use v1.1 for containers

cytomine · Sep 7, 2017 · b50ad35 · b50ad35
1 parent 9d50bb7
commit b50ad35
Show file tree

Hide file tree

Showing 21 changed files with 71 additions and 64 deletions.
diff --git a/auto_backup/Dockerfile b/auto_backup/Dockerfile
@@ -14,7 +14,7 @@
 # limitations under the License.
 #
 
-FROM cytomine/base
+FROM cytomine/base:v1.1
 MAINTAINER "Cytomine Team support@cytomine.be"
 
 RUN apt-get update -y && apt-get -y install \

diff --git a/bioformat/Dockerfile b/bioformat/Dockerfile
@@ -14,11 +14,11 @@
 # limitations under the License.
 #
 
-FROM cytomine/java8
+FROM cytomine/java8:v1.1
 
 MAINTAINER Cytomine Team "support@cytomine.be"
 
-RUN cd /tmp/ && wget -q http://cytomine.be/release/bioformat/BioFormatStandAlone.tar.gz -O BioFormatStandAlone.tar.gz && tar -zxvf BioFormatStandAlone.tar.gz
+RUN cd /tmp/ && wget -q https://github.com/cytomine/Cytomine-tools/releases/download/v1.1/BioFormatStandAlone.tar.gz -O BioFormatStandAlone.tar.gz && tar -zxvf BioFormatStandAlone.tar.gz
 
 ADD crontab /tmp/crontab
 ADD check_bioformat.py /tmp/check_bioformat.py

diff --git a/core/Dockerfile b/core/Dockerfile
@@ -14,14 +14,14 @@
 # limitations under the License.
 #
 
-FROM cytomine/tomcat7 
+FROM cytomine/tomcat7:v1.1
 
 MAINTAINER Cytomine Team "support@cytomine.be"
 
 ADD cytomineconfig.groovy /tmp/cytomineconfig.groovy
 
-RUN rm -r /var/lib/tomcat7/webapps/* && cd /var/lib/tomcat7/webapps/  && wget http://cytomine.be/release/core/last_ROOT.war -O ROOT.war
-RUN cd /var/lib/tomcat7/  && wget https://github.com/cytomine/Cytomine-core/releases/download/v1.0/restapidoc.json -O restapidoc.json
+RUN rm -r /var/lib/tomcat7/webapps/* && cd /var/lib/tomcat7/webapps/  && wget https://github.com/cytomine/Cytomine-core/releases/download/v1.1/cytomine.war -O ROOT.war
+RUN cd /var/lib/tomcat7/  && wget https://github.com/cytomine/Cytomine-core/releases/download/v1.1/restapidoc.json -O restapidoc.json
 
 ADD setenv.sh /tmp/setenv.sh
 RUN chmod +x /tmp/setenv.sh

diff --git a/data_for_test/Dockerfile b/data_for_test/Dockerfile
@@ -14,12 +14,12 @@
 # limitations under the License.
 #
 
-FROM cytomine/java8
+FROM cytomine/java8:v1.1
 
 MAINTAINER Cytomine Team "support@cytomine.be"
 
 RUN apt-get update -y && apt-get install -y groovy
-RUN cd /tmp/  && wget -q https://github.com/cytomine/Cytomine-java-client/releases/download/v1.1.1/cytomine-java-client-1.1.1.jar -O Cytomine-client-java.jar
+RUN cd /tmp/  && wget -q https://github.com/cytomine/Cytomine-java-client/releases/download/v1.1.2/cytomine-java-client.jar -O Cytomine-client-java.jar
 RUN cd /tmp/ && wget -q "http://cytomine.be/release/demo_script.zip" -O demo_script.zip && unzip demo_script.zip
 
 ADD injectdata.groovy /tmp/injectdata.groovy

diff --git a/iipCyto/Dockerfile b/iipCyto/Dockerfile
@@ -14,7 +14,7 @@
 # limitations under the License.
 #
 
-FROM cytomine/iipbase 
+FROM cytomine/iipbase:v1.1
 
 MAINTAINER Cytomine Team "support@cytomine.be"
 
@@ -23,7 +23,7 @@ RUN cd /tmp && wget http://launchpadlibrarian.net/147357170/libopenjpeg2_1.3%2Bd
 RUN cd /tmp && wget http://launchpadlibrarian.net/147357169/libopenjpeg-dev_1.3%2Bdfsg-4.6ubuntu2_amd64.deb && dpkg -i libopenjpeg-dev_1.3+dfsg-4.6ubuntu2_amd64.deb
 
 #openslide 2015/04/21
-RUN cd /tmp && git clone https://github.com/openslide/openslide && cd /tmp/openslide && git checkout 4cd4b83c3ffff0382126d0618c85407f2c469b28 && autoreconf -i && ./configure && make && make install
+RUN cd /tmp && git clone https://github.com/openslide/openslide && cd /tmp/openslide && git checkout tags/v3.4.1 && autoreconf -i && ./configure && make && make install
 
 #IIP Image Server
 RUN cd /tmp && git clone https://github.com/cytomine/iipsrv && cd /tmp/iipsrv && git checkout 6a42b2e28e07347be7e42048be72e078c8bc1ef7 && sh autogen.sh && LDFLAGS="-L/usr/local/lib -lopenslide" CPPFLAGS="-I/usr/local/include/openslide" ./configure && make 

diff --git a/iipOfficial/Dockerfile b/iipOfficial/Dockerfile
@@ -14,7 +14,7 @@
 # limitations under the License.
 #
 
-FROM cytomine/iipbase 
+FROM cytomine/iipbase:v1.1
 
 MAINTAINER Cytomine Team "support@cytomine.be"
 

diff --git a/iipbase/Dockerfile b/iipbase/Dockerfile
@@ -14,7 +14,7 @@
 # limitations under the License.
 #
 
-FROM cytomine/base
+FROM cytomine/base:v1.1
 
 MAINTAINER Cytomine Team "support@cytomine.be"
 
@@ -24,13 +24,24 @@ RUN apt-get -y update && \
       libjpeg8-dev \
       libmemcached-dev \
       libopenjpeg-dev \
+      libssl-dev \
       libtiff5-dev \
       psmisc \
       software-properties-common && \
-    apt-get -y build-dep iipimage-server nginx openslide
+      apt-get -y build-dep iipimage-server openslide
+
+
+RUN mkdir -p /opt/nginx
+WORKDIR /opt/nginx
+RUN wget http://nginx.org/download/nginx-1.10.1.tar.gz
+RUN tar -zxvf nginx-1.10.1.tar.gz
+
+RUN git clone https://github.com/vkholodkov/nginx-upload-module.git
+RUN cd nginx-upload-module/ && git checkout 2.2 && git reset --hard && git clean -f && git pull && git status
+
+WORKDIR /opt/nginx/nginx-1.10.1
+RUN ./configure --add-module=/opt/nginx/nginx-upload-module && make && sudo make install
 
-RUN cd /tmp && wget http://nginx.org/download/nginx-1.4.4.tar.gz && tar -zxvf ./nginx-1.4.4.tar.gz
-RUN cd /tmp/nginx-1.4.4 && ./configure && make && make install
 
 RUN mkdir -p /opt/cytomine/bin
 

diff --git a/ims/Dockerfile b/ims/Dockerfile
@@ -14,7 +14,7 @@
 # limitations under the License.
 #
 
-FROM cytomine/tomcat7
+FROM cytomine/tomcat7:v1.1
 
 MAINTAINER Cytomine Team "support@cytomine.be"
 
@@ -57,8 +57,8 @@ EXPOSE 8082
 
 RUN ldconfig -v
 
-RUN rm -r /var/lib/tomcat7/webapps/* && cd /var/lib/tomcat7/webapps/ && wget -q http://cytomine.be/release/ims/last_ROOT.war -O ROOT.war
-RUN cd /var/lib/tomcat7/  && wget -q https://github.com/cytomine/Cytomine-IMS/releases/download/v1.0/restapidoc.json -O restapidoc.json
+RUN rm -r /var/lib/tomcat7/webapps/* && cd /var/lib/tomcat7/webapps/ && wget -q https://github.com/cytomine/Cytomine-IMS/releases/download/v1.1/IMS.war -O ROOT.war
+RUN cd /var/lib/tomcat7/  && wget -q https://github.com/cytomine/Cytomine-IMS/releases/download/v1.1/restapidoc.json -O restapidoc.json
 
 ADD deploy.sh /tmp/deploy.sh
 RUN chmod +x /tmp/deploy.sh

diff --git a/iris/Dockerfile b/iris/Dockerfile
@@ -14,7 +14,7 @@
 # limitations under the License.
 #
 
-FROM cytomine/tomcat7 
+FROM cytomine/tomcat7:v1.1
 
 MAINTAINER Cytomine Team "support@cytomine.be"
 

diff --git a/java8/Dockerfile b/java8/Dockerfile
@@ -14,7 +14,7 @@
 # limitations under the License.
 #
 
-FROM cytomine/base
+FROM cytomine/base:v1.1
 
 MAINTAINER Cytomine Team "support@cytomine.be"
 

diff --git a/memcached/Dockerfile b/memcached/Dockerfile
@@ -14,7 +14,7 @@
 # limitations under the License.
 #
 
-FROM cytomine/base
+FROM cytomine/base:v1.1
 
 MAINTAINER Cytomine Team<support@cytomine.be>
 

diff --git a/mongodb/Dockerfile b/mongodb/Dockerfile
@@ -14,7 +14,7 @@
 # limitations under the License.
 #
 
-FROM cytomine/base
+FROM cytomine/base:v1.1
 MAINTAINER "Cytomine Team support@cytomine.be"
 
 # Install MongoDB.

diff --git a/nginx/Dockerfile b/nginx/Dockerfile
@@ -14,7 +14,7 @@
 # limitations under the License.
 #
 
-FROM cytomine/base
+FROM cytomine/base:v1.1
 
 MAINTAINER Cytomine Team "support@cytomine.be"
 

diff --git a/postgis/Dockerfile b/postgis/Dockerfile
@@ -14,7 +14,7 @@
 # limitations under the License.
 #
 
-FROM cytomine/postgres
+FROM cytomine/postgres:v1.1
 MAINTAINER "Cytomine Team support@cytomine.be"
 
 RUN apt-get update && apt-get -y -q install postgresql-9.3-postgis-2.1

diff --git a/postgres/Dockerfile b/postgres/Dockerfile
@@ -14,7 +14,7 @@
 # limitations under the License.
 #
 
-FROM cytomine/base
+FROM cytomine/base:v1.1
 MAINTAINER "Cytomine Team support@cytomine.be"
 
 # Add the PostgreSQL PGP key to verify their Debian packages.

diff --git a/rabbitmq/Dockerfile b/rabbitmq/Dockerfile
@@ -14,7 +14,7 @@
 # limitations under the License.
 #
 
-FROM cytomine/base
+FROM cytomine/base:v1.1
 
 MAINTAINER Cytomine Team "support@cytomine.be"
 

diff --git a/retrieval/Dockerfile b/retrieval/Dockerfile
@@ -14,7 +14,7 @@
 # limitations under the License.
 #
 
-FROM cytomine/java8
+FROM cytomine/java8:v1.1
 
 MAINTAINER "Cytomine Team support@cytomine.be"
 

diff --git a/software_router/Dockerfile b/software_router/Dockerfile
@@ -14,7 +14,7 @@
 # limitations under the License.
 #
 
-FROM cytomine/java8
+FROM cytomine/java8:v1.1
 
 MAINTAINER Cytomine Team "support@cytomine.be"
 
@@ -29,10 +29,10 @@ RUN conda install joblib=0.11 --yes
 RUN conda install pillow=3.4.2 --yes
 RUN conda install numpy=1.11.2 --yes
 RUN conda install shapely --yes
-#RUN conda install opencv --yes
 RUN conda install scipy=0.18.1 --yes
 RUN conda install scikit-learn=0.18.1 --yes
-RUN conda install opencv=3.1.0 --yes
+RUN conda install opencv=2.4.10 --yes
+RUN conda install libgfortran==1 --yes
 
 RUN apt-get -y update && apt-get install -y \
       apt-transport-https \
@@ -53,18 +53,17 @@ RUN dpkg-reconfigure locales
 
 # Cytomine-python-datamining
 
-RUN mkdir -p /root/Cytomine/ && cd /root/Cytomine/ && git clone https://github.com/cytomine/Cytomine-python-datamining.git && cd Cytomine-python-datamining/ && git checkout 11f23f28a1921af29ba7d9e05333a9386f87458c
-
+RUN mkdir -p /root/Cytomine/ && cd /root/Cytomine/ && git clone https://github.com/cytomine/Cytomine-python-datamining.git && cd Cytomine-python-datamining/ && git checkout tags/v1.1
 RUN cd /root/Cytomine/Cytomine-python-datamining/cytomine-datamining/algorithms/pyxit/ && cython _estimator.pyx && python setup.py build && python setup.py install
 
 
 # Cytomine-python-client
 
-RUN cd /root/Cytomine/ && git clone https://github.com/cytomine/Cytomine-python-client.git && cd Cytomine-python-client/ && git checkout tags/v1.0
+RUN cd /root/Cytomine/ && git clone https://github.com/cytomine/Cytomine-python-client.git && cd Cytomine-python-client/ && git checkout tags/v1.1
 RUN cd /root/Cytomine/Cytomine-python-client/client/ && python setup.py build && python setup.py install
 RUN cd /root/Cytomine/Cytomine-python-client/utilities/ &&  python setup.py build && python setup.py install
 
-RUN cd /root/Cytomine/ && git clone https://github.com/cytomine/Cytomine-tools.git && cd Cytomine-tools/ && git checkout tags/v1.0
+RUN cd /root/Cytomine/ && git clone https://github.com/cytomine/Cytomine-tools.git && cd Cytomine-tools/ && git checkout tags/v1.1
 
 
 # Groovy Installation
@@ -74,8 +73,8 @@ RUN cd /tmp/ && curl http://get.sdkman.io | bash
 RUN /bin/bash -c "source /root/.sdkman/bin/sdkman-init.sh && sdk install groovy 2.4.4 --yes"
 
 
-RUN mkdir -p /software_router && cd /software_router && wget http://cytomine.be/release/java/Cytomine-software-router.jar -O Cytomine-software-router.jar
-RUN cd /software_router && wget http://cytomine.be/release/java/cytomine-java-client.jar -O cytomine-java-client.jar
+RUN mkdir -p /software_router && cd /software_router && wget https://github.com/cytomine/Cytomine-software-router/releases/download/v1.1/Cytomine-software-router.jar -O Cytomine-software-router.jar
+RUN cd /software_router && wget https://github.com/cytomine/Cytomine-java-client/releases/download/v1.1.2/cytomine-java-client.jar -O cytomine-java-client.jar
 
 # Install Docker from Docker Inc. repositories.
 RUN curl -sSL https://get.docker.com/ | sh
@@ -85,9 +84,7 @@ ADD ./wrapdocker /usr/local/bin/wrapdocker
 RUN chmod +x /usr/local/bin/wrapdocker
 
 
-#RUN conda create -n sldc python=2.7 pillow numpy joblib shapely opencv scipy && source activate sldc
-
-RUN git clone https://github.com/waliens/sldc.git && cd sldc && python setup.py install
+#RUN git clone https://github.com/waliens/sldc.git && cd sldc && python setup.py install
 
 ADD config.groovy /tmp/config.groovy
 
@@ -96,14 +93,10 @@ ENV GROOVY_HOME /root/.sdkman/candidates/groovy/current
 ENV GROOVY_PATH /root/.sdkman/candidates/groovy/current/bin/groovy
 
 RUN mkdir -p /software_router/algo
-RUN echo "Maj tar"
-ADD cytomineEnv.tar.gz /root/miniconda2/envs
 
 ADD deploy.sh /tmp/deploy.sh
 RUN chmod +x /tmp/deploy.sh
 ADD injectSoftware.groovy /tmp/injectSoftware.groovy
 RUN chmod +x /tmp/injectSoftware.groovy
 
-ADD get_and_move.py /tmp/get_and_move.py
-
 ENTRYPOINT ["/tmp/deploy.sh"]
diff --git a/software_router/injectSoftware.groovy b/software_router/injectSoftware.groovy
@@ -45,7 +45,7 @@ println "LandMark added"
 SoftwareExample.addSoftwareExportLandmark(cytomine);
 println "Export LandMark added"
 
-SoftwareExample.addSoftwareGlmBuilder(cytomine);
+/*SoftwareExample.addSoftwareGlmBuilder(cytomine);
 println "GlmBuilder added"
 SoftwareExample.addSoftwareDmblLandmarkModelBuilder(cytomine);
 println "DmblLandmarkModelBuilder added"
@@ -56,7 +56,7 @@ println "LandmarkGenericPredictor added"
 SoftwareExample.addSoftwareLandmarkDmblPredictor(cytomine);
 println "LandmarkDmblPredictor added"
 SoftwareExample.addSoftwareLandmarkLcPredictor(cytomine);
-println "LandmarkLcPredictor added"
+println "LandmarkLcPredictor added"*/
 
 
 println "DONE"