4217 glassfish5

conf/docker/build.sh

@@ -28,14 +28,14 @@ else
 fi
 echo Images will be pushed to Docker Hub with the tag \"$TAG\".
 # Use "conf" directory as context so we can copy schema.xml into Solr image.
-docker build -t iqss/dataverse-solr:$TAG -f solr/Dockerfile ../../conf
-docker push iqss/dataverse-solr:$TAG
+#docker build -t iqss/dataverse-solr:$TAG -f solr/Dockerfile ../../conf
+#docker push iqss/dataverse-solr:$TAG
 # TODO: Think about if we really need dataverse.war because it's in dvinstall.zip.
 # FIXME: Automate the building of dataverse.war and dvinstall.zip. Think about https://github.com/IQSS/dataverse/issues/3974 and https://github.com/IQSS/dataverse/pull/3975
 cp ../../target/dataverse*.war dataverse-glassfish/dataverse.war
 cp ../../scripts/installer/dvinstall.zip dataverse-glassfish
 cp ../../doc/sphinx-guides/source/_static/util/default.config dataverse-glassfish
-cp ../../downloads/glassfish-4.1.zip dataverse-glassfish
+cp ../../downloads/glassfish-5.0.zip dataverse-glassfish
 cp ../../downloads/weld-osgi-bundle-2.2.10.Final-glassfish4.jar dataverse-glassfish
 docker build -t iqss/dataverse-glassfish:$TAG dataverse-glassfish
 # FIXME: Check the output of `docker build` and only push on success.

conf/docker/dataverse-glassfish/.gitignore

@@ -1,4 +1,4 @@
-glassfish-4.1.zip
+glassfish-5.0.zip
 weld-osgi-bundle-2.2.10.Final-glassfish4.jar
 dvinstall.zip
 dataverse.war

conf/docker/dataverse-glassfish/Dockerfile

@@ -1,7 +1,7 @@
 FROM centos:7.2.1511
 MAINTAINER Dataverse (support@dataverse.org)
 
-COPY glassfish-4.1.zip /tmp
+COPY glassfish-5.0.zip /tmp
 COPY weld-osgi-bundle-2.2.10.Final-glassfish4.jar /tmp
 COPY default.config /tmp
 COPY dvinstall.zip /tmp
@@ -33,16 +33,12 @@ RUN find /tmp
 #
 #RUN exitEarly
 
-# Install Glassfish 4.1
+# Install Glassfish 5.0
 
 RUN cd /tmp \ 
-    && unzip glassfish-4.1.zip \
-    && mv glassfish4 /usr/local \
-    && cd /usr/local/glassfish4/glassfish/modules \
-    && rm weld-osgi-bundle.jar \
-    && cp /tmp/weld-osgi-bundle-2.2.10.Final-glassfish4.jar . \
-    #FIXME: Patch Grizzly too!
-    && echo "Done installing and patching Glassfish"
+    && unzip glassfish-5.0.zip \
+    && mv glassfish5 /usr/local \
+    && echo "Done installing Glassfish"
 
 RUN chmod g=u /etc/passwd
 

doc/sphinx-guides/source/_static/util/default.config

@@ -1,7 +1,8 @@
 HOST_DNS_ADDRESS	localhost
-GLASSFISH_DIRECTORY	/usr/local/glassfish4
+GLASSFISH_DIRECTORY	/usr/local/glassfish5
 ADMIN_EMAIL	 
-MAIL_SERVER	mail.hmdc.harvard.edu
+MAIL_SERVER	localhost
+POSTGRES_ADMIN_USERNAME	postgres
 POSTGRES_ADMIN_PASSWORD	secret
 POSTGRES_SERVER	127.0.0.1
 POSTGRES_PORT	5432

doc/sphinx-guides/source/developers/dev-environment.rst

@@ -27,6 +27,8 @@ Glassfish
 
 As a `Java Enterprise Edition <http://en.wikipedia.org/wiki/Java_Platform,_Enterprise_Edition>`_ 7 (Java EE 7) application, Dataverse requires an applications server to run.
 
+FIXME: Update to Glassfish 5
+
 Glassfish 4.1 is required (not any earlier or later versions until https://github.com/IQSS/dataverse/issues/2628 is resolved), which can be downloaded from http://download.oracle.com/glassfish/4.1/release/glassfish-4.1.zip . If you have downloaded Glassfish as part of a Netbeans bundle, you can manually add the proper version by clicking "Tools", "Servers", "Add Server".
 
 By default, Glassfish reports analytics information. The administration guide suggests this can be disabled with ``asadmin create-jvm-options -Dcom.sun.enterprise.tools.admingui.NO_NETWORK=true``, should this be found to be undesirable for development purposes.
@@ -163,7 +165,7 @@ Run Installer
 Please note the following:
 
 - If you have trouble with the SMTP server, consider editing the installer script to disable the SMTP check.
-- Rather than running the installer in "interactive" mode, it's possible to put the values in a file. See "non-interactive mode" in the :doc:`/installation/installation-main` section of the Installation Guide.
+- Rather than running the installer in "interactive" mode, it's possible to put the values in a file. See "non-interactive mode" in the :doc:`/installation/installation-main` section of the Installation Guide. If you put a ``default.config`` file in place you can run ``./install -y -f -nogfpasswd -insecure`` to set up a dev environment, for example.
 
 Now that you have all the prerequisites in place, you need to configure the environment for the Dataverse app - configure the database connection, set some options, etc. We have an installer script that should do it all for you. Again, assuming that the clone on the Dataverse repository was retrieved using NetBeans and that it is saved in the path ~/NetBeansProjects:
 

doc/sphinx-guides/source/installation/prerequisites.rst

@@ -45,6 +45,8 @@ Installing Glassfish
 
 **Note:** The Dataverse installer need not be run as root, and it is recommended that Glassfish not run as root either. We suggest the creation of a glassfish service account for this purpose.
 
+FIXME: Update to Glassfish 5
+
 - Download and install Glassfish (installed in ``/usr/local/glassfish4`` in the example commands below)::
 
 	# wget http://dlc-cdn.sun.com/glassfish/4.1/release/glassfish-4.1.zip

downloads/.gitignore

@@ -1,4 +1,4 @@
-glassfish-4.1.zip
+glassfish-5.0.zip
 solr-4.6.0.tgz
 weld-osgi-bundle-2.2.10.Final-glassfish4.jar
 schemaSpy_5.0.0.jar

downloads/download.sh

@@ -1,5 +1,5 @@
 #!/bin/sh
-curl -L -O http://download.java.net/glassfish/4.1/release/glassfish-4.1.zip
+curl -L -O http://download.oracle.com/glassfish/5.0/release/glassfish-5.0.zip
 curl -L -O https://archive.apache.org/dist/lucene/solr/4.6.0/solr-4.6.0.tgz
 curl -L -O http://search.maven.org/remotecontent?filepath=org/jboss/weld/weld-osgi-bundle/2.2.10.Final/weld-osgi-bundle-2.2.10.Final-glassfish4.jar
 curl -s -L http://sourceforge.net/projects/schemaspy/files/schemaspy/SchemaSpy%205.0.0/schemaSpy_5.0.0.jar/download > schemaSpy_5.0.0.jar

scripts/installer/.gitignore

@@ -0,0 +1 @@
+default.config

scripts/installer/install

@@ -15,6 +15,7 @@ my $mailserver;
 my $yes;
 my $force;
 my $nogfpasswd;
+my $insecure;
 my $admin_email;
 my ($rez) = GetOptions(
     #"length=i" => \$length,    # numeric
@@ -28,6 +29,7 @@ my ($rez) = GetOptions(
     "y|yes"        => \$yes,
     "f|force"      => \$force,
     "nogfpasswd"   => \$nogfpasswd,
+    "insecure"     => \$insecure,
     "admin_email=s" => \$admin_email,
 );
 
@@ -54,6 +56,7 @@ else
 
 	'POSTGRES_SERVER',
 	'POSTGRES_PORT',
+	'POSTGRES_ADMIN_USERNAME',
 	'POSTGRES_ADMIN_PASSWORD',
 	'POSTGRES_DATABASE',
 	'POSTGRES_USER',
@@ -79,6 +82,7 @@ my %CONFIG_DEFAULTS = (
     'ADMIN_EMAIL',         '',
     'MAIL_SERVER',         'mail.hmdc.harvard.edu',
 
+    'POSTGRES_ADMIN_USERNAME', 'postgres',
     'POSTGRES_ADMIN_PASSWORD', 'secret',
     'POSTGRES_SERVER',   '127.0.0.1',
     'POSTGRES_PORT',     5432,
@@ -105,6 +109,7 @@ my %CONFIG_PROMPTS = (
 
     'POSTGRES_SERVER',   'Postgres Server Address',
     'POSTGRES_PORT',     'Postgres Server Port',
+    'POSTGRES_ADMIN_USERNAME', 'Postgres ADMIN username',
     'POSTGRES_ADMIN_PASSWORD', 'Postgres ADMIN password',
     'POSTGRES_DATABASE', 'Name of the Postgres Database',
     'POSTGRES_USER',     'Name of the Postgres User',
@@ -131,6 +136,7 @@ my %CONFIG_COMMENTS = (
 
     'POSTGRES_SERVER',   '',
     'POSTGRES_PORT',     '',
+    'POSTGRES_ADMIN_USERNAME', ":\n - We will need this to create the user and database that the Dataverse application will be using.\n (Hit RETURN if access control is set to \"trust\" for this connection in pg_hba.conf)\n: ",
     'POSTGRES_ADMIN_PASSWORD', ":\n - We will need this to create the user and database that the Dataverse application will be using.\n (Hit RETURN if access control is set to \"trust\" for this connection in pg_hba.conf)\n: ",
     'POSTGRES_USER',     ":\n - This is the Postgres user that the Dataverse app will be using to talk to the database\n: ",
     'POSTGRES_DATABASE', '',
@@ -713,14 +719,20 @@ if ( $psql_exec eq "" )
     $psql_admin_exec = "PGPASSWORD=" . $CONFIG_DEFAULTS{'POSTGRES_ADMIN_PASSWORD'} . "; export PGPASSWORD; " . $psql_exec; 
     $psql_exec = "PGPASSWORD=" . $CONFIG_DEFAULTS{'POSTGRES_PASSWORD'} . "; export PGPASSWORD; " . $psql_exec; 
 
-    print "Checking if we can talk to Postgres as the admin user...\n";
+    print "Checking if we can talk to Postgres as the admin user (" . $CONFIG_DEFAULTS{'POSTGRES_ADMIN_USERNAME'} . ")...\n";
 }
 
 # 4. CONFIGURE POSTGRES:
 
 # 4a. BUT FIRST, CHECK IF WE CAN TALK TO POSTGRES AS THE ADMIN:
 
-if ( $psql_admin_exec eq "" || system( $psql_admin_exec . "/psql -h " . $CONFIG_DEFAULTS{'POSTGRES_SERVER'} . " -U postgres -d postgres -c 'SELECT * FROM pg_roles' > /dev/null 2>&1" ) ) 
+print "\$psql_admin_exec: $psql_admin_exec\n";
+
+my $foo = $psql_admin_exec . "/psql -h " . $CONFIG_DEFAULTS{'POSTGRES_SERVER'} . " -U " . $CONFIG_DEFAULTS{'POSTGRES_ADMIN_USERNAME'} . " -d postgres -c 'SELECT * FROM pg_roles'";
+
+print "\$foo: $foo\n";
+
+if ( $psql_admin_exec eq "" || system( $psql_admin_exec . "/psql -h " . $CONFIG_DEFAULTS{'POSTGRES_SERVER'} . " -U " . $CONFIG_DEFAULTS{'POSTGRES_ADMIN_USERNAME'} . " -d postgres -c 'SELECT * FROM pg_roles' > /dev/null 2>&1" ) ) 
 {
     # No, we can't. :(
     if ($pg_local_connection) 
@@ -1099,7 +1111,11 @@ else {
 # the username and password for every asadmin command, if
 # access to :4848 is password-protected:
 
-system( $glassfish_dir. "/bin/asadmin login" );
+# If you you have a "default.config" file in place and run `./install -y -f -nogfpasswd`
+# you can keep the installation process non-interactive.
+unless ($nogfpasswd) {
+    system( $glassfish_dir. "/bin/asadmin login" );
+}
 
 # NEW: configure glassfish using ASADMIN commands:
 
@@ -1285,10 +1301,15 @@ for my $script ( "setup-all.sh" ) {
     #    $run_script = "tmpscript.sh";
     #}
     #else {
-    $run_script = $script;
+    #    $run_script = $script;
     #}
+    if ($insecure) {
+        $run_script = "$script --insecure";
+    } else {
+        $run_script = $script;
+    }
 
-    unless ( my $exit_code = system( "./" . $run_script . " > $run_script.$$.log 2>&1") == 0 ) 
+    unless ( my $exit_code = system( "./" . $run_script . " > $script.$$.log 2>&1") == 0 )
     {
         print "\nERROR executing script " . $script . "!\n";
         exit 1;

scripts/installer/resetgf5anddb

@@ -0,0 +1,6 @@
+#!/bin/sh
+/usr/local/glassfish5/glassfish/bin/asadmin stop-domain
+rm -rf /usr/local/glassfish5/glassfish/domains/domain1/generated
+psql -c 'DROP DATABASE "dvndb"' template1
+../search/clear
+rm -rf ~/dataverse/files

scripts/vagrant/setup.sh

@@ -28,6 +28,7 @@ GLASSFISH_USER=glassfish
 echo "Ensuring Unix user '$GLASSFISH_USER' exists"
 useradd $GLASSFISH_USER || :
 DOWNLOAD_DIR='/dataverse/downloads'
+# FIXME: update to Glassfish 5
 GLASSFISH_ZIP="$DOWNLOAD_DIR/glassfish-4.1.zip"
 SOLR_TGZ="$DOWNLOAD_DIR/solr-4.6.0.tgz"
 WELD_PATCH="$DOWNLOAD_DIR/weld-osgi-bundle-2.2.10.Final-glassfish4.jar"
@@ -37,6 +38,7 @@ if [ ! -f $GLASSFISH_ZIP ] || [ ! -f $SOLR_TGZ ]; then
     echo "Done running download script."
 fi
 GLASSFISH_USER_HOME=~glassfish
+# FIXME: update to Glassfish 5
 GLASSFISH_ROOT=$GLASSFISH_USER_HOME/glassfish4
 if [ ! -d $GLASSFISH_ROOT ]; then
   echo "Copying $GLASSFISH_ZIP to $GLASSFISH_USER_HOME and unzipping"

src/main/java/edu/harvard/iq/dataverse/search/SearchIncludeFragment.java

@@ -307,6 +307,10 @@ public void search(boolean onlyDataRelatedToMe) {
         String allTypesFilterQuery = SearchFields.TYPE + ":(dataverses OR datasets OR files)";
         filterQueriesFinalAllTypes.add(allTypesFilterQuery);
 
+        if (page == 0) {
+            logger.info("Variable 'page' was zero. Changing it one. What does this have to do with upgrading to Glassfish 5?");
+            page = 1;
+        }
         int paginationStart = (page - 1) * paginationGuiRows;
         /**
          * @todo

src/main/webapp/dataverse.xhtml

@@ -18,7 +18,11 @@
             <ui:define name="body">
                 <f:metadata>
                     <f:viewParam name="id" value="#{DataversePage.dataverse.id}"/>
-                    <f:viewParam name="alias" value="#{DataversePage.dataverse.alias}"/>
+                    <!--Commenting out this "DataversePage.dataverse.alias" line because Glassfish 5 doesn't like it.
+                    No error message appears in server.log, DataversePage.init never fires, and the page shows this error:
+                    "Validation Error – Required fields were missed or there was a validation error. Please scroll down to see details."
+                    -->
+                    <!--<f:viewParam name="alias" value="# {DataversePage.dataverse.alias}"/>-->
                     <f:viewParam name="ownerId" value="#{DataversePage.ownerId}"/>
                     <f:viewParam name="editMode" value="#{DataversePage.editMode}"/>
                     <f:viewAction action="#{DataversePage.init}"/>