initial commit

SVN: 16118

plasmid/build/antrun.sh

+#! /bin/bash
+
+ME="$0"
+MYDIR=${ME%/*}
+cd $MYDIR
+ant -lib ../../build_resources/lib/ecj.jar "$@"

plasmid/build/build.xml

+<project name="plasmid" default="ci" basedir="..">
+	<import file="../../datastore_server/build/build.xml" />
+	<project-classpath name="ecp" classes="${classes}" />
+
+	<property name="original.dist" value="dist" />
+	<property name="mainfolder" value="plasmid" />
+	<property name="variant" value="-plasmid" />
+
+	<target name="compile" depends="build-common.compile, clean" />
+
+	<target name="run-tests">
+		<antcall target="build-common.run-tests">
+			<param name="test.suite" value="tests.xml" />
+		</antcall>
+	</target>
+
+	<!--
+        // Task for creating distributions
+  -->
+	<target name="dist" depends="datastore_server.make-dist" />
+
+	<!--
+        // Task for continuous integration server.
+  -->
+	<target name="ci" depends="build-common.ci, dist, check-dependencies" />
+
+	<target name="dss-jar" depends="datastore_server.dss-jar">
+		<jar update="true" destfile="${dss-jar.file}">
+			<fileset dir="source">
+				<include name="**/*.sql" />
+			</fileset>
+		</jar>
+	</target>
+
+</project>
\ No newline at end of file

plasmid/etc/log.xml

+<?xml version="1.0" encoding="UTF-8" ?>
+<!DOCTYPE log4j:configuration SYSTEM "log4j.dtd">
+
+<log4j:configuration xmlns:log4j='http://jakarta.apache.org/log4j/'>
+
+  <appender name="STDOUT" class="org.apache.log4j.ConsoleAppender">
+     <layout class="org.apache.log4j.PatternLayout">
+       <param name="ConversionPattern" value="%d %-5p [%t] %c - %m%n"/>
+     </layout>
+  </appender>
+
+  <appender name="NULL" class="org.apache.log4j.varia.NullAppender" />
+
+  <root>
+     <priority value ="info" />
+     <appender-ref ref="STDOUT" />
+  </root>
+
+</log4j:configuration>

plasmid/etc/service.properties

+# Unique code of this Data Store Server. Not more than 40 characters.
+data-store-server-code = DSS1
+
+data-folder = targets/playground/data
+
+# The root directory of the data store
+storeroot-dir = ${data-folder}/store
+
+# The directory where the command queue file is located; defaults to storeroot-dir 
+commandqueue-dir =
+
+# Port
+port = 8889
+
+# Session timeout in minutes
+session-timeout = 720
+
+# Set to 'false' for development/testing without deployed server. In this mode datastore will not use
+# SSL when connecting to openbis. Otherwise all 'keystore' properties need to be set for SSL connection 
+# (default when use-ssl property is not set so there is no need to specify it on production servers).
+use-ssl = false
+
+# Path to the keystore
+keystore.path = ../datastore_server/dist/etc/openBIS.keystore
+
+# Password of the keystore
+keystore.password = changeit
+
+# Key password of the keystore
+keystore.key-password = changeit
+
+# The check interval (in seconds)
+check-interval = 5
+
+# The time-out for clean up work in the shutdown sequence (in seconds).
+# Note that that the maximal time for the shutdown sequence to complete can be as large 
+# as twice this time.
+# Remark: On a network file system, it is not recommended to turn this value to something 
+# lower than 180.
+shutdown-timeout = 2
+
+# If free disk space goes below value defined here, a notification email will be sent.
+# Value must be specified in kilobytes (1048576 = 1024 * 1024 = 1GB). If no high water mark is
+# specified or if value is negative, the system will not be watching.
+highwater-mark = -1
+
+# If a data set is successfully registered it sends out an email to the registrator. 
+# If this property is not specified, no email is sent to the registrator. This property
+# does not affect the mails which are sent, when the data set could not be registered.
+notify-successful-registration = false
+
+# The URL of the openBIS server
+server-url = http://localhost:8888
+
+# The username to use when contacting the openBIS server
+username = etlserver
+
+# The password to use when contacting the openBIS server
+password = etlserver
+
+# The base URL for Web client access.
+download-url = https://localhost:${port}
+
+# SMTP properties (must start with 'mail' to be considered). 
+mail.smtp.host = file://targets/playground/email
+mail.from = datastore_server@localhost
+
+# ---------------- Timing parameters for file system operations on remote shares.
+
+# Time (in seconds) to wait for any file system operation to finish. Operations exceeding this 
+# timeout will be terminated. 
+timeout = 60
+# Number of times that a timed out operation will be tried again (0 means: every file system 
+# operation will only ever be performed once).
+max-retries = 11
+# Time (in seconds) to wait after an operation has been timed out before re-trying.  
+failure-interval = 10 
+
+# The period of no write access that needs to pass before an incoming data item is considered 
+# complete and ready to be processed (in seconds) [default: 300]. 
+# Valid only when auto-detection method is used to determine if an incoming data are ready to be processed.
+quiet-period = 10
+
+# Comma separated names of processing threads. Each thread should have configuration properties prefixed with its name.
+# E.g. 'code-extractor' property for the thread 'my-etl' should be specified as 'my-etl.code-extractor'
+inputs = main-thread
+
+# ---------------------------------------------------------------------------
+# main thread configuration
+# ---------------------------------------------------------------------------
+# The directory to watch for incoming data.
+main-thread.incoming-dir = ${data-folder}/incoming
+
+# Determines when the incoming data should be considered complete and ready to be processed.
+# Allowed values: 
+#  - auto-detection - when no write access will be detected for a specified 'quite-period'
+#  - marker-file		- when an appropriate marker file for the data exists. 
+# The default value is 'marker-file'.
+main-thread.incoming-data-completeness-condition = auto-detection
+main-thread.delete-unidentified = true
+# ---------------- Plugin properties
+# TODO
+# The extractor class to use for code extraction
+main-thread.data-set-info-extractor = ch.systemsx.cisd.cina.dss.info.CinaDataSetInfoExtractor
+main-thread.data-set-info-extractor = eu.basysbio.cisd.dss.DataSetInfoExtractor
+
+# The extractor class to use for type extraction
+main-thread.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
+main-thread.type-extractor.file-format-type = GB
+main-thread.type-extractor.locator-type = RELATIVE_LOCATION
+main-thread.type-extractor.data-set-type = PLASMID
+main-thread.type-extractor.is-measured = true
+#main-thread.type-extractor = ch.systemsx.cisd.cina.dss.info.CinaTypeExtractor
+#main-thread.type-extractor = ch.systemsx.cisd.etlserver.cifex.CifexTypeExtractor
+
+# The storage processor (IStorageProcessor implementation)
+main-thread.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
+# Cifex?
\ No newline at end of file

plasmid/resource/dependency-structure.ddf

+#show allResults
+
+{root} = ch.systemsx.cisd.plasmid
+{dss} = ${root}.dss
+{openbis} = ch.systemsx.cisd.openbis
+
+######################################################################
+# Check dependencies to openbis
+
+[dss] = ${dss}.*
+[private_openbis] = ${openbis}.* excluding [dss] ${openbis}.dss.generic.shared.* ${openbis}.generic.shared.* ${openbis}.dss.generic.server.plugins.*
+
+check sets [dss]
+
+check [dss] independentOf [private_openbis]
+