simple 29-Sep-2019 19:48:04 Build Clowder - pyclowder - develop - Default Job #2 (CATS-PYC32-JOB1-2) started building on agent buildserver-2.os.ncsa.edu simple 29-Sep-2019 19:48:04 Remote agent on host buildserver-2.os.ncsa.edu simple 29-Sep-2019 19:48:04 Build working directory is /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PYC32-JOB1 simple 29-Sep-2019 19:48:04 Executing build Clowder - pyclowder - develop - Default Job #2 (CATS-PYC32-JOB1-2) simple 29-Sep-2019 19:48:04 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 29-Sep-2019 19:48:04 Checking out into /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PYC32-JOB1 simple 29-Sep-2019 19:48:04 Updating source code to revision: 0b3e2e8f213e3b233245a9867ffb5e152ee05de3 simple 29-Sep-2019 19:48:04 Enforcing full fetch as requested revision has not been found on the configured branch simple 29-Sep-2019 19:48:04 Fetching 'refs/heads/*' from 'ssh://git@opensource.ncsa.illinois.edu:7999/cats/pyclowder.git'. Will try to do a shallow fetch. simple 29-Sep-2019 19:48:04 Warning: Permanently added '[127.0.0.1]:39245' (RSA) to the list of known hosts. simple 29-Sep-2019 19:48:04 From ssh://127.0.0.1:39245/cats/pyclowder simple 29-Sep-2019 19:48:04 * [new branch] Add-redirect-option -> Add-redirect-option simple 29-Sep-2019 19:48:04 * [new branch] CATS-784-python3-compatible -> CATS-784-python3-compatible simple 29-Sep-2019 19:48:04 * [new branch] CATSPYC-19-add-anonymous-email-receiver-on-the-email-message -> CATSPYC-19-add-anonymous-email-receiver-on-the-email-message simple 29-Sep-2019 19:48:04 * [new branch] SYN-63-Remove-data-from-geoserver -> SYN-63-Remove-data-from-geoserver simple 29-Sep-2019 19:48:04 * [new branch] add-get-or-create-methods -> add-get-or-create-methods simple 29-Sep-2019 19:48:04 * [new branch] add-sphinx-docs -> add-sphinx-docs simple 29-Sep-2019 19:48:04 * [new branch] boxhack -> boxhack simple 29-Sep-2019 19:48:04 * [new branch] bugfix/BD-2344-update-pip-in-simple-extractor-wrapper -> bugfix/BD-2344-update-pip-in-simple-extractor-wrapper simple 29-Sep-2019 19:48:04 * [new branch] bugfix/BD-2345-open-extractor-info-json-with-utf-8-encoding -> bugfix/BD-2345-open-extractor-info-json-with-utf-8-encoding simple 29-Sep-2019 19:48:04 * [new branch] bugfix/CATS-729-copy-dataset-extractor-fix -> bugfix/CATS-729-copy-dataset-extractor-fix simple 29-Sep-2019 19:48:04 * [new branch] bugfix/GLGVO-343-parser-vm-spawning-many-jobs-update -> bugfix/GLGVO-343-parser-vm-spawning-many-jobs-update simple 29-Sep-2019 19:48:04 * [new branch] check_duplicate-flag -> check_duplicate-flag simple 29-Sep-2019 19:48:04 * [new branch] clowder-clients-clean -> clowder-clients-clean simple 29-Sep-2019 19:48:04 + 727b1d7...0b3e2e8 develop -> develop (forced update) simple 29-Sep-2019 19:48:04 * [new branch] extractor-bugfix -> extractor-bugfix simple 29-Sep-2019 19:48:04 * [new branch] feature/GEOD-927-fix-add-test-for-pyclowder2-geostreams -> feature/GEOD-927-fix-add-test-for-pyclowder2-geostreams simple 29-Sep-2019 19:48:04 * [new branch] geostreams -> geostreams simple 29-Sep-2019 19:48:04 * [new branch] hotfix/extractor-info.json -> hotfix/extractor-info.json simple 29-Sep-2019 19:48:04 * [new branch] master -> master simple 29-Sep-2019 19:48:04 * [new branch] rename_functions -> rename_functions simple 29-Sep-2019 19:48:04 * [new branch] seven-miles-changes -> seven-miles-changes simple 29-Sep-2019 19:48:04 * [new tag] 2.0.2 -> 2.0.2 simple 29-Sep-2019 19:48:04 * [new tag] v2.0.3 -> v2.0.3 simple 29-Sep-2019 19:48:04 * [new tag] v2.1.0 -> v2.1.0 simple 29-Sep-2019 19:48:04 * [new tag] v2.1.1 -> v2.1.1 simple 29-Sep-2019 19:48:04 * [new tag] v2.2.0 -> v2.2.0 simple 29-Sep-2019 19:48:04 * [new tag] v2.2.2 -> v2.2.2 simple 29-Sep-2019 19:48:04 Checking out revision 0b3e2e8f213e3b233245a9867ffb5e152ee05de3. simple 29-Sep-2019 19:48:04 Already on 'develop' simple 29-Sep-2019 19:48:04 Updated source code to revision: 0b3e2e8f213e3b233245a9867ffb5e152ee05de3 simple 29-Sep-2019 19:48:04 Finished task 'Checkout Default Repository' with result: Success simple 29-Sep-2019 19:48:04 Running pre-build action: VCS Version Collector simple 29-Sep-2019 19:48:04 Starting task 'docker build and push' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' command 29-Sep-2019 19:48:04 Beginning to execute external process for build 'Clowder - pyclowder - develop - Default Job #2 (CATS-PYC32-JOB1-2)'\n ... running command line: \n/bin/sh docker.sh\n ... in: /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PYC32-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=develop\nbamboo_capability_system_builder_command_npm_6=/home/bamboo/node-v6.9.1/bin/npm\nbamboo_capability_system_builder_command_buckminster_4_3=/home/bamboo/buckminster-4.3/buckminster\nbamboo_capability_system_builder_node_Node_js_v6_9_1=/home/bamboo/node-v6.9.1/bin/node\nbamboo_capability_system_builder_command_buckminster_4_4=/home/bamboo/buckminster-4.4/buckminster\nbamboo_capability_system_builder_command_buckminster_4_2=/home/bamboo/buckminster-4.2/buckminster\nbamboo_planRepository_1_branchDisplayName=develop\nbamboo_repository_revision_number=0b3e2e8f213e3b233245a9867ffb5e152ee05de3\nbamboo_resultsUrl=https://opensource.ncsa.illinois.edu/bamboo/browse/CATS-PYC32-JOB1-2\nbamboo_capability_system_builder_command_sphinx=/usr/bin/sphinx-build\nbamboo_build_working_directory=/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PYC32-JOB1\nbamboo_planRepository_1_name=pyclowder\nbamboo_buildKey=CATS-PYC32-JOB1\nbamboo_capability_system_os=linux\nbamboo_repository_177831947_git_branch=develop\nbamboo_shortPlanName=pyclowder\nbamboo_planRepository_name=pyclowder\nbamboo_buildNumber=2\nbamboo_capability_system_builder_node_grunt_6=/home/bamboo/node-v6.9.1/bin/grunt\nbamboo_repository_177831947_branch_name=develop\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://opensource.ncsa.illinois.edu/bamboo/browse/CATS-PYC32-JOB1-2\nbamboo_planRepository_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/pyclowder.git\nbamboo_agentId=140673028\nbamboo_planName=Clowder - pyclowder - develop\nbamboo_shortPlanKey=PYC32\nbamboo_capability_system_builder_command_sbt_0_13=/home/bamboo/sbt-0.13.2/bin/sbt\nbamboo_capability_system_builder_node_Node_js_v0_10_28=/home/bamboo/node-v0.10.28/bin/node\nbamboo_shortJobKey=JOB1\nbamboo_planRepository_revision=0b3e2e8f213e3b233245a9867ffb5e152ee05de3\nbamboo_buildTimeStamp=2019-09-29T19:48:04.198-05:00\nbamboo_repository_previous_revision_number=727b1d7f7657d2cc231ec2a623577d79454b25ec\nbamboo_capability_system_builder_command_npm=/home/bamboo/node-v0.10.28/bin/npm\nbamboo_capability_system_builder_mvn2_Maven_2=/home/bamboo/apache-maven-2.2.1\nbamboo_planRepository_previousRevision=727b1d7f7657d2cc231ec2a623577d79454b25ec\nbamboo_repository_177831947_revision_number=0b3e2e8f213e3b233245a9867ffb5e152ee05de3\nbamboo_repository_git_branch=develop\nbamboo_buildResultKey=CATS-PYC32-JOB1-2\nbamboo_repository_branch_name=develop\nbamboo_buildPlanName=Clowder - pyclowder - develop - Default Job\nbamboo_planRepository_1_revision=0b3e2e8f213e3b233245a9867ffb5e152ee05de3\nbamboo_capability_system_builder_command_python3=/usr/bin/python3\nbamboo_repository_name=pyclowder\nbamboo_repository_177831947_git_username=\nbamboo_buildFailed=false\nbamboo_capability_system_docker_executable=/usr/bin/docker\nbamboo_capability_system_builder_command_grunt=/home/bamboo/node-v0.10.28/bin/grunt\nbamboo_planRepository_branch=develop\nbamboo_repository_177831947_name=pyclowder\nbamboo_agentWorkingDirectory=/home/bamboo/bamboo-agent-home/xml-data/build-dir\nbamboo_repository_177831947_git_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/pyclowder.git\nbamboo_capability_system_git_executable=/usr/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=727b1d7f7657d2cc231ec2a623577d79454b25ec\nbamboo_capability_system_builder_sbt_SBT_0_13_13=/home/bamboo/sbt-0.13.13\nbamboo_planRepository_branchDisplayName=develop\nbamboo_capability_system_builder_command_phantomjs=/home/bamboo/phantomjs-1.9.8/bin/phantomjs\nbamboo_planRepository_1_type=bbserver\nbamboo_planRepository_branchName=develop\nbamboo_capability_system_builder_command_python2_7=/usr/bin/python2.7\nbamboo_capability_system_hostname=buildserver-1\nbamboo_capability_system_jdk_JDK=/home/bamboo/jdk1.8.0_66\nbamboo_capability_system_software_mongo=/usr/bin/mongo\nbamboo_plan_storageTag=plan-177700875\nbamboo_hg_cache_directory=/home/bamboo/bamboo-agent-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_capability_system_builder_command_casperjs=/home/bamboo/node-v0.10.28/bin/casperjs\nbamboo_capability_system_software_rabbitmq=/usr/sbin/rabbitmqctl\nbamboo_capability_system_jdk_JDK_1_8_0_66=/home/bamboo/jdk1.8.0_66\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=bbserver\nbamboo_git_cache_directory=/home/bamboo/bamboo-agent-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_177831947_previous_revision_number=727b1d7f7657d2cc231ec2a623577d79454b25ec\nbamboo_repository_git_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/pyclowder.git\nbamboo_capability_system_builder_node_Node_js=/home/bamboo/node-v0.10.28/bin/node\nbamboo_capability_system_builder_ant_Ant=/home/bamboo/apache-ant-1.9.4\nbamboo_capability_system_builder_mvn3_Maven_3=/home/bamboo/apache-maven-3.3.9\nbamboo_tmp_directory=/home/bamboo/bamboo-agent-home/temp\nbamboo_working_directory=/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PYC32-JOB1\nbamboo_planKey=CATS-PYC32\nbamboo_planRepository_1_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/pyclowder.git\nbamboo_planRepository_username=\nbamboo_capability_system_jdk_JDK_1_8=/home/bamboo/jdk1.8.0_66\nbamboo_capability_system_jdk_JDK_1_6=/home/bamboo/jdk1.6.0_41\nbamboo_capability_system_builder_command_mkcrx=/home/bamboo/mkcrx/mkcrx.sh\nbamboo_capability_system_jdk_JDK_1_7=/home/bamboo/jdk1.7.0_60\nbamboo_planRepository_1_branchName=develop\n build 29-Sep-2019 19:48:05 Sending build context to Docker daemon 267.8kB build 29-Sep-2019 19:48:05 build 29-Sep-2019 19:48:05 Step 1/10 : FROM ubuntu:16.04 build 29-Sep-2019 19:48:05 ---> 657d80a6401d build 29-Sep-2019 19:48:05 Step 2/10 : ARG PYTHON_VERSION="2.7" build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> 7d071fce2822 build 29-Sep-2019 19:48:05 Step 3/10 : ENV PYTHON_VERSION=${PYTHON_VERSION} RABBITMQ_URI="amqp://guest:guest@rabbitmq:5672/%2F" RABBITMQ_EXCHANGE="clowder" RABBITMQ_QUEUE="" REGISTRATION_ENDPOINTS="" EMAIL_SERVER="" EMAIL_SENDER="extractor" MAIN_SCRIPT="" build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> 6d4fba816a1e build 29-Sep-2019 19:48:05 Step 4/10 : RUN apt-get -q -q update && apt-get install -y --no-install-recommends python${PYTHON_VERSION} curl && if [ ! -e /usr/bin/python ]; then ln -s /usr/bin/python${PYTHON_VERSION} /usr/bin/python; fi && curl -k https://bootstrap.pypa.io/get-pip.py -o /tmp/get-pip.py && python /tmp/get-pip.py && pip install --upgrade setuptools && rm -rf /var/lib/apt/lists/* /tmp/get-pip.py build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> 120aa51655ff build 29-Sep-2019 19:48:05 Step 5/10 : COPY pyclowder /tmp/pyclowder/pyclowder build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> 6d76b3beb121 build 29-Sep-2019 19:48:05 Step 6/10 : COPY setup.py description.rst /tmp/pyclowder/ build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> 860cbc248fe1 build 29-Sep-2019 19:48:05 Step 7/10 : RUN pip install --upgrade /tmp/pyclowder && rm -rf /tmp/pyclowder build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> 62eafaf985b6 build 29-Sep-2019 19:48:05 Step 8/10 : WORKDIR /home/clowder build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> 3489a864819b build 29-Sep-2019 19:48:05 Step 9/10 : COPY notifications.json /home/clowder/ build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> 54a193a02c9b build 29-Sep-2019 19:48:05 Step 10/10 : CMD python "./${MAIN_SCRIPT}" build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> dd7058a2620a build 29-Sep-2019 19:48:05 Successfully built dd7058a2620a build 29-Sep-2019 19:48:05 Successfully tagged clowder/pyclowder:latest build 29-Sep-2019 19:48:05 Sending build context to Docker daemon 265.7kB build 29-Sep-2019 19:48:05 build 29-Sep-2019 19:48:05 Step 1/7 : ARG PYCLOWDER_PYTHON="" build 29-Sep-2019 19:48:05 Step 2/7 : FROM clowder/pyclowder${PYCLOWDER_PYTHON}:latest build 29-Sep-2019 19:48:05 ---> dd7058a2620a build 29-Sep-2019 19:48:05 Step 3/7 : ONBUILD COPY packages.* Dockerfile /home/clowder/ build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> 7a85fa61aaf7 build 29-Sep-2019 19:48:05 Step 4/7 : ONBUILD RUN if [ -e packages.apt ]; then apt-get -q -q update && xargs apt-get -y install --no-install-recommends < packages.apt && rm -rf /var/lib/apt/lists/*; fi build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> d31de910b23f build 29-Sep-2019 19:48:05 Step 5/7 : ONBUILD COPY requirements.txt* Dockerfile /home/clowder/ build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> a127f8631bf4 build 29-Sep-2019 19:48:05 Step 6/7 : ONBUILD RUN if [ -e requirements.txt ]; then pip install --no-cache-dir -r requirements.txt; fi build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> 31a54614f4f4 build 29-Sep-2019 19:48:05 Step 7/7 : ONBUILD ADD . /home/clowder/ build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> 85b511f58633 build 29-Sep-2019 19:48:05 Successfully built 85b511f58633 build 29-Sep-2019 19:48:05 Successfully tagged clowder/pyclowder:onbuild build 29-Sep-2019 19:48:05 Sending build context to Docker daemon 12.8kB build 29-Sep-2019 19:48:05 build 29-Sep-2019 19:48:05 Step 1/6 : ARG PYCLOWDER_PYTHON="" build 29-Sep-2019 19:48:05 Step 2/6 : FROM clowder/pyclowder${PYCLOWDER_PYTHON}:onbuild build 29-Sep-2019 19:48:05 # Executing 5 build triggers build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> 4c2524540888 build 29-Sep-2019 19:48:05 Step 3/6 : ENV MAIN_SCRIPT="binary_extractor.py" RABBITMQ_QUEUE="" IMAGE_BINARY="" IMAGE_TYPE="" IMAGE_THUMBNAIL_COMMAND="" IMAGE_PREVIEW_COMMAND="" PREVIEW_BINARY="" PREVIEW_TYPE="" PREVIEW_COMMAND="" build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> 845cdb818202 build 29-Sep-2019 19:48:05 Step 4/6 : ONBUILD COPY packages.* Dockerfile /home/clowder/ build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> ced1525ab9d4 build 29-Sep-2019 19:48:05 Step 5/6 : ONBUILD RUN if [ -e packages.apt ]; then apt-get -q -q update && xargs apt-get -y install --no-install-recommends < packages.apt && rm -rf /var/lib/apt/lists/*; fi build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> e12ec7dd47a4 build 29-Sep-2019 19:48:05 Step 6/6 : ONBUILD COPY extractor_info.json /home/clowder/ build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> c018300631b2 build 29-Sep-2019 19:48:05 Successfully built c018300631b2 build 29-Sep-2019 19:48:05 Successfully tagged clowder/extractors-binary-preview:onbuild build 29-Sep-2019 19:48:05 Sending build context to Docker daemon 6.656kB build 29-Sep-2019 19:48:05 build 29-Sep-2019 19:48:05 Step 1/11 : ARG PYCLOWDER_PYTHON="" build 29-Sep-2019 19:48:05 Step 2/11 : FROM clowder/pyclowder${PYCLOWDER_PYTHON}:latest build 29-Sep-2019 19:48:05 ---> dd7058a2620a build 29-Sep-2019 19:48:05 Step 3/11 : ENV EXTRACTION_FUNC="" build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> 5ec3bcc0f133 build 29-Sep-2019 19:48:05 Step 4/11 : ENV EXTRACTION_MODULE="" build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> 8f744f833e01 build 29-Sep-2019 19:48:05 Step 5/11 : COPY simple_extractor.py . build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> 54ad9dd74034 build 29-Sep-2019 19:48:05 Step 6/11 : ONBUILD COPY packages.* Dockerfile /home/clowder/ build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> 15386f72c1de build 29-Sep-2019 19:48:05 Step 7/11 : ONBUILD RUN if [ -e packages.apt ]; then apt-get -q -q update && xargs apt-get -y install --no-install-recommends < packages.apt && rm -rf /var/lib/apt/lists/*; fi build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> 1d3529747c3f build 29-Sep-2019 19:48:05 Step 8/11 : ONBUILD COPY requirements.txt* Dockerfile /home/clowder/ build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> 6e906ddef1eb build 29-Sep-2019 19:48:05 Step 9/11 : ONBUILD RUN if [ -e requirements.txt ]; then pip install --no-cache-dir -r requirements.txt; fi build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> d455c2a07b85 build 29-Sep-2019 19:48:05 Step 10/11 : ONBUILD ADD . /home/clowder/ build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> fd992774021c build 29-Sep-2019 19:48:05 Step 11/11 : CMD python -c "from simple_extractor import SimplePythonExtractor; from ${EXTRACTION_MODULE} import *; SimplePythonExtractor(${EXTRACTION_FUNC}).start()" build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> e1c0f4dce633 build 29-Sep-2019 19:48:05 Successfully built e1c0f4dce633 build 29-Sep-2019 19:48:05 Successfully tagged clowder/extractors-simple-extractor:onbuild build 29-Sep-2019 19:48:05 Sending build context to Docker daemon 13.31kB build 29-Sep-2019 19:48:05 build 29-Sep-2019 19:48:05 Step 1/11 : ARG PYCLOWDER_PYTHON="" build 29-Sep-2019 19:48:05 Step 2/11 : FROM clowder/pyclowder${PYCLOWDER_PYTHON}:latest build 29-Sep-2019 19:48:05 ---> dd7058a2620a build 29-Sep-2019 19:48:05 Step 3/11 : ENV R_SCRIPT="" R_FUNCTION="" build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> 7e0269fcd318 build 29-Sep-2019 19:48:05 Step 4/11 : RUN echo "deb http://cran.rstudio.com/bin/linux/ubuntu xenial/" > /etc/apt/sources.list.d/R.list && apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 && apt-get -q -q update && apt-get -y install --no-install-recommends r-base-core r-base-dev && rm -rf /var/lib/apt/lists/* && Rscript --vanilla -e "install.packages('jsonlite', repos='http://cran.rstudio.com/'); print(system.file(package = 'jsonlite')); q(status=as.integer(system.file(package = 'jsonlite') == ''))" build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> eb86c380f98c build 29-Sep-2019 19:48:05 Step 5/11 : COPY r_extractor.py launcher.R /home/clowder/ build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> 7fd806a6b3c4 build 29-Sep-2019 19:48:05 Step 6/11 : ONBUILD COPY packages.* Dockerfile /home/clowder/ build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> 2583e497a0e8 build 29-Sep-2019 19:48:05 Step 7/11 : ONBUILD RUN if [ -e packages.apt ]; then apt-get -q -q update && xargs apt-get -y install --no-install-recommends < packages.apt && rm -rf /var/lib/apt/lists/*; fi build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> f2b28b70c6d5 build 29-Sep-2019 19:48:05 Step 8/11 : ONBUILD COPY docker.R* Dockerfile /home/clowder/ build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> a99f1906b661 build 29-Sep-2019 19:48:05 Step 9/11 : ONBUILD RUN if [ -e docker.R ]; then Rscript docker.R; fi build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> ba5f0a968440 build 29-Sep-2019 19:48:05 Step 10/11 : ONBUILD ADD . /home/clowder/ build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> a15d3dfaaf94 build 29-Sep-2019 19:48:05 Step 11/11 : CMD python r_extractor.py build 29-Sep-2019 19:48:05 ---> Using cache build 29-Sep-2019 19:48:05 ---> 0dc22bddc90f build 29-Sep-2019 19:48:05 Successfully built 0dc22bddc90f build 29-Sep-2019 19:48:05 Successfully tagged clowder/extractors-simple-r-extractor:onbuild build 29-Sep-2019 19:48:06 Sending build context to Docker daemon 267.8kB build 29-Sep-2019 19:48:06 build 29-Sep-2019 19:48:06 Step 1/10 : FROM ubuntu:16.04 build 29-Sep-2019 19:48:06 ---> 657d80a6401d build 29-Sep-2019 19:48:06 Step 2/10 : ARG PYTHON_VERSION="2.7" build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> 7d071fce2822 build 29-Sep-2019 19:48:06 Step 3/10 : ENV PYTHON_VERSION=${PYTHON_VERSION} RABBITMQ_URI="amqp://guest:guest@rabbitmq:5672/%2F" RABBITMQ_EXCHANGE="clowder" RABBITMQ_QUEUE="" REGISTRATION_ENDPOINTS="" EMAIL_SERVER="" EMAIL_SENDER="extractor" MAIN_SCRIPT="" build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> f6fbf60fc5c0 build 29-Sep-2019 19:48:06 Step 4/10 : RUN apt-get -q -q update && apt-get install -y --no-install-recommends python${PYTHON_VERSION} curl && if [ ! -e /usr/bin/python ]; then ln -s /usr/bin/python${PYTHON_VERSION} /usr/bin/python; fi && curl -k https://bootstrap.pypa.io/get-pip.py -o /tmp/get-pip.py && python /tmp/get-pip.py && pip install --upgrade setuptools && rm -rf /var/lib/apt/lists/* /tmp/get-pip.py build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> f1bc58800597 build 29-Sep-2019 19:48:06 Step 5/10 : COPY pyclowder /tmp/pyclowder/pyclowder build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> 597c3f5e2968 build 29-Sep-2019 19:48:06 Step 6/10 : COPY setup.py description.rst /tmp/pyclowder/ build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> 21751dcbe393 build 29-Sep-2019 19:48:06 Step 7/10 : RUN pip install --upgrade /tmp/pyclowder && rm -rf /tmp/pyclowder build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> 9cb08c3eb887 build 29-Sep-2019 19:48:06 Step 8/10 : WORKDIR /home/clowder build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> 56066ba6ea87 build 29-Sep-2019 19:48:06 Step 9/10 : COPY notifications.json /home/clowder/ build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> 1708a9940a2a build 29-Sep-2019 19:48:06 Step 10/10 : CMD python "./${MAIN_SCRIPT}" build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> 4e0a5b6aa8a3 build 29-Sep-2019 19:48:06 Successfully built 4e0a5b6aa8a3 build 29-Sep-2019 19:48:06 Successfully tagged clowder/pyclowder-python3:latest build 29-Sep-2019 19:48:06 Sending build context to Docker daemon 265.7kB build 29-Sep-2019 19:48:06 build 29-Sep-2019 19:48:06 Step 1/7 : ARG PYCLOWDER_PYTHON="" build 29-Sep-2019 19:48:06 Step 2/7 : FROM clowder/pyclowder${PYCLOWDER_PYTHON}:latest build 29-Sep-2019 19:48:06 ---> 4e0a5b6aa8a3 build 29-Sep-2019 19:48:06 Step 3/7 : ONBUILD COPY packages.* Dockerfile /home/clowder/ build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> 66ecf93f77a4 build 29-Sep-2019 19:48:06 Step 4/7 : ONBUILD RUN if [ -e packages.apt ]; then apt-get -q -q update && xargs apt-get -y install --no-install-recommends < packages.apt && rm -rf /var/lib/apt/lists/*; fi build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> e466cf6346ef build 29-Sep-2019 19:48:06 Step 5/7 : ONBUILD COPY requirements.txt* Dockerfile /home/clowder/ build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> ad4c2be545c8 build 29-Sep-2019 19:48:06 Step 6/7 : ONBUILD RUN if [ -e requirements.txt ]; then pip install --no-cache-dir -r requirements.txt; fi build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> b31c60631fa8 build 29-Sep-2019 19:48:06 Step 7/7 : ONBUILD ADD . /home/clowder/ build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> 1027a3d0825a build 29-Sep-2019 19:48:06 Successfully built 1027a3d0825a build 29-Sep-2019 19:48:06 Successfully tagged clowder/pyclowder-python3:onbuild build 29-Sep-2019 19:48:06 Sending build context to Docker daemon 12.8kB build 29-Sep-2019 19:48:06 build 29-Sep-2019 19:48:06 Step 1/6 : ARG PYCLOWDER_PYTHON="" build 29-Sep-2019 19:48:06 Step 2/6 : FROM clowder/pyclowder${PYCLOWDER_PYTHON}:onbuild build 29-Sep-2019 19:48:06 # Executing 5 build triggers build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> b3f1064f0640 build 29-Sep-2019 19:48:06 Step 3/6 : ENV MAIN_SCRIPT="binary_extractor.py" RABBITMQ_QUEUE="" IMAGE_BINARY="" IMAGE_TYPE="" IMAGE_THUMBNAIL_COMMAND="" IMAGE_PREVIEW_COMMAND="" PREVIEW_BINARY="" PREVIEW_TYPE="" PREVIEW_COMMAND="" build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> 6b0049c301d4 build 29-Sep-2019 19:48:06 Step 4/6 : ONBUILD COPY packages.* Dockerfile /home/clowder/ build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> 6123aff22e13 build 29-Sep-2019 19:48:06 Step 5/6 : ONBUILD RUN if [ -e packages.apt ]; then apt-get -q -q update && xargs apt-get -y install --no-install-recommends < packages.apt && rm -rf /var/lib/apt/lists/*; fi build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> ec70c8469c80 build 29-Sep-2019 19:48:06 Step 6/6 : ONBUILD COPY extractor_info.json /home/clowder/ build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> f566c3ef3474 build 29-Sep-2019 19:48:06 Successfully built f566c3ef3474 build 29-Sep-2019 19:48:06 Successfully tagged clowder/extractors-binary-preview-python3:onbuild build 29-Sep-2019 19:48:06 Sending build context to Docker daemon 6.656kB build 29-Sep-2019 19:48:06 build 29-Sep-2019 19:48:06 Step 1/11 : ARG PYCLOWDER_PYTHON="" build 29-Sep-2019 19:48:06 Step 2/11 : FROM clowder/pyclowder${PYCLOWDER_PYTHON}:latest build 29-Sep-2019 19:48:06 ---> 4e0a5b6aa8a3 build 29-Sep-2019 19:48:06 Step 3/11 : ENV EXTRACTION_FUNC="" build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> 3ae37fd01aa4 build 29-Sep-2019 19:48:06 Step 4/11 : ENV EXTRACTION_MODULE="" build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> b81bd25614b6 build 29-Sep-2019 19:48:06 Step 5/11 : COPY simple_extractor.py . build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> 973592e3e7e2 build 29-Sep-2019 19:48:06 Step 6/11 : ONBUILD COPY packages.* Dockerfile /home/clowder/ build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> 30739eac93b0 build 29-Sep-2019 19:48:06 Step 7/11 : ONBUILD RUN if [ -e packages.apt ]; then apt-get -q -q update && xargs apt-get -y install --no-install-recommends < packages.apt && rm -rf /var/lib/apt/lists/*; fi build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> 779d1a7c719b build 29-Sep-2019 19:48:06 Step 8/11 : ONBUILD COPY requirements.txt* Dockerfile /home/clowder/ build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> 5ccfda9c9dcc build 29-Sep-2019 19:48:06 Step 9/11 : ONBUILD RUN if [ -e requirements.txt ]; then pip install --no-cache-dir -r requirements.txt; fi build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> e6754308238b build 29-Sep-2019 19:48:06 Step 10/11 : ONBUILD ADD . /home/clowder/ build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> 6bb00e7c3b74 build 29-Sep-2019 19:48:06 Step 11/11 : CMD python -c "from simple_extractor import SimplePythonExtractor; from ${EXTRACTION_MODULE} import *; SimplePythonExtractor(${EXTRACTION_FUNC}).start()" build 29-Sep-2019 19:48:06 ---> Using cache build 29-Sep-2019 19:48:06 ---> 2d62b6b3d71c build 29-Sep-2019 19:48:06 Successfully built 2d62b6b3d71c build 29-Sep-2019 19:48:07 Successfully tagged clowder/extractors-simple-extractor-python3:onbuild build 29-Sep-2019 19:48:07 Sending build context to Docker daemon 13.31kB build 29-Sep-2019 19:48:07 build 29-Sep-2019 19:48:07 Step 1/11 : ARG PYCLOWDER_PYTHON="" build 29-Sep-2019 19:48:07 Step 2/11 : FROM clowder/pyclowder${PYCLOWDER_PYTHON}:latest build 29-Sep-2019 19:48:07 ---> 4e0a5b6aa8a3 build 29-Sep-2019 19:48:07 Step 3/11 : ENV R_SCRIPT="" R_FUNCTION="" build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> 63579f8b2a95 build 29-Sep-2019 19:48:07 Step 4/11 : RUN echo "deb http://cran.rstudio.com/bin/linux/ubuntu xenial/" > /etc/apt/sources.list.d/R.list && apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 && apt-get -q -q update && apt-get -y install --no-install-recommends r-base-core r-base-dev && rm -rf /var/lib/apt/lists/* && Rscript --vanilla -e "install.packages('jsonlite', repos='http://cran.rstudio.com/'); print(system.file(package = 'jsonlite')); q(status=as.integer(system.file(package = 'jsonlite') == ''))" build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> b188d7e98305 build 29-Sep-2019 19:48:07 Step 5/11 : COPY r_extractor.py launcher.R /home/clowder/ build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> ca0d6f759af1 build 29-Sep-2019 19:48:07 Step 6/11 : ONBUILD COPY packages.* Dockerfile /home/clowder/ build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> 2febded5a55d build 29-Sep-2019 19:48:07 Step 7/11 : ONBUILD RUN if [ -e packages.apt ]; then apt-get -q -q update && xargs apt-get -y install --no-install-recommends < packages.apt && rm -rf /var/lib/apt/lists/*; fi build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> 03ddd40d9f7a build 29-Sep-2019 19:48:07 Step 8/11 : ONBUILD COPY docker.R* Dockerfile /home/clowder/ build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> 973620bd7ad3 build 29-Sep-2019 19:48:07 Step 9/11 : ONBUILD RUN if [ -e docker.R ]; then Rscript docker.R; fi build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> e000d0bef514 build 29-Sep-2019 19:48:07 Step 10/11 : ONBUILD ADD . /home/clowder/ build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> c9e4c02a38dc build 29-Sep-2019 19:48:07 Step 11/11 : CMD python r_extractor.py build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> ffb662004f5f build 29-Sep-2019 19:48:07 Successfully built ffb662004f5f build 29-Sep-2019 19:48:07 Successfully tagged clowder/extractors-simple-r-extractor-python3:onbuild build 29-Sep-2019 19:48:07 Sending build context to Docker daemon 9.216kB build 29-Sep-2019 19:48:07 build 29-Sep-2019 19:48:07 Step 1/3 : ARG PYCLOWDER_PYTHON="" build 29-Sep-2019 19:48:07 Step 2/3 : FROM clowder/pyclowder${PYCLOWDER_PYTHON}:onbuild build 29-Sep-2019 19:48:07 # Executing 5 build triggers build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> 7bfedae08fe2 build 29-Sep-2019 19:48:07 Step 3/3 : ENV MAIN_SCRIPT="wordcount.py" build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> f3d37a75c60d build 29-Sep-2019 19:48:07 Successfully built f3d37a75c60d build 29-Sep-2019 19:48:07 Successfully tagged clowder/extractors-wordcount:latest build 29-Sep-2019 19:48:07 Sending build context to Docker daemon 5.12kB build 29-Sep-2019 19:48:07 build 29-Sep-2019 19:48:07 Step 1/4 : ARG PYCLOWDER_PYTHON="" build 29-Sep-2019 19:48:07 Step 2/4 : FROM clowder/extractors-simple-extractor${PYCLOWDER_PYTHON}:onbuild build 29-Sep-2019 19:48:07 # Executing 5 build triggers build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> d8bc2bd30019 build 29-Sep-2019 19:48:07 Step 3/4 : ENV EXTRACTION_FUNC="wordcount" build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> e4ee5dc93504 build 29-Sep-2019 19:48:07 Step 4/4 : ENV EXTRACTION_MODULE="wordcount" build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> c88d1c3b8999 build 29-Sep-2019 19:48:07 Successfully built c88d1c3b8999 build 29-Sep-2019 19:48:07 Successfully tagged clowder/extractors-wordcount-simple-extractor:latest build 29-Sep-2019 19:48:07 Sending build context to Docker daemon 5.12kB build 29-Sep-2019 19:48:07 build 29-Sep-2019 19:48:07 Step 1/3 : ARG PYCLOWDER_PYTHON="" build 29-Sep-2019 19:48:07 Step 2/3 : FROM clowder/extractors-simple-r-extractor${PYCLOWDER_PYTHON}:onbuild build 29-Sep-2019 19:48:07 # Executing 5 build triggers build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> dbbfd93ab5e7 build 29-Sep-2019 19:48:07 Step 3/3 : ENV R_SCRIPT="wordcount.R" R_FUNCTION="process_file" build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> f17ed902f072 build 29-Sep-2019 19:48:07 Successfully built f17ed902f072 build 29-Sep-2019 19:48:07 Successfully tagged clowder/extractors-wordcount-simple-r-extractor:latest build 29-Sep-2019 19:48:07 Sending build context to Docker daemon 8.192kB build 29-Sep-2019 19:48:07 build 29-Sep-2019 19:48:07 Step 1/7 : FROM python:3.5 build 29-Sep-2019 19:48:07 ---> 67f4589d3c88 build 29-Sep-2019 19:48:07 Step 2/7 : ENV RABBITMQ_URI="amqp://guest:guest@rabbitmq/%2F" build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> 780c06a38965 build 29-Sep-2019 19:48:07 Step 3/7 : EXPOSE 9999 build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> e35b498b2fe3 build 29-Sep-2019 19:48:07 Step 4/7 : RUN pip install pika==0.11.2 requests==2.18.4 build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> bc90da966d93 build 29-Sep-2019 19:48:07 Step 5/7 : WORKDIR /src build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> c4f7ae366418 build 29-Sep-2019 19:48:07 Step 6/7 : COPY monitor.py /src/ build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> f20e0c8c8326 build 29-Sep-2019 19:48:07 Step 7/7 : CMD python monitor.py build 29-Sep-2019 19:48:07 ---> Using cache build 29-Sep-2019 19:48:07 ---> ea2efd4a43d1 build 29-Sep-2019 19:48:07 Successfully built ea2efd4a43d1 build 29-Sep-2019 19:48:07 Successfully tagged clowder/extractors-monitor:latest simple 29-Sep-2019 19:48:07 Finished task 'docker build and push' with result: Success simple 29-Sep-2019 19:48:07 Running post build plugin 'Docker Container Cleanup' simple 29-Sep-2019 19:48:07 Running post build plugin 'NCover Results Collector' simple 29-Sep-2019 19:48:07 Running post build plugin 'Clover Results Collector' simple 29-Sep-2019 19:48:07 Running post build plugin 'npm Cache Cleanup' simple 29-Sep-2019 19:48:07 Running post build plugin 'Artifact Copier' simple 29-Sep-2019 19:48:07 Finalising the build... simple 29-Sep-2019 19:48:07 Stopping timer. simple 29-Sep-2019 19:48:07 Build CATS-PYC32-JOB1-2 completed. simple 29-Sep-2019 19:48:07 Running on server: post build plugin 'NCover Results Collector' simple 29-Sep-2019 19:48:07 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 29-Sep-2019 19:48:07 Running on server: post build plugin 'Clover Delta Calculator' simple 29-Sep-2019 19:48:07 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 29-Sep-2019 19:48:07 All post build plugins have finished simple 29-Sep-2019 19:48:07 Generating build results summary... simple 29-Sep-2019 19:48:07 Saving build results to disk... simple 29-Sep-2019 19:48:08 Logging substituted variables... simple 29-Sep-2019 19:48:08 Indexing build results... simple 29-Sep-2019 19:48:08 Finished building CATS-PYC32-JOB1-2.