diff --git a/openbis_standard_technologies/dist/server/etc/log.xml b/openbis_standard_technologies/dist/server/etc/log.xml new file mode 100644 index 0000000000000000000000000000000000000000..e806ca7986a35e36f5fcd0b4aacfbe7454acb202 --- /dev/null +++ b/openbis_standard_technologies/dist/server/etc/log.xml @@ -0,0 +1,118 @@ +<?xml version="1.0" encoding="UTF-8" ?> +<!DOCTYPE log4j:configuration SYSTEM "log4j.dtd"> + +<log4j:configuration xmlns:log4j='http://jakarta.apache.org/log4j/'> + + <appender name="DEFAULT" class="org.apache.log4j.DailyRollingFileAppender"> + + <param name="File" value="logs/openbis_log.txt" /> + <param name="DatePattern" value="'.'yyyy-MM-dd" /> + + <layout class="org.apache.log4j.PatternLayout"> + <!-- + // %d: outputs the date of the logging event. + // %-5p: priority (i.e. level) of the logging event should be left justified to + // a width of five characters. + // %t: outputs the name of the thread that generated the logging event. + // %c: outputs the category of the logging event. + // %m: outputs the application supplied message associated with the logging event. + // %X: outputs the MDC (mapped diagnostic context) associated with the thread that generated the logging event. + --> + <param name="ConversionPattern" value="%d %-5p [%t]%X{sessionInfo} %c - %m%n" /> + </layout> + + </appender> + <appender name="AUTH" class="org.apache.log4j.DailyRollingFileAppender"> + + <param name="File" value="logs/openbis_auth_log.txt" /> + <param name="DatePattern" value="'.'yyyy-MM-dd" /> + + <layout class="org.apache.log4j.PatternLayout"> + <param name="ConversionPattern" value="%d %-5p [%t]%X{sessionInfo} %c - %m%n" /> + </layout> + </appender> + + <appender name="USAGE" class="org.apache.log4j.DailyRollingFileAppender"> + + <param name="File" value="logs/openbis_usage_log.txt" /> + <param name="DatePattern" value="'.'yyyy-MM-dd" /> + + <layout class="org.apache.log4j.PatternLayout"> + <param name="ConversionPattern" value="%d %-5p [%t]%X{sessionInfo} %c - %m%n" /> + </layout> + </appender> + + <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> + + <!-- + // Defined but not used right now. + --> + <appender name="NULL" class="org.apache.log4j.varia.NullAppender" /> + + <appender name="EMAIL" class="org.apache.log4j.net.SMTPAppender"> + + <param name="BufferSize" value="512" /> + <param name="SMTPHost" value="localhost" /> + <param name="From" value="openbis@localhost" /> + <param name="To" value="openbis@localhost" /> + <param name="Subject" value="ATTENTION: openBIS Server" /> + <param name="EvaluatorClass" + value="ch.systemsx.cisd.common.logging.AlwaysTrueTriggeringEventEvaluator" /> + + <layout class="org.apache.log4j.PatternLayout"> + <param name="ConversionPattern" value="%d %-5p [%t] %c - %m%n" /> + </layout> + + </appender> + + <!-- + // If we have the category 'NOTIFY' and we send a logging event with priority 'info', then an email will be sent. + --> + <category name="NOTIFY"> + <priority value="info" /> + <appender-ref ref="DEFAULT" /> + <appender-ref ref="EMAIL" /> + </category> + + <!-- + // If we have the category 'AUTH' and we send a logging event with priority 'info', then log to AUTH and USAGE. + --> + <category name="AUTH"> + <priority value="info" /> + <appender-ref ref="AUTH" /> + <appender-ref ref="USAGE" /> + </category> + + <!-- + // If we have the category 'TRACKING' and we send a logging event with priority 'info', then log to USAGE. + --> + <category name="TRACKING"> + <priority value="info" /> + <appender-ref ref="USAGE" /> + </category> + + <!-- + // If we have the category 'ACCESS' and we send a logging event with priority 'info', then log to USAGE. + --> + <category name="ACCESS"> + <priority value="info" /> + <appender-ref ref="USAGE" /> + </category> + + <!-- + // Do not use log level debug otherwise plain passwords are readable. + --> + <logger name="httpclient.wire"> + <level value="ERROR" /> + </logger> + + <root> + <priority value="info" /> + <appender-ref ref="DEFAULT" /> + </root> + +</log4j:configuration> diff --git a/openbis_standard_technologies/dist/server/etc/passwd b/openbis_standard_technologies/dist/server/etc/passwd new file mode 100644 index 0000000000000000000000000000000000000000..9a706e68a26f1e4e39733914a319ec5dfe169f3d --- /dev/null +++ b/openbis_standard_technologies/dist/server/etc/passwd @@ -0,0 +1,4 @@ +a:a@admins.com:A:The Admin:J3fII6Pex7jnCBwF+uXz2mFuB1QVhPUi +u:u@users.com:U:The User:dmbGKaGRmbX8YKfslMxUHObmYfjywkuT +o:o@observers.com:O:The Observer:t53ADCnFnEFhBvHB7FPoHhbHeW2O1KJc +etlserver::::SHGHSPawL/B3NKXD5nsu4fSrj5LwR2MX diff --git a/openbis_standard_technologies/dist/server/openbis.conf b/openbis_standard_technologies/dist/server/openbis.conf new file mode 100644 index 0000000000000000000000000000000000000000..6c5055b8023ca0d4c43cc2916239c0558d00efc9 --- /dev/null +++ b/openbis_standard_technologies/dist/server/openbis.conf @@ -0,0 +1,18 @@ +# +# openBIS configuration file +# + +# +# Home directory of the JRE that should be used +# +#JAVA_HOME=${JAVA_HOME:=/usr/java/latest} + +# +# General options to the JRE +# +JAVA_OPTS=${JAVA_OPTS:=-server -d64 -Djavax.net.ssl.trustStore=etc/openBIS.keystore} + +# +# Memory options to the JRE +# +JAVA_MEM_OPTS="-Xmx2048m -Xms512m -XX:MaxPermSize=256m" diff --git a/openbis_standard_technologies/dist/server/service.properties b/openbis_standard_technologies/dist/server/service.properties new file mode 100644 index 0000000000000000000000000000000000000000..5f6bd14c5ecb793654914bddea613b167b18a755 --- /dev/null +++ b/openbis_standard_technologies/dist/server/service.properties @@ -0,0 +1,98 @@ +# Supported: 'file-authentication-service' and 'crowd-authentication-service' +authentication-service = file-authentication-service + +# The time after which an inactive session is expired by the service (in minutes). +session-timeout = 720 + +# Authorization +# Supported: 'no-authorization' and 'active-authorization' +authorization-component-factory = active-authorization + +script-folder = . + +# Supported: currently only 'postgresql' is supported +database.engine = postgresql +database.create-from-scratch = false +# For debugging set this value to true. +database.script-single-step-mode = false +database.url-host-part = +database.kind = standard +database.owner = +database.owner-password = +database.admin-user = +database.admin-password = + +proteomics.database.engine = postgresql +proteomics.database.create-from-scratch = false +proteomics.database.script-single-step-mode = false +proteomics.database.url-host-part = +proteomics.database.basic-name = proteomics +proteomics.database.kind = productive +proteomics.database.owner = +proteomics.database.owner-password = +proteomics.database.admin-user = +proteomics.database.admin-password = +proteomics.script-folder = proteomics + +data-source-provider = dss-based-data-source-provider + +dss-based-data-source-provider.data-store-servers = dss-screening +dss-based-data-source-provider.dss-screening.database-driver = org.postgresql.Driver +dss-based-data-source-provider.dss-screening.database-url = jdbc:postgresql://localhost/imaging_productive + +crowd.service.host = crowd.systemsx.ch +crowd.service.port = 8443 +crowd.application.name = openbis +crowd.application.password = + +# The database instance local unique identifier. Used when the new database is created. +database-instance = STANDARD + +# The URL of the CIFEX server +cifex-url = https://cifex.ethz.ch:443 + +# Hibernate Search +# The working directory. +hibernate.search.index-base = ./indices +# One of NO_INDEX, SKIP_IF_MARKER_FOUND, INDEX_FROM_SCRATCH. +# If not specified, default (SKIP_IF_MARKER_FOUND) is taken. +hibernate.search.index-mode = SKIP_IF_MARKER_FOUND +# Defines the maximum number of elements indexed before flushing the transaction-bound queue. +# Default is 1000. +hibernate.search.batch-size = 1000 +# Maximum number of search results +hibernate.search.maxResults = 100000 +# If 'async', the update of indices will be done in a separate thread. +hibernate.search.worker.execution=async + +# Name of the file that stores Web Client configuration +web-client-configuration-file = etc/web-client.properties + +# --------------------------------------------------------------------------- +# anonymous login configuration +# --------------------------------------------------------------------------- +# Login of the existing user whose settings will be used for anonymous login +#user-for-anonymous-login = <user-login> + +core-plugins-folder=./webapps/openbis/core-plugins + +# When set to "true" enables the system to store material codes containing non-alphanumeric characters. +# Regardless of the value of this property no white spaces are allowed in the material codes. +#material-relax-code-constraints=false + +# A comma-separated list of trusted cross-origin domains, that are allowed to +# query openBIS content. Typically these are lightweight webapps that integrate with openBIS +# via JSON-RPC services, but are not directly hosted within the openBIS application. +# +# Example 1 (two different domains configured): +# +# trusted-cross-origin-domains=https://myapp.domain.com:8443, http://other.domain.com +# +# Example 2 (match every domain): +# +# trusted-cross-origin-domains= * +# +# The '*' matches any arbitrary domain. It should be used with care as it opens openBIS +# for potential cross-site scripting attacks. +# +#trusted-cross-origin-domains= diff --git a/openbis_standard_technologies/dist/server/web-client.properties b/openbis_standard_technologies/dist/server/web-client.properties new file mode 100644 index 0000000000000000000000000000000000000000..9962d22f69902c4b6df838daab19f34d387f0750 --- /dev/null +++ b/openbis_standard_technologies/dist/server/web-client.properties @@ -0,0 +1,95 @@ +# Enable moving entities to trash (non-permanent deletion). +# Default value: true +enable-trash = true + +# Default view mode that should be used if user doesn't have it specified in URL. +# Options: +# 'NORMAL' (standard mode - default), +# 'SIMPLE' (readonly mode with simplified GUI), +# 'EMBEDDED' (similar to 'SIMPLE', suitable to be embedded on external pages) +# +#default-view-mode = SIMPLE + +# Maximal number of visible columns in tables. Default: 50. +#max-visible-columns = 20 + +# (optional) List of data set types for which there should be an image overview shown in dataset tables. +# If not specified image overview will not be shown for any datasets +# even if some overview plugins have been configured. +# +data-set-types-with-image-overview = MICROSCOPY_IMAGE, .*IMG.* + +# Configuration of entity (experiment, sample, data set, material) detail views. +# Allows to hide chosen sections. +# +# Mandatory properties: +# - view (entity detail view id) +# - types (list of entity type codes) +# Optional properties: +# - hide-sections (list of section ids) +# - hide-smart-view (removes "Smart View" from Data Set Detail View -> Data View) (generic_dataset_viewer) +# - hide-file-view (removes "File View" from Data Set Detail View -> Data View) (generic_dataset_viewer) +# Available sections in entity-detail-views: +# generic_dataset_viewer +# data-set-data-section +# data-set-parents-section +# data-set-children-section +# query-section +# generic_experiment_viewer +# data-sets-section +# attachment-section +# query-section +# container-sample-section +# generic_sample_viewer +# container-sample-section +# derived-samples-section +# parent-samples-section +# data-sets-section +# attachment-section +# query-section +# generic_material_viewer +# query-section +# +# Example: +# +detail-views = plate-or-well-view, image-data-view, image-analysis-data-view, microscopy-dataset-view + +#experiment-view.view = generic_experiment_viewer +#experiment-view.types = SIRNA_HCS +#experiment-view.hide-sections = data-sets-section, attachment-section + +plate-or-well-view.view = generic_sample_viewer +plate-or-well-view.types = PLATE.*, .*WELL.* +plate-or-well-view.hide-sections = container-sample-section, derived-samples-section, parent-samples-section + +image-data-view.view = generic_dataset_viewer +image-data-view.types = HCS_IMAGE.* +image-data-view.hide-sections = data-set-parents-section, data-set-children-section, plate-layout-dataset-section +image-data-view.hide-smart-view = false +image-data-view.hide-file-view = true + +image-analysis-data-view.view = generic_dataset_viewer +image-analysis-data-view.types = HCS_ANALYSIS_WELL_FEATURES.* +image-analysis-data-view.hide-sections = data-set-parents-section, data-set-children-section +image-analysis-data-view.hide-smart-view = true +image-analysis-data-view.hide-file-view = true + +microscopy-dataset-view.view = generic_dataset_viewer +microscopy-dataset-view.types = MICROSCOPY_IMAGE, .*IMG.* +microscopy-dataset-view.hide-sections = data-set-children-section, data-set-parents-section +microscopy-dataset-view.hide-smart-view = false +microscopy-dataset-view.hide-file-view = true + +technologies = proteomics, screening + +# Relative path of cache. Default value is 'cache'. +proteomics.cache-folder = ../../../web-client-data-cache +# Minimum free disk space needed for the cache. Default value is 1 GB. +#proteomics.minimum-free-disk-space-in-MB = 1024 +# Maximum retention time. Data older than this time will be removed from cache. Default value is a week. +#proteomics.maximum-retention-time-in-days = 7 + +screening.image-viewer-enabled = true +# Material properties of the configured type will be rendered as links +# to the material detail view. +#screening.material-details-property-type = GENE_SYMBOLS