New API endpoints for TRSA (Trusted Remote Storage Agent) of ImPACT project: stage 1

conf/docker-aio/c7.dockerfile

@@ -12,8 +12,8 @@ COPY testdata/solrconfig.xml /tmp/dv
 # IPv6 and localhost appears to be related to some of the intermittant connection issues
 COPY disableipv6.conf /etc/sysctl.d/
 RUN rm /etc/httpd/conf/*
-COPY httpd.conf /etc/httpd/conf 
-RUN cd /opt ; tar zxf /tmp/dv/deps/solr-7.3.1dv.tgz 
+COPY httpd.conf /etc/httpd/conf
+RUN cd /opt ; tar zxf /tmp/dv/deps/solr-7.3.1dv.tgz
 RUN cd /opt ; tar zxf /tmp/dv/deps/glassfish4dv.tgz
 
 # this copy of domain.xml is the result of running `asadmin set server.monitoring-service.module-monitoring-levels.jvm=LOW` on a default glassfish installation (aka - enable the glassfish REST monitir endpoint for the jvm`
@@ -24,6 +24,7 @@ RUN sudo -u postgres /usr/pgsql-9.6/bin/initdb -D /var/lib/pgsql/data
 
 # copy configuration related files
 RUN cp /tmp/dv/pg_hba.conf /var/lib/pgsql/data/
+RUN cp /tmp/dv/postgresql.conf /var/lib/pgsql/data/
 RUN cp -r /opt/solr-7.3.1/server/solr/configsets/_default /opt/solr-7.3.1/server/solr/collection1
 RUN cp /tmp/dv/schema.xml /opt/solr-7.3.1/server/solr/collection1/conf/schema.xml
 RUN cp /tmp/dv/solrconfig.xml /opt/solr-7.3.1/server/solr/collection1/conf/solrconfig.xml
@@ -71,7 +72,7 @@ ENV doi_username=${doi_username}
 ENV doi_password=${doi_password}
 COPY configure_doi.bash /opt/dv
 
-# healthcheck for glassfish only (assumes modified domain.xml); 
+# healthcheck for glassfish only (assumes modified domain.xml);
 #  does not check dataverse application status.
 HEALTHCHECK CMD curl --fail http://localhost:4848/monitoring/domain/server.json || exit 1
 CMD ["/opt/dv/entrypoint.bash"]

conf/docker-aio/configure_doi.bash

@@ -7,7 +7,7 @@ if [ ! -z "${DoiProvider}" ]; then
         curl -X PUT -d ${DoiProvider} http://localhost:8080/api/admin/settings/:DoiProvider
 fi
 if [ ! -z "${doi_username}" ]; then
-        bin/asadmin create-jvm-options "-Ddoi.username=${doi_password}"
+        bin/asadmin create-jvm-options "-Ddoi.username=${doi_username}"
 fi
 if [ ! -z "${doi_password}" ]; then
         bin/asadmin create-jvm-options "-Ddoi.password=${doi_password}"

conf/docker-aio/dv/postgresql.conf

@@ -0,0 +1,185 @@
+					# (change requires restart)
+					# (change requires restart)
+					# (change requires restart)
+					# (change requires restart)
+listen_addresses = '*'		# what IP address(es) to listen on;
+					# comma-separated list of addresses;
+					# defaults to 'localhost'; use '*' for all
+					# (change requires restart)
+max_connections = 100			# (change requires restart)
+					# (change requires restart)
+					# (change requires restart)
+					# (change requires restart)
+					# (change requires restart)
+					# (change requires restart)
+					# 0 selects the system default
+					# 0 selects the system default
+					# 0 selects the system default
+shared_buffers = 128MB			# min 128kB
+					# (change requires restart)
+					# (change requires restart)
+					# (change requires restart)
+dynamic_shared_memory_type = posix	# the default is the first option
+					# supported by the operating system:
+					#   posix
+					#   sysv
+					#   windows
+					#   mmap
+					# use none to disable dynamic shared memory
+					# (change requires restart)
+					# in kB, or -1 for no limit
+					# (change requires restart)
+					# (change requires restart)
+					# (change requires restart)
+						# (turning this off can cause
+						# unrecoverable data corruption)
+					# off, local, remote_write, remote_apply, or on
+					# supported by the operating system:
+					#   open_datasync
+					#   fdatasync (default on Linux)
+					#   fsync
+					#   fsync_writethrough
+					#   open_sync
+					# (change requires restart)
+					# (change requires restart)
+				# (change requires restart)
+				# placeholders: %p = path of file to archive
+				#               %f = file name only
+				# e.g. 'test ! -f /mnt/server/archivedir/%f && cp %p /mnt/server/archivedir/%f'
+				# number of seconds; 0 disables
+				# (change requires restart)
+				# (change requires restart)
+				# (change requires restart)
+				# number of sync standbys and comma-separated list of application_name
+				# from standby(s); '*' = all
+					# (change requires restart)
+					# when reading WAL from archive;
+					# -1 allows indefinite delay
+					# when reading streaming WAL;
+					# -1 allows indefinite delay
+					# 0 disables
+					# query conflicts
+					# communication from master
+					# in milliseconds; 0 disables
+					# retrieve WAL after a failed attempt
+					# JOIN clauses
+log_destination = 'stderr'		# Valid values are combinations of
+					# stderr, csvlog, syslog, and eventlog,
+					# depending on platform.  csvlog
+					# requires logging_collector to be on.
+logging_collector = on			# Enable capturing of stderr and csvlog
+					# into log files. Required to be on for
+					# csvlogs.
+					# (change requires restart)
+log_directory = 'pg_log'		# directory where log files are written,
+					# can be absolute or relative to PGDATA
+log_filename = 'postgresql-%a.log'	# log file name pattern,
+					# can include strftime() escapes
+					# begin with 0 to use octal notation
+log_truncate_on_rotation = on		# If on, an existing log file with the
+					# same name as the new log file will be
+					# truncated rather than appended to.
+					# But such truncation only occurs on
+					# time-driven rotation, not on restarts
+					# or size-driven rotation.  Default is
+					# off, meaning append to existing files
+					# in all cases.
+log_rotation_age = 1d			# Automatic rotation of logfiles will
+					# happen after that time.  0 disables.
+log_rotation_size = 0			# Automatic rotation of logfiles will
+					# happen after that much log output.
+					# 0 disables.
+					#   debug5
+					#   debug4
+					#   debug3
+					#   debug2
+					#   debug1
+					#   log
+					#   notice
+					#   warning
+					#   error
+					#   debug5
+					#   debug4
+					#   debug3
+					#   debug2
+					#   debug1
+					#   info
+					#   notice
+					#   warning
+					#   error
+					#   log
+					#   fatal
+					#   panic
+					#   debug5
+					#   debug4
+					#   debug3
+					#   debug2
+					#   debug1
+					#   info
+					#   notice
+					#   warning
+					#   error
+					#   log
+					#   fatal
+					#   panic (effectively off)
+					# and their durations, > 0 logs only
+					# statements running at least this number
+					# of milliseconds
+log_line_prefix = '< %m > '			# special values:
+					#   %a = application name
+					#   %u = user name
+					#   %d = database name
+					#   %r = remote host and port
+					#   %h = remote host
+					#   %p = process ID
+					#   %t = timestamp without milliseconds
+					#   %m = timestamp with milliseconds
+					#   %n = timestamp with milliseconds (as a Unix epoch)
+					#   %i = command tag
+					#   %e = SQL state
+					#   %c = session ID
+					#   %l = session line number
+					#   %s = session start timestamp
+					#   %v = virtual transaction ID
+					#   %x = transaction ID (0 if none)
+					#   %q = stop here in non-session
+					#        processes
+					#   %% = '%'
+					# e.g. '<%u%%%d> '
+					# than the specified size in kilobytes;
+					# -1 disables, 0 logs all temp files
+log_timezone = 'UTC'
+					# (change requires restart)
+					# requires track_counts to also be on.
+					# their durations, > 0 logs only
+					# actions running at least this number
+					# of milliseconds.
+					# (change requires restart)
+					# vacuum
+					# analyze
+					# (change requires restart)
+					# before forced vacuum
+					# (change requires restart)
+					# autovacuum, in milliseconds;
+					# -1 means use vacuum_cost_delay
+					# autovacuum, -1 means use
+					# vacuum_cost_limit
+					# only default tablespace
+datestyle = 'iso, mdy'
+timezone = 'UTC'
+					# abbreviations.  Currently, there are
+					#   Default
+					#   Australia (historical usage)
+					#   India
+					# You can create your own file in
+					# share/timezonesets/.
+					# encoding
+lc_messages = 'C'			# locale for system error message
+					# strings
+lc_monetary = 'C'			# locale for monetary formatting
+lc_numeric = 'C'			# locale for number formatting
+lc_time = 'C'				# locale for time formatting
+default_text_search_config = 'pg_catalog.english'
+					# (change requires restart)
+					# (change requires restart)
+					# directory 'conf.d'

conf/docker-aio/entrypoint.bash

@@ -2,6 +2,7 @@
 export LANG=en_US.UTF-8
 #sudo -u postgres /usr/bin/postgres -D /var/lib/pgsql/data &
 sudo -u postgres /usr/pgsql-9.6/bin/postgres -D /var/lib/pgsql/data &
+sleep 15
 cd /opt/solr-7.3.1/
 # TODO: Run Solr as non-root and remove "-force".
 bin/solr start -force
@@ -11,7 +12,7 @@ bin/solr create_core -c collection1 -d server/solr/collection1/conf -force
 apachectl -DFOREGROUND &
 
 # TODO: Run Glassfish as non-root.
-cd /opt/glassfish4
-bin/asadmin start-domain --debug
+cd /opt/glassfish4/
+bin/asadmin start-domain
 sleep infinity
 

conf/docker-aio/prep_it.bash

@@ -10,7 +10,7 @@ n_retries=10
 # glassfish healthy/ready retries
 n_wait=5
 
-cd conf/docker-aio
+#cd conf/docker-aio
 ./0prep_deps.sh
 ./1prep.sh
 docker build -t dv0 -f c7.dockerfile .
@@ -21,7 +21,7 @@ do
 	# cleanup from previous runs if necessary
 	docker rm -f dv
 	# start container
-	docker run -d -p 8084:80 -p 8083:8080 -p 9010:9009 --name dv dv0
+	docker run -d -p 5432:5432 -p 80:80 -p 8080:8080 --name dv dv0
 
 	# wait for glassfish to be healthy
 	i_wait=0
@@ -35,7 +35,7 @@ do
 			sleep $d_wait
 		fi
 		i_wait=$(( $i_wait + 1 ))
-		
+
 	done
 
 	# try setupIT.bash
@@ -69,6 +69,5 @@ docker exec -it dv /opt/dv/configure_doi.bash
 
 cd ../..
 echo "docker-aio ready to run integration tests ($i_retry)"
-curl http://localhost:8084/api/info/version
+curl http://localhost:8080/api/info/version
 echo $?
-

conf/docker-aio/setJvmOptions.bash

@@ -0,0 +1,18 @@
+#!/usr/bin/env bash
+set -a
+. $1
+set +a
+
+echo "SITE_URL=${SITE_URL}"
+echo "DOI_USERNAME=${DOI_USERNAME}"
+echo "DOI_PASSWORD=${DOI_PASSWORD}"
+echo "DOI_BASEURL=${DOI_BASEURL}"
+
+
+docker exec -it dv /usr/local/glassfish4/bin/asadmin create-jvm-options "\"-Ddataverse.siteUrl=${SITE_URL}\""
+sleep 15
+docker exec -it dv /usr/local/glassfish4/bin/asadmin create-jvm-options "\"-Ddoi.username=${DOI_USERNAME}\""
+sleep 15
+docker exec -it dv /usr/local/glassfish4/bin/asadmin create-jvm-options "\"-Ddoi.password=${DOI_PASSWORD}\""
+sleep 15
+docker exec -it dv /usr/local/glassfish4/bin/asadmin create-jvm-options "\"-Ddoi.baseurlstring=${DOI_BASEURL}\""

doc/Architecture/TRSA.adoc

@@ -0,0 +1,2 @@
+=== major changes to version 4.8.6
+* ImportType.IMPORT_METADATA_ONLY was added to ImportUtil