diff --git a/rtd_phosphonetx/etc/log.xml b/rtd_phosphonetx/etc/log.xml new file mode 100644 index 0000000000000000000000000000000000000000..5cee0a68436a19a6c4ec4b14b580e6d9f75bf84f --- /dev/null +++ b/rtd_phosphonetx/etc/log.xml @@ -0,0 +1,19 @@ +<?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> diff --git a/rtd_phosphonetx/etc/passwd b/rtd_phosphonetx/etc/passwd new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/rtd_phosphonetx/etc/passwd.sv b/rtd_phosphonetx/etc/passwd.sv new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/rtd_phosphonetx/etc/passwd.tmp b/rtd_phosphonetx/etc/passwd.tmp new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/rtd_phosphonetx/etc/service.properties b/rtd_phosphonetx/etc/service.properties new file mode 100644 index 0000000000000000000000000000000000000000..bb9148a121ef17aa55c7b6b0ceb4320f8fe31023 --- /dev/null +++ b/rtd_phosphonetx/etc/service.properties @@ -0,0 +1,127 @@ +# Unique code of this Data Store Server. Not more than 40 characters. +data-store-server-code = DSS1 + +# The root directory of the data store +storeroot-dir = targets/playground/data/store + +# Port +port = 8889 + +# Session timeout in minutes +session-timeout = 720 + +# 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/openbis + +# 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:8889 + +# SMTP properties (must start with 'mail' to be considered). +# mail.smtp.host = localhost +# 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 + +# Globally used separator character which separates entities in a data set file name +data-set-file-name-entity-separator = _ + +# Specifies what should happen if an error occurs during dataset processing. +# By default this flag is set to false and user has to modify the 'faulty paths file' +# each time the faulty dataset should be processed again. +# Set this flag to true if the processing should be repeated after some time without manual intervention. +# Note that this can increase the server load. +# reprocess-faulty-datasets = false + +# 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' thread configuration +# --------------------------------------------------------------------------- +# The directory to watch for incoming data. +main-thread.incoming-dir = targets/playground/data/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 + +# The group the samples extracted by this thread belong to. If commented out or empty, then samples +# are considered associated to a database instance (not group private). +# main-thread.group-code = <change this> + +# ---------------- Plugin properties +# The extractor class to use for code extraction +main-thread.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor +main-thread.data-set-info-extractor.strip-file-extension = true +main-thread.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator} +main-thread.data-set-info-extractor.group-code = TEST +# Location of file containing data set properties +#main-thread.data-set-info-extractor.data-set-properties-file-name = data-set.properties + +# The extractor class to use for type extraction +main-thread.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor +main-thread.type-extractor.file-format-type = XML +main-thread.type-extractor.locator-type = RELATIVE_LOCATION +main-thread.type-extractor.data-set-type = PROT_RESULT +main-thread.type-extractor.is-measured = true + +main-thread.dataset-handler = ch.systemsx.cisd.openbis.etlserver.phosphonetx.ResultDataSetHandler +main-thread.dataset-handler.database.kind = dev +main-thread.dataset-handler.database.owner = +main-thread.dataset-handler.database.password = + +# The storage processor (IStorageProcessor implementation) +main-thread.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor