Merge pull request #6200 from joshmoore/bin-omero

Remove bin/omero
ome · Jan 9, 2020 · b8b3037 · b8b3037
2 parents f694061 + 2b2fdd5
commit b8b3037
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Showing 31 changed files with 190 additions and 1,561 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -24,18 +24,41 @@ ARG RUN_IMAGE=openmicroscopy/omero-${COMPONENT}:5.6
 FROM ${BUILD_IMAGE} as build
 USER root
 ARG DEBIAN_FRONTEND=noninteractive
+
+# From omero-install: step01_ubuntu1804_ice_deps.sh
+RUN apt-get update && \
+    apt-get install -y -q \
+        build-essential \
+        wget \
+        db5.3-util \
+        libbz2-dev \
+        libdb++-dev \
+        libdb-dev \
+        libexpat-dev \
+        libmcpp-dev \
+        libssl-dev \
+        mcpp \
+        zlib1g-dev \
+ && cd /tmp \
+ && wget -q https://github.com/ome/zeroc-ice-ubuntu1804/releases/download/0.3.0/ice-3.6.5-0.3.0-ubuntu1804-amd64.tar.gz \
+ && tar xf ice-3.6.5-0.3.0-ubuntu1804-amd64.tar.gz \
+ && rm ice-3.6.5-0.3.0-ubuntu1804-amd64.tar.gz \
+ && mv ice-3.6.5-0.3.0 /opt \
+ && echo /opt/ice-3.6.5-0.3.0/lib/x86_64-linux-gnu > /etc/ld.so.conf.d/ice-x86_64.conf \
+ && ldconfig
+
 RUN apt-get update \
  && apt-get install -y ant git gradle maven python3 python3-pip python3-venv \
-      zlib1g-dev python-pillow python-numpy python-sphinx \
-      libssl-dev libbz2-dev libmcpp-dev libdb++-dev libdb-dev \
-      zeroc-ice-all-dev
+      python-pillow python-numpy python-sphinx
+
 ENV VIRTUAL_ENV=/opt/omero/server/venv3
-ENV PATH=$VIRTUAL_ENV/bin/:$PATH
+ENV PATH=/opt/ice-3.6.5-0.3.0/bin:$VIRTUAL_ENV/bin/:$PATH
 RUN mkdir -p /opt/omero/server/ \
  && python3 -m venv $VIRTUAL_ENV
 RUN python -m pip install --upgrade pip setuptools
 RUN python -m pip install https://github.com/ome/zeroc-ice-ubuntu1804/releases/download/0.2.0/zeroc_ice-3.6.5-cp36-cp36m-linux_x86_64.whl
 RUN python -m pip install flake8 future pytest
+RUN python -m pip install 'omero-py>=5.6.0.dev10'
 RUN id 1000 || useradd -u 1000 -ms /bin/bash build
 
 # TODO: would be nice to not need to copy .git since it invalidates the build frequently and takes more time
@@ -77,8 +100,7 @@ RUN rm -rf /opt/omero/server/OMERO.server
 COPY --chown=omero-server:omero-server --from=build /src/dist /opt/omero/server/OMERO.server
 USER root
 RUN yum install -y git
-RUN /opt/omero/server/venv3/bin/pip install future
-RUN sed -i 's/#!\/usr\/bin\/env python/#!\/opt\/omero\/server\/venv3\/bin\/python/' /opt/omero/server/OMERO.server/bin/omero
+
 USER omero-server
 WORKDIR /opt/omero/server/OMERO.server
 ENV VIRTUAL_ENV=/opt/omero/server/venv3

diff --git a/build.xml b/build.xml
@@ -272,11 +272,7 @@ To get started using Eclipse, execute "ant build-dev" and import the top-level
 
     <target name="release-zip" description="Zip the dist directory into ${product.name}-${omero.version}.zip">
         <zip destfile="${omero.home}/target/${product.name}-${omero.version}.zip">
-            <zipfileset dir="${dist.dir}" prefix="${product.name}-${omero.version}"
-                excludes="bin/omero"/>
-            <zipfileset dir="${dist.dir}" prefix="${product.name}-${omero.version}"
-                includes="bin/omero"
-                filemode="755"/>
+            <zipfileset dir="${dist.dir}" prefix="${product.name}-${omero.version}"/>
         </zip>
     </target>
 
@@ -308,9 +304,8 @@ To get started using Eclipse, execute "ant build-dev" and import the top-level
     <target name="release-clients" description="Zip the Python and Java zips">
         <zip destfile="${omero.home}/target/OMERO.py-${omero.version}.zip">
             <zipfileset dir="${dist.dir}" prefix="OMERO.py-${omero.version}"
-                includes="bin/**,etc/**,lib/python/**,lib/fallback/**,sql/**,share/web/**" excludes="bin/omero"/>
-            <zipfileset dir="${dist.dir}" prefix="OMERO.py-${omero.version}"
-                includes="bin/omero" filemode="755"/>
+                includes="bin/**,etc/**,lib/fallback/**,sql/**,share/web/**"/>
+            <zipfileset dir="${dist.dir}" prefix="OMERO.py-${omero.version}"/>
         </zip>
         <zip destfile="${omero.home}/target/OMERO.java-${omero.version}.zip">
             <zipfileset dir="${dist.dir}/lib/client"    prefix="OMERO.java-${omero.version}/libs" includes="**/*.jar"/>
@@ -320,11 +315,7 @@ To get started using Eclipse, execute "ant build-dev" and import the top-level
 
     <target name="release-tar" description="Tar the dist directory into ${product-name}-${omero.version}.tar.bz2">
         <tar destfile="${product.name}-${omero.version}.tar.bz2" compression="bzip2">
-            <zipfileset dir="${dist.dir}" prefix="${product.name}-${omero.version}"
-                excludes="bin/omero"/>
-            <zipfileset dir="${dist.dir}" prefix="${product.name}-${omero.version}"
-                includes="bin/omero"
-                filemode="755"/>
+            <zipfileset dir="${dist.dir}" prefix="${product.name}-${omero.version}"/>
         </tar>
     </target>
 
@@ -484,8 +475,7 @@ omero.version=${omero.version}
     <macrodef name="ice-admin">
         <element name="args" implicit="yes"/>
         <sequential>
-            <exec executable="python" dir="${dist.dir}" failonerror="true">
-                <arg value="bin/omero"/>
+            <exec executable="omero" dir="${dist.dir}" failonerror="true">
                 <arg value="admin"/>
                 <arg value="ice"/>
                 <args/>

diff --git a/components/antlib/resources/global.xml b/components/antlib/resources/global.xml
@@ -538,13 +538,54 @@
             <sequential>
                 <exec executable="python" failonerror="@{failonerror}">
                     <env key="ICE_CONFIG" value="${env.ICE_CONFIG}"/>
-                    <env key="PYTHONPATH" path="test:build/lib:${basedir}/../target/lib/python:${env.PYTHONPATH}"/>
+                    <env key="PYTHONPATH" path="test:build/lib:${env.PYTHONPATH}"/>
                     <arg value="${basedir}/setup.py"/>
                     <args/>
                 </exec>
             </sequential>
         </macrodef>
 
+        <macrodef name="download">
+            <attribute name="pkg"/>
+            <attribute name="file"/>
+            <attribute name="expected"/>
+            <attribute name="where"/>
+            <sequential>
+                <mkdir dir="@{where}"/>
+                <mkdir dir="../target/build/lib"/>
+                <local name="url_input"/>
+                <local name="url_output"/>
+                <local name="dest"/>
+                <local name="calculated"/>
+                <local name="mismatch"/>
+                <property name="dest" value="@{where}/@{file}"/>
+                <property name="url_input" value="${versions.@{pkg}-url}"/>
+                <propertyregex property="url_output"
+                  input="${url_input}"
+                  regexp="PACKAGE"
+                  replace="@{pkg}"
+                  global="true"
+                  casesensitive="true" />
+                <get dest="${dest}" usetimestamp="true">
+                    <url url="${url_output}/@{file}"/>
+                </get>
+                <checksum file="${dest}" algorithm="MD5" fileext=".md5"/>
+                <loadfile property="calculated" srcFile="${dest}.md5"/>
+                <condition property="mismatch">
+                    <and>
+                        <isset property="versions.@{pkg}-md5"/><!-- TODO: remove others -->
+                        <not>
+                            <equals arg1="@{expected}" arg2="" trim="true"/>
+                        </not>
+                        <not>
+                            <equals arg1="@{expected}" arg2="${calculated}" trim="true"/>
+                        </not>
+                    </and>
+                </condition>
+                <fail if="${mismatch}" message="@{file}: checksum error"/>
+            </sequential>
+        </macrodef>
+
         <macrodef name="makeManifest">
             <attribute name="property"/>
             <sequential>

diff --git a/components/tests/ui/README.md b/components/tests/ui/README.md
@@ -78,7 +78,7 @@ robot plugin, e.g. for a  local server:
 ```
 cd ../
 mv dist/robot_ice.config components/tests/ui/resources/
-ICE_CONFIG=$(pwd)/components/tests/ui/resources/robot_ice.config dist/bin/omero --path components/tests/ui/plugins robot config > components/tests/ui/resources/config.txt
+ICE_CONFIG=$(pwd)/components/tests/ui/resources/robot_ice.config omero --path components/tests/ui/plugins robot config > components/tests/ui/resources/config.txt
 ```
 
 Note this command will create the Robot configuration file using the

diff --git a/components/tests/ui/resources/robot.template b/components/tests/ui/resources/robot.template
@@ -36,4 +36,4 @@ ${WEBCLIENT LOGIN URL}      ${LOGIN URL}?url=%(QWEBPREFIX)s%(QSEP)swebclient%(QS
 ${USERS URL}            ${WEBADMIN WELCOME URL}experimenters/
 ${GROUPS URL}           ${WEBADMIN WELCOME URL}groups/
 
-${COMMAND}       		bin/omero
+${COMMAND}       		omero
diff --git a/components/tests/ui/robot_setup.sh b/components/tests/ui/robot_setup.sh
@@ -28,12 +28,12 @@ FILE_ANNOTATION=${FILE_ANNOTATION:-robot_file_annotation.txt}
 FILE_ANNOTATION2=${FILE_ANNOTATION2:-robot_file_annotation2.txt}
 
 # Create robot user and group
-bin/omero login root@$HOSTNAME:$PORT -w $ROOT_PASSWORD
-bin/omero group add $GROUP_NAME --ignore-existing --perms $GROUP_PERMS
-bin/omero group add $GROUP_NAME_2 --ignore-existing
-bin/omero user add $USER_NAME $USER_NAME $USER_NAME $GROUP_NAME $GROUP_NAME_2 --ignore-existing -P $USER_PASSWORD
-bin/omero user joingroup --name $USER_NAME --group-name $GROUP_NAME --as-owner
-bin/omero logout
+omero login root@$HOSTNAME:$PORT -w $ROOT_PASSWORD
+omero group add $GROUP_NAME --ignore-existing --perms $GROUP_PERMS
+omero group add $GROUP_NAME_2 --ignore-existing
+omero user add $USER_NAME $USER_NAME $USER_NAME $GROUP_NAME $GROUP_NAME_2 --ignore-existing -P $USER_PASSWORD
+omero user joingroup --name $USER_NAME --group-name $GROUP_NAME --as-owner
+omero logout
 
 # Create fake files
 touch $IMAGE_NAME
@@ -58,104 +58,104 @@ echo "Robot test file annotations" > "$FILE_ANNOTATION"
 echo "Another test file annotation" > "$FILE_ANNOTATION2"
 
 # Create robot setup
-bin/omero login $USER_NAME@$HOSTNAME:$PORT -w $USER_PASSWORD
+omero login $USER_NAME@$HOSTNAME:$PORT -w $USER_PASSWORD
 # Parse the sessions file to get session key
-key=$(bin/omero sessions key)
+key=$(omero sessions key)
 echo "Session key: $key"
 nProjects=1
 nDatasets=1
 nImages=10
 echo "Creating projects and datasets"
 for (( i=1; i<=$nProjects; i++ ))
 do
-  project=$(bin/omero obj new Project name='Project '$i)
+  project=$(omero obj new Project name='Project '$i)
   for (( j=1; j<=$nDatasets; j++ ))
   do
-    dataset=$(bin/omero obj new Dataset name='Dataset '$i-$j)
-    bin/omero obj new ProjectDatasetLink parent=$project child=$dataset
+    dataset=$(omero obj new Dataset name='Dataset '$i-$j)
+    omero obj new ProjectDatasetLink parent=$project child=$dataset
     echo "Importing images into dataset"
     for (( k=1; k<=$nImages; k++ ))
     do
-      bin/omero import -d $dataset $IMAGE_NAME --debug ERROR > show_import.log 2>&1
+      omero import -d $dataset $IMAGE_NAME --debug ERROR > show_import.log 2>&1
       imageid=$(sed -n -e 's/^Image://p' show_import.log)
-      bin/omero obj update Image:$imageid name=test_view$k
+      omero obj update Image:$imageid name=test_view$k
     done
   done
 done
 
 # Create Dataset with images for deleting
-delDs=$(bin/omero obj new Dataset name='Delete')
+delDs=$(omero obj new Dataset name='Delete')
 for (( k=1; k<=10; k++ ))
 do
-  bin/omero import -d $delDs $TINY_IMAGE_NAME --debug ERROR
+  omero import -d $delDs $TINY_IMAGE_NAME --debug ERROR
 done
 
 # Create Dataset with MIF images
-mifDs=$(bin/omero obj new Dataset name='MIF Images')
+mifDs=$(omero obj new Dataset name='MIF Images')
 for (( k=1; k<=2; k++ ))
 do
-  bin/omero import -d $mifDs $MIF_IMAGE_NAME --debug ERROR
+  omero import -d $mifDs $MIF_IMAGE_NAME --debug ERROR
 done
 
 # Create Dataset with multi channel images
-mcDs=$(bin/omero obj new Dataset name='MultiChannel Images')
+mcDs=$(omero obj new Dataset name='MultiChannel Images')
 for (( k=1; k<=2; k++ ))
 do
-  bin/omero import -d $mcDs $MULTI_C_IMAGE_NAME --debug ERROR
+  omero import -d $mcDs $MULTI_C_IMAGE_NAME --debug ERROR
 done
 
 # Create Dataset with Big Image
-bigDs=$(bin/omero obj new Dataset name='Big Images')
-bin/omero import -d $bigDs $BIG_IMAGE_NAME --debug ERROR
+bigDs=$(omero obj new Dataset name='Big Images')
+omero import -d $bigDs $BIG_IMAGE_NAME --debug ERROR
 
 # Import Plate and rename
-bin/omero import $PLATE_NAME --debug ERROR > plate_import.log 2>&1
+omero import $PLATE_NAME --debug ERROR > plate_import.log 2>&1
 plateid=$(sed -n -e 's/^Plate://p' plate_import.log)
-bin/omero obj update Plate:$plateid name=spwTests
+omero obj update Plate:$plateid name=spwTests
 # Use populate_metadata to upload and attach bulk annotation csv
 # We use testtables to only try populate if tables are working
 export OMERO_DEV_PLUGINS=1      # required to enable 'metadata' CLI
-bin/omero metadata testtables && bin/omero metadata populate Plate:$plateid --file $BULK_ANNOTATION_CSV
+omero metadata testtables && omero metadata populate Plate:$plateid --file $BULK_ANNOTATION_CSV
 
 # Run script to populate WellSamples with posX and posY values
-PYTHONPATH=./lib/python python $WELLSCRIPT $HOSTNAME $PORT $key $plateid
+python $WELLSCRIPT $HOSTNAME $PORT $key $plateid
 
 # Import Tiny Plate (single acquisition & well) and rename
-bin/omero import $TINY_PLATE_NAME --debug ERROR > show_import.log 2>&1
+omero import $TINY_PLATE_NAME --debug ERROR > show_import.log 2>&1
 plateid=$(sed -n -e 's/^Plate://p' show_import.log)
-bin/omero obj update Plate:$plateid name=tinyPlate
+omero obj update Plate:$plateid name=tinyPlate
 # Import Image into Project/Dataset and rename for test
-showP=$(bin/omero obj new Project name='showProject')
-showD=$(bin/omero obj new Dataset name='showDataset')
-bin/omero obj new ProjectDatasetLink parent=$showP child=$showD
+showP=$(omero obj new Project name='showProject')
+showD=$(omero obj new Dataset name='showDataset')
+omero obj new ProjectDatasetLink parent=$showP child=$showD
 for (( k=1; k<=2; k++ ))
 do
-  bin/omero import -d $showD $IMAGE_NAME --debug ERROR > show_import.log 2>&1
+  omero import -d $showD $IMAGE_NAME --debug ERROR > show_import.log 2>&1
   imageid=$(sed -n -e 's/^Image://p' show_import.log)
-  bin/omero obj update Image:$imageid name=testShowImage$k
+  omero obj update Image:$imageid name=testShowImage$k
 done
 
 # Create Screen with empty plates for Create Scenario
-scrDs=$(bin/omero obj new Screen name='CreateScenario')
+scrDs=$(omero obj new Screen name='CreateScenario')
 for (( k=1; k<=6; k++ ))
 do
-  bin/omero import -r $scrDs $TINY_PLATE_NAME --debug ERROR
+  omero import -r $scrDs $TINY_PLATE_NAME --debug ERROR
 done
 
 # Create Orphaned Images for Create Scenario
 for (( k=1; k<=10; k++ ))
 do
-  bin/omero import $TINY_IMAGE_NAME --debug ERROR
+  omero import $TINY_IMAGE_NAME --debug ERROR
 done
 
 # Upload files and create FileAnnotations
-ofile=$(bin/omero upload $FILE_ANNOTATION)
-bin/omero obj new FileAnnotation file=$ofile
-ofile2=$(bin/omero upload $FILE_ANNOTATION2)
-bin/omero obj new FileAnnotation file=$ofile2
+ofile=$(omero upload $FILE_ANNOTATION)
+omero obj new FileAnnotation file=$ofile
+ofile2=$(omero upload $FILE_ANNOTATION2)
+omero obj new FileAnnotation file=$ofile2
 
 # Logout
-bin/omero logout
+omero logout
 
 # Create ice.config file
 echo "omero.host=$HOSTNAME" > "$CONFIG_FILENAME"

diff --git a/components/tools/OmeroFS/build.xml b/components/tools/OmeroFS/build.xml
@@ -32,7 +32,7 @@
 
     <target name="integration" depends="python-integration" unless="env.NOPYTHON"/>
 
-    <target name="tools-init" depends="python-download" unless="env.NOPYTHON"/>
+    <target name="tools-init" unless="env.NOPYTHON"/>
 
     <target name="tools-build" depends="tools-init" description="Creates all artifacts for tools/target" unless="env.NOPYTHON"/>