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Started by upstream project "BIOFORMATS-test-repo" build number 18 originally caused by: Started by upstream project "Trigger" build number 21 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins12965034967530914293.sh + '[' i2i = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_2113_merge_ci -v /uod/idr/repos/curated/i2i:/data -v /uod/idr-scratch/merge-ci/curated/i2i:/config snoopycrimecop/bioformats:merge_ci -Dtestng.memory=15g -Dtestng.threadCount=12 Buildfile: /bio-formats-build/bioformats/components/test-suite/build.xml [echo] isSnapshot = true init-title: [echo] ----------=========== bio-formats-testing-framework ===========---------- init-timestamp: init: copy-resources: compile: [resolver:resolve] Resolving artifacts compile-tests: [resolver:resolve] Resolving artifacts [javac] Compiling 1 source file to /bio-formats-build/bioformats/components/test-suite/test [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] 1 warning test-automated: [testng] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 00:20:13,800 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:20:13,802 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 00:20:13,802 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:20:13,804 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:20:13,805 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:20:13,805 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:20:13,805 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:20:13,805 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:20:13,806 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:20:13,807 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:20:13,808 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:20:13,808 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:20:14,023 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:20:14,023 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:20:14,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:20:14,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:20:14,054 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:20:14,054 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:20:14,054 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:20:14,055 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:20:14,055 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 00:20:14,055 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 00:20:14,056 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 250 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-31 00:20:14,066] [main] java.version = 17.0.2 [testng] 00:20:14,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:20:14,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:14,139 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-31_00-20-14.log] [testng] 00:20:14,141 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-03-31 00:20:14,144] [main] testng.directory = /data [testng] [2024-03-31 00:20:14,145] [main] testng.configDirectory = /config [testng] [2024-03-31 00:20:14,159] [main] testng.multiplier = 1.0 [testng] [2024-03-31 00:20:14,160] [main] testng.in-memory = false [testng] [2024-03-31 00:20:14,160] [main] testng.allow-missing = false [testng] [2024-03-31 00:20:14,161] [main] user.language = en [testng] [2024-03-31 00:20:14,161] [main] user.country = ${user.country} [testng] [2024-03-31 00:20:14,161] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-31 00:20:15,814] [main] ---------------------------------------- [testng] [2024-03-31 00:20:15,814] [main] Total files: 108 [testng] [2024-03-31 00:20:15,814] [main] Scan time: 1.653 s (15 ms/file) [testng] [2024-03-31 00:20:15,814] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 103 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-31 00:20:25,068] [pool-1-thread-1] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000048_491-TIRF_000.tif: [testng] 00:20:25,069 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:20:25,069 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:25,071 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-31_00-20-25.log] [testng] 00:20:25,071 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6690ab32 - End of configuration. [testng] [2024-03-31 00:20:25,177] [pool-1-thread-12] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000078_491-TIRF_000.tif: [testng] 00:20:25,177 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:20:25,177 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:25,178 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-31_00-20-25.log] [testng] 00:20:25,179 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54793062 - End of configuration. [testng] [2024-03-31 00:20:25,283] [pool-1-thread-11] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000073_491-TIRF_000.tif: [testng] 00:20:25,283 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:20:25,283 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:25,284 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-31_00-20-25.log] [testng] 00:20:25,285 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d1e0648 - End of configuration. [testng] [2024-03-31 00:20:25,338] [pool-1-thread-10] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000009_491-TIRF_000.tif: [testng] 00:20:25,339 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:20:25,339 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:25,340 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-31_00-20-25.log] [testng] 00:20:25,341 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35feb0d0 - End of configuration. [testng] [2024-03-31 00:20:25,383] [pool-1-thread-9] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000067_491-TIRF_000.tif: [testng] 00:20:25,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:20:25,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:25,384 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-31_00-20-25.log] [testng] 00:20:25,384 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5827249a - End of configuration. [testng] [2024-03-31 00:20:25,429] [pool-1-thread-8] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000077_491-TIRF_000.tif: [testng] 00:20:25,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:20:25,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:25,430 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-31_00-20-25.log] [testng] 00:20:25,431 |-INFO in ch.qos.logback.core.sift.SiftProcessor@262f9fe8 - End of configuration. [testng] [2024-03-31 00:20:25,471] [pool-1-thread-7] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000035_491-TIRF_000.tif: [testng] 00:20:25,471 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:20:25,471 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:25,472 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-31_00-20-25.log] [testng] 00:20:25,472 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78bee4bb - End of configuration. [testng] [2024-03-31 00:20:25,503] [pool-1-thread-6] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000059_491-TIRF_000.tif: [testng] 00:20:25,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:20:25,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:25,504 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-31_00-20-25.log] [testng] 00:20:25,505 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33d3b67f - End of configuration. [testng] [2024-03-31 00:20:25,541] [pool-1-thread-5] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000036_491-TIRF_000.tif: [testng] 00:20:25,542 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:20:25,542 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:25,542 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-31_00-20-25.log] [testng] 00:20:25,543 |-INFO in ch.qos.logback.core.sift.SiftProcessor@771c5da1 - End of configuration. [testng] [2024-03-31 00:20:25,576] [pool-1-thread-4] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000052_491-TIRF_000.tif: [testng] 00:20:25,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:20:25,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:25,577 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-31_00-20-25.log] [testng] 00:20:25,577 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72f5b3af - End of configuration. [testng] [2024-03-31 00:20:25,626] [pool-1-thread-3] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000047_491-TIRF_000.tif: [testng] 00:20:25,627 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:20:25,627 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:25,627 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-31_00-20-25.log] [testng] 00:20:25,628 |-INFO in ch.qos.logback.core.sift.SiftProcessor@452991c3 - End of configuration. [testng] [2024-03-31 00:20:25,660] [pool-1-thread-2] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000043_491-TIRF_000.tif: [testng] 00:20:25,660 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:20:25,660 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:25,661 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-31_00-20-25.log] [testng] 00:20:25,661 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7be77972 - End of configuration. [testng] [2024-03-31 00:20:28,345] [pool-1-thread-8] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000003_491-TIRF_000.tif: [testng] [2024-03-31 00:20:28,381] [pool-1-thread-5] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000017_491-TIRF_000.tif: [testng] [2024-03-31 00:20:28,418] [pool-1-thread-3] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000064_491-TIRF_000.tif: [testng] [2024-03-31 00:20:28,455] [pool-1-thread-2] Initializing /data/sample files/TESM_microscope/TESM_i2i_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF.i2i: [testng] [2024-03-31 00:20:28,478] [pool-1-thread-12] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000010_491-TIRF_000.tif: [testng] [2024-03-31 00:20:28,516] [pool-1-thread-10] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000051_491-TIRF_000.tif: [testng] [2024-03-31 00:20:28,555] [pool-1-thread-9] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000015_491-TIRF_000.tif: [testng] [2024-03-31 00:20:28,601] [pool-1-thread-4] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000025_491-TIRF_000.tif: [testng] [2024-03-31 00:20:28,642] [pool-1-thread-7] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000038_491-TIRF_000.tif: [testng] [2024-03-31 00:20:28,677] [pool-1-thread-11] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000055_491-TIRF_000.tif: [testng] [2024-03-31 00:20:28,713] [pool-1-thread-1] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000079_491-TIRF_000.tif: [testng] [2024-03-31 00:20:28,749] [pool-1-thread-6] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000080_491-TIRF_000.tif: [testng] [2024-03-31 00:20:29,573] [pool-1-thread-2] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000032_491-TIRF_000.tif: [testng] [2024-03-31 00:20:29,854] [pool-1-thread-7] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000001_491-TIRF_000.tif: [testng] [2024-03-31 00:20:29,944] [pool-1-thread-4] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000016_491-TIRF_000.tif: [testng] [2024-03-31 00:20:30,021] [pool-1-thread-5] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000074_491-TIRF_000.tif: [testng] [2024-03-31 00:20:30,142] [pool-1-thread-12] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000002_491-TIRF_000.tif: [testng] [2024-03-31 00:20:30,182] [pool-1-thread-10] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000000_491-TIRF_000.tif: [testng] [2024-03-31 00:20:30,241] [pool-1-thread-8] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000028_491-TIRF_000.tif: [testng] [2024-03-31 00:20:30,278] [pool-1-thread-6] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000066_491-TIRF_000.tif: [testng] [2024-03-31 00:20:30,319] [pool-1-thread-9] Initializing /data/sample 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