pulled the latest and resolved conflicts

VirtualFlyBrain · Jul 1, 2019 · 0922f63 · 0922f63
2 parents 05ed84d + 2c64c4e
commit 0922f63
Show file tree

Hide file tree

Showing 9 changed files with 103 additions and 49 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -49,6 +49,12 @@ RUN ../copy.sh https://github.com/VirtualFlyBrain/uk.ac.vfb.geppetto.git "${targ
   mvn -Dhttps.protocols=TLSv1.2 -DskipTests --quiet install &&\
   rm -rf src
 
+RUN ../copy.sh https://github.com/openworm/org.geppetto.model.swc.git "${targetBranch}" "${originBranch}" "${defaultBranch}" &&\
+  cd org.geppetto.model.swc &&\
+  /bin/echo -e "\e[96mMaven install org.geppetto.model.swc\e[0m" &&\
+  mvn -Dhttps.protocols=TLSv1.2 -DskipTests --quiet install &&\
+  rm -rf src
+
 RUN ../copy.sh https://github.com/openworm/org.geppetto.frontend.git "${targetBranch}" "${originBranch}" "${defaultBranch}"
 
 RUN cd $HOME/workspace/org.geppetto.frontend/src/main &&\
@@ -63,11 +69,16 @@ RUN cd $HOME/workspace/org.geppetto.frontend &&\
   grep -rnwl "$HOME/workspace/" -e "UA-45841517-1" | xargs sed -i "s|UA-45841517-1|${googleAnalyticsSiteCode}|g" &&\
   mvn -Dhttps.protocols=TLSv1.2 -DcontextPath=org.geppetto.frontend -DuseSsl=false -DskipTests install &&\
   rm -rf src
-
+
+COPY dockerFiles/geppetto.plan $HOME/workspace/org.geppetto/geppetto.plan
+COPY dockerFiles/config.json $HOME/workspace/org.geppetto/utilities/source_setup/config.json
+COPY dockerFiles/startup.sh /
+
 WORKDIR $HOME
 RUN mkdir rm $SERVER_HOME/./repository/usr
 RUN cd $HOME/workspace/org.geppetto/utilities/source_setup && python update_server.py
 
 
 EXPOSE 8080
-CMD [ "/bin/bash", "-c", "$SERVER_HOME/bin/startup.sh" ]
+EXPOSE 8443
+CMD [ "/bin/bash", "-c", "/startup.sh" ]
diff --git a/components/VFBMain.js b/components/VFBMain.js
@@ -844,14 +844,16 @@ export default class VFBMain extends React.Component {
           showButtonBar={true}
           termInfoName={this.termInfoName}
           termInfoId={this.termInfoId}
-          order={['Name',
-                  'Alternative Names',
-                  'Query For',
-                  'Depicts',
+          order={['Label',
+                  'Types',
+                  'Parents',
                   'Thumbnail',
-                  'Relationship',
+                  'Examples',
+                  'Relationships',
+                  'Query For',
                   'Description',
                   'References',
+                  'Cross References',
                   'Aligned To',
                   'Download']} /></div>)
     } else if (component === "sliceViewer") {

diff --git a/components/configuration/spotlightConfiguration.js b/components/configuration/spotlightConfiguration.js
@@ -71,7 +71,7 @@ var spotlightConfig = {
 
 var spotlightDataSourceConfig = {
   VFB: {
-    url: "http://solr.virtualflybrain.org/solr/ontology/select?fl=short_form,label,synonym,id,type,has_narrow_synonym_annotation,has_broad_synonym_annotation&start=0&fq=ontology_name:(vfb)&rows=250&bq=is_obsolete:false%5E100.0%20shortform_autosuggest:VFB*%5E110.0%20shortform_autosuggest:FBbt*%5E100.0%20is_defining_ontology:true%5E100.0%20label_s:%22%22%5E2%20synonym_s:%22%22%20in_subset_annotation:BRAINNAME%5E3%20short_form:FBbt_00003982%5E2&q=$SEARCH_TERM$%20OR%20$SEARCH_TERM$*%20OR%20*$SEARCH_TERM$*&defType=edismax&qf=label%20synonym%20label_autosuggest_ws%20label_autosuggest_e%20label_autosuggest%20synonym_autosuggest_ws%20synonym_autosuggest_e%20synonym_autosuggest%20shortform_autosuggest%20has_narrow_synonym_annotation%20has_broad_synonym_annotation&wt=json&indent=true", 
+    url: "https://solr.virtualflybrain.org/solr/ontology/select?fl=short_form,label,synonym,id,type,has_narrow_synonym_annotation,has_broad_synonym_annotation&start=0&fq=ontology_name:(vfb)&rows=100&bq=is_obsolete:false%5E100.0%20shortform_autosuggest:VFB*%5E110.0%20shortform_autosuggest:FBbt*%5E100.0%20is_defining_ontology:true%5E100.0%20label_s:%22%22%5E2%20synonym_s:%22%22%20in_subset_annotation:BRAINNAME%5E3%20short_form:FBbt_00003982%5E2&q=$SEARCH_TERM$%20OR%20$SEARCH_TERM$*%20OR%20*$SEARCH_TERM$*&defType=edismax&qf=label%20synonym%20label_autosuggest_ws%20label_autosuggest_e%20label_autosuggest%20synonym_autosuggest_ws%20synonym_autosuggest_e%20synonym_autosuggest%20shortform_autosuggest%20has_narrow_synonym_annotation%20has_broad_synonym_annotation&wt=json&indent=true", 
     crossDomain: true,
     id: "short_form",
     label: { field: "label", formatting: "$VALUE$" },

diff --git a/css/VFBMain.less b/css/VFBMain.less
@@ -217,3 +217,8 @@
     background-color: #252323;
     color: #11bffe;
 }
+
+// query results rows 
+.griddle-body {
+	font-size: 14px !important;
+}
diff --git a/css/VFBTermInfo.less b/css/VFBTermInfo.less
@@ -278,7 +278,7 @@ li>span.label.types{
     background-color:darkgreen !Important;
 }
 
- .label.types>.label.label-Publication {
+ .label.types>.label.label-pub {
     background-color:blue !Important;
 }
 
@@ -287,7 +287,7 @@ li>span.label.types{
 }
 
  .label.types>.label.label-Person {
-    background-color:#22ceec !Important;
+    background-color:#0f8398 !Important;
 }
 
   .label.types>.label.label-Neuron {
@@ -307,27 +307,27 @@ li>span.label.types{
 }
 
  .label.types>.label.label-GABAergic {
-    background-color:#d3e912 !Important;
+    background-color:#ab6f09 !Important;
 }
 
  .label.types>.label.label-Dopaminergic {
-    background-color:#d3e912 !Important;
+    background-color:#ab6f09 !Important;
 }
 
  .label.types>.label.label-Cholinergic {
-    background-color:#d3e912 !Important;
+    background-color:#ab6f09 !Important;
 }
 
  .label.types>.label.label-Glutamatergic {
-    background-color:#d3e912 !Important;
+    background-color:#ab6f09 !Important;
 }
 
  .label.types>.label.label-Octopaminergic {
-    background-color:#d3e912 !Important;
+    background-color:#ab6f09 !Important;
 }
 
  .label.types>.label.label-Serotonergic {
-    background-color:#d3e912 !Important;
+    background-color:#ab6f09 !Important;
 }
 
  .label.types>.label.label-Motor_neuron {

diff --git a/dockerFiles/config.json b/dockerFiles/config.json
@@ -0,0 +1,40 @@
+{
+  "sourcesdir": "..//..//..//",
+  "repos": [
+    {
+      "name": "org.geppetto.core",
+      "url": "",
+      "auto_install": "yes"
+    },
+    {
+      "name": "org.geppetto.datasources",
+      "url": "",
+      "auto_install": "yes"
+    },
+    {
+      "name": "org.geppetto.frontend",
+      "url": "",
+      "auto_install": "yes"
+    },
+    {
+      "name": "org.geppetto.model",
+      "url": "",
+      "auto_install": "yes"
+    },
+    {
+      "name": "org.geppetto.model.swc",
+      "url": "",
+      "auto_install": "yes"
+    },
+    {
+      "name": "org.geppetto.simulation",
+      "url": "",
+      "auto_install": "yes"
+    },
+    {
+      "name": "uk.ac.vfb.geppetto",
+      "url": "",
+      "auto_install": "yes"
+    }
+  ]
+}
diff --git a/dockerFiles/geppetto.plan b/dockerFiles/geppetto.plan
@@ -1,10 +1,10 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <plan name="multi-artifact.plan" version="1.0.0" scoped="true" atomic="true" xmlns="http://www.springsource.org/schema/dm-server/plan" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.springsource.org/schema/dm-server/plan http://www.springsource.org/schema/dm-server/plan/springsource-dm-server-plan.xsd">
-	<artifact type="bundle" name="org.geppetto.model" version="%VERSION%"/>
-	<artifact type="bundle" name="org.geppetto.core" version="%VERSION%"/>
-	<artifact type="bundle" name="org.geppetto.model.swc" version="%VERSION%"/>
-	<artifact type="bundle" name="org.geppetto.simulation" version="%VERSION%"/>
-	<artifact type="bundle" name="org.geppetto.datasources" version="%VERSION%"/>
-	<artifact type="bundle" name="uk.ac.vfb.geppetto" version="%VERSION%"/>
-	<artifact type="bundle" name="org.geppetto.frontend" version="%VERSION%"/>
-</plan>
+	<artifact type="bundle" name="org.geppetto.model" version="1.0.0"/>
+	<artifact type="bundle" name="org.geppetto.core" version="1.0.0"/>
+	<artifact type="bundle" name="org.geppetto.model.swc" version="1.0.0"/>
+	<artifact type="bundle" name="org.geppetto.simulation" version="1.0.0"/>
+	<artifact type="bundle" name="org.geppetto.datasources" version="1.0.0"/>
+	<artifact type="bundle" name="uk.ac.vfb.geppetto" version="1.0.0"/>
+	<artifact type="bundle" name="org.geppetto.frontend" version="1.0.0"/>
+</plan>
diff --git a/dockerFiles/startup.sh b/dockerFiles/startup.sh
@@ -1,24 +1,20 @@
 #!/bin/bash
 
 # Swap servers
-grep -rls pdb.virtualflybrain.org /home/ | xargs sed -i "s@pdb.virtualflybrain.org@$VFB_PDB_SERVER@g" &
-grep -rls owl.virtualflybrain.org /opt/geppetto/ | xargs sed -iv "s@owl.virtualflybrain.org@$VFB_OWL_SERVER@g"	grep -rls owl.virtualflybrain.org /home/ | xargs sed -i "s@owl.virtualflybrain.org@$VFB_OWL_SERVER@g" &
-grep -rls solr.virtualflybrain.org /opt/geppetto/ | xargs sed -iv "s@http://solr.virtualflybrain.org/solr/ontology/select@$SOLR_SERVER@g"	grep -rls solr.virtualflybrain.org /home/ | xargs sed -i "s@http://solr.virtualflybrain.org/solr/ontology/select@$SOLR_SERVER@g" &
+grep -rls pdb.virtualflybrain.org $HOME/ | xargs sed -i "s@pdb.virtualflybrain.org@$VFB_PDB_SERVER@g" &
+grep -rls owl.virtualflybrain.org $HOME/workspace/ | xargs sed -iv "s@owl.virtualflybrain.org@$VFB_OWL_SERVER@g"	grep -rls owl.virtualflybrain.org /home/ | xargs sed -i "s@owl.virtualflybrain.org@$VFB_OWL_SERVER@g" &
+grep -rls solr.virtualflybrain.org $HOME/workspace/ | xargs sed -iv "s@http://solr.virtualflybrain.org/solr/ontology/select@$SOLR_SERVER@g"	grep -rls solr.virtualflybrain.org /home/ | xargs sed -i "s@http://solr.virtualflybrain.org/solr/ontology/select@$SOLR_SERVER@g" &
 
 #Start a logfile
 mkdir -p $SERVER_HOME/serviceability/logs
 echo 'Start of log...' > $SERVER_HOME/serviceability/logs/log.log
 
-# deploy Geppetto
-cd /opt/geppetto/org.geppetto/utilities/source_setup 
-python update_server.py
+# re-deploy Geppetto
+cd $HOME/workspace/org.geppetto/utilities/source_setup && python update_server.py
 
 # set java memory maximum 
 sed 's/XX:MaxPermSize=512m/XX:MaxPermSize=$MAXSIZE/g' -i $SERVER_HOME/bin/dmk.sh
 sed 's/Xmx512m/Xmx$MAXSIZE/' -i $SERVER_HOME/bin/dmk.sh
-# Remove redirect in tomcat config
-sed 's\redirectPort="8443"\\g' -i $SERVER_HOME/configuration/tomcat-server.xml
-
 
 # output log
 tail -F --retry $SERVER_HOME/serviceability/logs/log.log &