cdp: ws://localhost:42393/devtoo..., se:cdpVersion: 119.0.6045.199, 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: 372c7a54be5e17e4ac3b67477588ea4f
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AnalysisDetailsPageIT.testSamplesPage():
src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/analysis/AnalysisDetailsPageIT.java#L235
org.openqa.selenium.StaleElementReferenceException: stale element reference: stale element not found
(Session info: headless chrome=119.0.6045.199)
For documentation on this error, please visit: https://selenium.dev/exceptions/#stale_element_reference
Build info: version: '4.1.4', revision: '535d840ee2'
System info: host: 'fv-az1394-568', ip: '10.1.0.19', os.name: 'Linux', os.arch: 'amd64', os.version: '5.15.0-1052-azure', java.version: '11.0.21'
Driver info: org.openqa.selenium.chrome.ChromeDriver
Command: [372c7a54be5e17e4ac3b67477588ea4f, getElementAttribute {id=DB78E19D5CF7DF49ABA7A027E7463E29_element_2162, name=data-error}]
Capabilities {acceptInsecureCerts: false, browserName: chrome, browserVersion: 119.0.6045.199, chrome: {chromedriverVersion: 119.0.6045.105 (38c72552c5e..., userDataDir: /tmp/.org.chromium.Chromium...}, fedcm:accounts: true, goog:chromeOptions: {debuggerAddress: localhost:42393}, javascriptEnabled: true, networkConnectionEnabled: false, pageLoadStrategy: normal, platform: LINUX, platformName: LINUX, proxy: Proxy(), se:cdp: ws://localhost:42393/devtoo..., se:cdpVersion: 119.0.6045.199, 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}
Element: [[ChromeDriver: chrome on LINUX (372c7a54be5e17e4ac3b67477588ea4f)] -> tag name: main]
Session ID: 372c7a54be5e17e4ac3b67477588ea4f
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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-az1394-568', ip: '10.1.0.19', os.name: 'Linux', os.arch: 'amd64', os.version: '5.15.0-1052-azure', java.version: '11.0.21'
Driver info: org.openqa.selenium.chrome.ChromeDriver
Capabilities {acceptInsecureCerts: false, browserName: chrome, browserVersion: 119.0.6045.199, chrome: {chromedriverVersion: 119.0.6045.105 (38c72552c5e..., userDataDir: /tmp/.org.chromium.Chromium...}, fedcm:accounts: true, goog:chromeOptions: {debuggerAddress: localhost:42393}, javascriptEnabled: true, networkConnectionEnabled: false, pageLoadStrategy: normal, platform: LINUX, platformName: LINUX, proxy: Proxy(), se:cdp: ws://localhost:42393/devtoo..., se:cdpVersion: 119.0.6045.199, 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: 372c7a54be5e17e4ac3b67477588ea4f
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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-az1394-568', ip: '10.1.0.19', os.name: 'Linux', os.arch: 'amd64', os.version: '5.15.0-1052-azure', java.version: '11.0.21'
Driver info: org.openqa.selenium.chrome.ChromeDriver
Capabilities {acceptInsecureCerts: false, browserName: chrome, browserVersion: 119.0.6045.199, chrome: {chromedriverVersion: 119.0.6045.105 (38c72552c5e..., userDataDir: /tmp/.org.chromium.Chromium...}, fedcm:accounts: true, goog:chromeOptions: {debuggerAddress: localhost:42393}, javascriptEnabled: true, networkConnectionEnabled: false, pageLoadStrategy: normal, platform: LINUX, platformName: LINUX, proxy: Proxy(), se:cdp: ws://localhost:42393/devtoo..., se:cdpVersion: 119.0.6045.199, 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: 372c7a54be5e17e4ac3b67477588ea4f
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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 (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 (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 (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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