java.lang.NullPointerException: Cannot invoke "ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC.getOverrepresentedSequences()" because "analysis" is null

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>

AnalysisExecutionServiceGalaxyIT.testTransferAnalysisResultsSuccessPhylogenomicsPairedNoParameters(): src/test/java/ca/corefacility/bioinformatics/irida/service/analysis/execution/galaxy/impl/integration/AnalysisExecutionServiceGalaxyIT.java#L862

java.util.concurrent.ExecutionException: java.lang.IllegalStateException: path 11/1/testReference7769239184825239551.fasta does not exist

AnalysisExecutionServiceGalaxyIT.testTransferAnalysisResultsFailInvalidId(): src/test/java/ca/corefacility/bioinformatics/irida/service/analysis/execution/galaxy/impl/integration/AnalysisExecutionServiceGalaxyIT.java#L1374

java.util.concurrent.ExecutionException: java.lang.IllegalStateException: path 24/1/testReference11914492372003693425.fasta does not exist

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/testReference12620555510122825652.fasta does not exist

AnalysisExecutionScheduledTaskImplIT.testFullAnalysisRunSuccessOneSubmissionOneError(): src/test/java/ca/corefacility/bioinformatics/irida/service/impl/integration/AnalysisExecutionScheduledTaskImplIT.java#L247

java.util.concurrent.ExecutionException: java.lang.IllegalStateException: path 30/1/testReference3659657960953186539.fasta does not exist

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/testReference16086931055096640707.fasta does not exist

LoginPageLdapNoServerIT.testLoginNoLdapServer(): src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/LoginPageLdapNoServerIT.java#L41

org.opentest4j.AssertionFailedError: expected: <http://127.0.0.1:41305/irida/login?ldap-error=6> but was: <http://127.0.0.1:41305/irida/login?error=true>

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>

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-az565-732', ip: '10.1.0.102', os.name: 'Linux', os.arch: 'amd64', os.version: '5.15.0-1078-azure', java.version: '17.0.14' Driver info: org.openqa.selenium.chrome.ChromeDriver Capabilities {acceptInsecureCerts: false, browserName: chrome, browserVersion: 132.0.6834.159, chrome: {chromedriverVersion: 132.0.6834.159 (2d77d3fc445..., userDataDir: /tmp/.org.chromium.Chromium...}, fedcm:accounts: true, goog:chromeOptions: {debuggerAddress: localhost:36571}, javascriptEnabled: true, networkConnectionEnabled: false, pageLoadStrategy: normal, platform: LINUX, platformName: LINUX, proxy: Proxy(), se:cdp: ws://localhost:36571/devtoo..., se:cdpVersion: 132.0.6834.159, 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: 1519eb637eed7d94f01dd41fe7c59246

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-az565-732', ip: '10.1.0.102', os.name: 'Linux', os.arch: 'amd64', os.version: '5.15.0-1078-azure', java.version: '17.0.14' Driver info: org.openqa.selenium.chrome.ChromeDriver Capabilities {acceptInsecureCerts: false, browserName: chrome, browserVersion: 132.0.6834.159, chrome: {chromedriverVersion: 132.0.6834.159 (2d77d3fc445..., userDataDir: /tmp/.org.chromium.Chromium...}, fedcm:accounts: true, goog:chromeOptions: {debuggerAddress: localhost:36571}, javascriptEnabled: true, networkConnectionEnabled: false, pageLoadStrategy: normal, platform: LINUX, platformName: LINUX, proxy: Proxy(), se:cdp: ws://localhost:36571/devtoo..., se:cdpVersion: 132.0.6834.159, 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: 1519eb637eed7d94f01dd41fe7c59246

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-az565-732', ip: '10.1.0.102', os.name: 'Linux', os.arch: 'amd64', os.version: '5.15.0-1078-azure', java.version: '17.0.14' Driver info: org.openqa.selenium.chrome.ChromeDriver Capabilities {acceptInsecureCerts: false, browserName: chrome, browserVersion: 132.0.6834.159, chrome: {chromedriverVersion: 132.0.6834.159 (2d77d3fc445..., userDataDir: /tmp/.org.chromium.Chromium...}, fedcm:accounts: true, goog:chromeOptions: {debuggerAddress: localhost:36571}, javascriptEnabled: true, networkConnectionEnabled: false, pageLoadStrategy: normal, platform: LINUX, platformName: LINUX, proxy: Proxy(), se:cdp: ws://localhost:36571/devtoo..., se:cdpVersion: 132.0.6834.159, 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: 1519eb637eed7d94f01dd41fe7c59246

AnalysisDetailsPageIT.testSamplesPage(): src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/analysis/AnalysisDetailsPageIT.java#L236

org.openqa.selenium.NoSuchElementException: no such element: Unable to locate element: {"method":"css selector","selector":"span[title='Samples']"} (Session info: chrome=132.0.6834.159) For documentation on this error, please visit: https://selenium.dev/exceptions/#no_such_element Build info: version: '4.1.4', revision: '535d840ee2' System info: host: 'fv-az565-732', ip: '10.1.0.102', os.name: 'Linux', os.arch: 'amd64', os.version: '5.15.0-1078-azure', java.version: '17.0.14' Driver info: org.openqa.selenium.chrome.ChromeDriver Command: [1519eb637eed7d94f01dd41fe7c59246, findChildElement {id=f.593675AB9BA511295E01DBEDC2BCB0E8.d.23CC08F0650E3B26C6CFFEA64F5A2371.e.4072, using=css selector, value=span[title='Samples']}] Capabilities {acceptInsecureCerts: false, browserName: chrome, browserVersion: 132.0.6834.159, chrome: {chromedriverVersion: 132.0.6834.159 (2d77d3fc445..., userDataDir: /tmp/.org.chromium.Chromium...}, fedcm:accounts: true, goog:chromeOptions: {debuggerAddress: localhost:36571}, javascriptEnabled: true, networkConnectionEnabled: false, pageLoadStrategy: normal, platform: LINUX, platformName: LINUX, proxy: Proxy(), se:cdp: ws://localhost:36571/devtoo..., se:cdpVersion: 132.0.6834.159, 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: 1519eb637eed7d94f01dd41fe7c59246

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>

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-az565-732', ip: '10.1.0.102', os.name: 'Linux', os.arch: 'amd64', os.version: '5.15.0-1078-azure', java.version: '17.0.14' Driver info: org.openqa.selenium.chrome.ChromeDriver Capabilities {acceptInsecureCerts: false, browserName: chrome, browserVersion: 132.0.6834.159, chrome: {chromedriverVersion: 132.0.6834.159 (2d77d3fc445..., userDataDir: /tmp/.org.chromium.Chromium...}, fedcm:accounts: true, goog:chromeOptions: {debuggerAddress: localhost:36571}, javascriptEnabled: true, networkConnectionEnabled: false, pageLoadStrategy: normal, platform: LINUX, platformName: LINUX, proxy: Proxy(), se:cdp: ws://localhost:36571/devtoo..., se:cdpVersion: 132.0.6834.159, 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: 1519eb637eed7d94f01dd41fe7c59246

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-az565-732', ip: '10.1.0.102', os.name: 'Linux', os.arch: 'amd64', os.version: '5.15.0-1078-azure', java.version: '17.0.14' Driver info: org.openqa.selenium.chrome.ChromeDriver Capabilities {acceptInsecureCerts: false, browserName: chrome, browserVersion: 132.0.6834.159, chrome: {chromedriverVersion: 132.0.6834.159 (2d77d3fc445..., userDataDir: /tmp/.org.chromium.Chromium...}, fedcm:accounts: true, goog:chromeOptions: {debuggerAddress: localhost:36571}, javascriptEnabled: true, networkConnectionEnabled: false, pageLoadStrategy: normal, platform: LINUX, platformName: LINUX, proxy: Proxy(), se:cdp: ws://localhost:36571/devtoo..., se:cdpVersion: 132.0.6834.159, 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: 1519eb637eed7d94f01dd41fe7c59246

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>

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/

gradle-build (file_system_testing)