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MINGYJ
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korydraughn
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iRODS: Replace Jargon with irods4j
1 parent 535c8ef commit 4a69ec5

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-616
lines changed

‎irods/bin/pom.xml‎

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<!--
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~ Copyright (c) 2002-2016 iterate GmbH. All rights reserved.
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~ https://cyberduck.io/
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~
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~ This program is free software; you can redistribute it and/or modify
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~ it under the terms of the GNU General Public License as published by
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~ the Free Software Foundation; either version 2 of the License, or
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~ (at your option) any later version.
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~
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~ This program is distributed in the hope that it will be useful,
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~ but WITHOUT ANY WARRANTY; without even the implied warranty of
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~ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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~ GNU General Public License for more details.
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-->
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<parent>
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<groupId>ch.cyberduck</groupId>
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<artifactId>parent</artifactId>
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<version>9.2.0-SNAPSHOT</version>
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</parent>
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<artifactId>irods</artifactId>
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<packaging>jar</packaging>
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<dependencies>
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<dependency>
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<groupId>ch.cyberduck</groupId>
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<artifactId>core</artifactId>
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<version>${project.version}</version>
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</dependency>
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<dependency>
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<groupId>ch.cyberduck</groupId>
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<artifactId>test</artifactId>
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<type>pom</type>
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<scope>test</scope>
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<version>${project.version}</version>
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</dependency>
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<!--
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<dependency>
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<groupId>ch.iterate.jargon</groupId>
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<artifactId>jargon-core</artifactId>
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<version>4.2.0.1</version>
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<exclusions>
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<exclusion>
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<groupId>com.claymoresystems</groupId>
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<artifactId>puretls</artifactId>
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</exclusion>
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<exclusion>
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<groupId>org.globus.jglobus</groupId>
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<artifactId>cog-jglobus</artifactId>
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</exclusion>
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<exclusion>
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<groupId>org.perf4j</groupId>
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<artifactId>perf4j</artifactId>
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</exclusion>
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<exclusion>
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<groupId>log4j</groupId>
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<artifactId>log4j</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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-->
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</dependencies>
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<build>
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<plugins>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-failsafe-plugin</artifactId>
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<configuration>
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<skipTests>true</skipTests>
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</configuration>
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</plugin>
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</plugins>
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</build>
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</project>
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‎irods/bin/src/test/resources/iRODS (iPlant Collaborative).cyberduckprofile‎

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<?xml version="1.0" encoding="UTF-8"?>
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<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
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<plist version="1.0">
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<dict>
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<key>Protocol</key>
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<string>irods</string>
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<key>Vendor</key>
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<string>iplant</string>
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<key>Description</key>
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<string>iPlant Data Store</string>
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<key>Hostname Configurable</key>
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<false/>
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<key>Port Configurable</key>
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<false/>
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<key>Default Hostname</key>
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<string>data.iplantcollaborative.org</string>
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<key>Region</key>
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<string>iplant</string>
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<key>Default Port</key>
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<string>1247</string>
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<key>Username Placeholder</key>
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<string>iPlant username</string>
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<key>Password Placeholder</key>
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<string>iPlant password</string>
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<key>Authorization</key>
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<string>STANDARD</string>
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</dict>
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</plist>

‎irods/output.txt‎

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irods.host=172.20.0.2
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irods.port=1247
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irods.zoneName=tempZone
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# STANDARD | PAM AUTH
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irods.auth.scheme=STANDARD
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default.storage.resource=
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# sets jargon ssl negotiation policy for the client. Leaving to DONT_CARE defers to the server, and is recommended
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# NO_NEGOTIATION, CS_NEG_REFUSE, CS_NEG_REQUIRE, CS_NEG_DONT_CARE
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ssl.negotiation.policy=CS_NEG_REFUSE
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##########################################################
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# jargon properties settings
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utilize.packing.streams=true
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# jargon now supports checksum calculation for streaming uploads. This does not currently verify, but does store if set to true
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compute.checksum=true
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######################################
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# other irods environment
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# HTTP connection for RMD
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rmd.connection.timeout=500
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rmd.connection.port=8000
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# Reverse DNS lookup on dashboard
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reverse.dns.lookup=false
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######################################
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# msi props
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populate.msi.enabled=false
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illumina.msi.enabled=true
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# MSI API version supported by this application
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msi.api.version=1.X.X
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msi.metalnx.list=libmsiget_illumina_meta.so,libmsiobjget_microservices.so,libmsiobjget_version.so,libmsiobjjpeg_extract.so,libmsiobjput_mdbam.so,libmsiobjput_mdbam.so,libmsiobjput_mdmanifest.so,libmsiobjput_mdvcf.so,libmsiobjput_populate.so
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msi.irods.list=libmsisync_to_archive.so,libmsi_update_unixfilesystem_resource_free_space.so,libmsiobjput_http.so,libmsiobjput_irods.so,libmsiobjget_irods.so,libmsiobjget_http.so,libmsiobjput_slink.so,libmsiobjget_slink.so
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msi.irods.42.list=libmsisync_to_archive.so,libmsi_update_unixfilesystem_resource_free_space.so
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msi.other.list=
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######################################
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# global feature flags that serve as defaults. Note that the info handling will manipulate aspects of the data profiler,
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# so by default some things are set to null to be turned on by the service depending on the view requested (e.g. acl, metadata, replicas) and should be left 'false' as a default,
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# but other aspects, such as metadata templating and mime type detection, can be globally turned on or off depending on the implmenetation.
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# controls access to features globally
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metalnx.enable.tickets=false
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# disable automatic detection and running of rules on upload
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metalnx.enable.upload.rules=false
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# download size limit in megabytes (6000=6GB)
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metalnx.download.limit=6000
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# show dashboard (off by default due to performance issues)
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metalnx.enable.dashboard=false
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######################################
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# info home page feature flags
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# this controls the behavior of the data profiler and what information it will gather
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irodsext.dataprofiler.retrieve.tickets=false
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# process starred or favorites
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irodsext.dataprofiler.retrieve.starred=true
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# process shared
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irodsext.dataprofiler.retrieve.shared=false
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# tags and comments
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irodsext.dataprofiler.retrieve.tags.and.comments=false
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# metadata templates (currently not implemented)
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irodsext.dataprofiler.retrieve.metadata.templates=false
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# save data type information for later use
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irodsext.datatyper.persist.data.types=false
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# perform a detailed versus a lightweight data typing, which may involve processing the file contents
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irodsext.datatyper.detailed.determination=false
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#############################
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# misc ui configuration niceties
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#############################
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# allow translation of iRODS auth types to user friendly names in login
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# in the form irodstype:displaytype|
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metalnx.authtype.mappings=PAM:PAM|STANDARD:Standard
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#############################
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# JWT configuration (necessary when using search and notification services). Otherwise can be left as-is and ignored
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#############################
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jwt.issuer=metalnx
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jwt.secret=thisisasecretthatisverysecretyouwillneverguessthiskey
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jwt.algo=HS384
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#############################
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# Pluggable search configuration. Turn on and off pluggable search globally, and configure search endpoints.
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# N.B. pluggable search also requires provisioning of the jwt.* information above
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#############################
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# configured endpoints, comma delimited in form https://host.com/v1
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# Note the commented out URL which matches up to the irods-contrib/file-and-metadata-indexer docker compose assembly. In order to
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# utilize this assembly you need to uncomment the URL and set pluggablesearch.enabled to true
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pluggablesearch.endpointRegistryList=
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# enable pluggable search globally and show the search GUI components
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pluggablesearch.enabled=false
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# display the older file and properties search in the menu, if you are running the elasticsearch standard plugin this is probably
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# a menu item to turn off
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classicsearch.enabled=true
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# JWT subject claim used to access search endpoint for data gathering. User searches will utilize the name of the individual
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pluggablesearch.endpointAccessSubject=metalnx
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# timeout for info/attribute gathering, set to 0 for no timeout
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pluggablesearch.info.timeout=0
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# timeout for actual search, set to 0 for no timeout
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pluggablesearch.search.timeout=0
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#############################
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# Pluggable shopping cart and export plugin configuration.
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# Turn on and off pluggable shopping cart globally, and configure export endpoints.
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# N.B. plugins also requires provisioning of the jwt.* information above
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#############################
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# enable pluggable export globally and show the export GUI components
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pluggableshoppingcart.enabled=false
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# configured endpoints, comma delimited in form https://host.com/v1
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pluggablepublishing.endpointRegistryList=
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# timeout for info/attribute gathering, set to 0 for no timeout
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pluggablepublishing.info.timeout=0
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# timeout for actual publishing, set to 0 for no timeout
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pluggablepublishing.publishing.timeout=0
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# server rule engine instance that will provide the galleryview listing
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gallery_view.rule_engine_plugin.instance_name=irods_rule_engine_plugin-irods_rule_language-instance
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##########################################################
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# Metadata Masking Properties
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#
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# Excludes metadata when the attribute name starts with at least one prefix.
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# Multiple prefixes can be defined by separating them with the character sequence defined
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# by metalnx.metadata.mask.delimiter.
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#
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# For example, the configuration below will hide any metadata that contains an attribute
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# starting with "irods::", "metalnx-", or "_system_".
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#
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# metalnx.metadata.mask.prefixes=irods::;metalnx-;_system_
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# metalnx.metadata.mask.delimiter=;
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#
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# Use the iRODS Metadata Guard rule engine plugin to protect your metadata namespaces from
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# being modified.
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metalnx.metadata.mask.prefixes=
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metalnx.metadata.mask.delimiter=,
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##########################################################
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# Setting to enable/disable the "Public" sidebar link.
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# The default is "false" (hidden)
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##########################################################
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sidebar.show.public=false

‎irods/pom.xml‎

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<packaging>jar</packaging>
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<dependencies>
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<dependency>
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<groupId>org.irods</groupId>
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<artifactId>irods4j</artifactId>
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<version>0.2.0-java8</version>
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</dependency>
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<dependency>
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<groupId>ch.cyberduck</groupId>
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<artifactId>core</artifactId>
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<scope>test</scope>
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<version>${project.version}</version>
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</dependency>
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<dependency>
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<groupId>ch.iterate.jargon</groupId>
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<artifactId>jargon-core</artifactId>
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<version>4.2.0.1</version>
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<exclusions>
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<exclusion>
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<groupId>com.claymoresystems</groupId>
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<artifactId>puretls</artifactId>
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</exclusion>
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<exclusion>
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<groupId>org.globus.jglobus</groupId>
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<artifactId>cog-jglobus</artifactId>
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</exclusion>
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<exclusion>
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<groupId>org.perf4j</groupId>
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<artifactId>perf4j</artifactId>
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</exclusion>
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<exclusion>
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<groupId>log4j</groupId>
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<artifactId>log4j</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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</dependencies>
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<build>

‎irods/src/main/java/ch/cyberduck/core/irods/ChunkWorker.java‎

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package ch.cyberduck.core.irods;
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import java.io.IOException;
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import java.io.RandomAccessFile;
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import org.irods.irods4j.high_level.io.IRODSDataObjectInputStream;
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import org.irods.irods4j.high_level.io.IRODSDataObjectOutputStream;
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import org.irods.irods4j.high_level.io.IRODSDataObjectStream.SeekDirection;
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import org.irods.irods4j.low_level.api.IRODSException;
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public class ChunkWorker implements Runnable{
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private final Object stream;
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private final RandomAccessFile file;
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private final long offset;
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private final long chunkSize;
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private final byte[] buffer;
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public ChunkWorker(Object stream, String localfilePath,long offset, long chunkSize, int bufferSize) throws IOException, IRODSException {
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this.stream= stream;
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this.file=new RandomAccessFile(localfilePath,"rw");
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this.offset=offset;
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this.chunkSize=chunkSize;
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this.buffer=new byte[bufferSize];
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file.seek(offset);
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}
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@Override
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public void run(){
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try {
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if (stream instanceof IRODSDataObjectInputStream) {
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IRODSDataObjectInputStream in = (IRODSDataObjectInputStream) (stream);
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in.seek((int) offset, SeekDirection.CURRENT);
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long remaining = chunkSize;
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while (remaining > 0) {
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int readLength = (int) Math.min(buffer.length, remaining);
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int read = in.read(buffer, 0, readLength);
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file.write(buffer, 0, read);
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remaining -= read;
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}
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}else if (stream instanceof IRODSDataObjectOutputStream) {
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IRODSDataObjectOutputStream out = (IRODSDataObjectOutputStream) (stream);
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out.seek((int) offset, SeekDirection.CURRENT);
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long remaining = chunkSize;
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while (remaining > 0) {
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int writeLength = (int) Math.min(buffer.length, remaining);
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int read = file.read(buffer, 0, writeLength);
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if (read == -1) break;
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out.write(buffer, 0, read);
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remaining -= read;
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}
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}else {
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throw new IllegalArgumentException("Unsupported stream type");
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}
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} catch (IOException | IRODSException e) {
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e.printStackTrace();
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}
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try {
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close();
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} catch (IOException e) {
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e.printStackTrace();
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}
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}
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public void close() throws IOException {
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file.close();
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if (stream instanceof IRODSDataObjectInputStream) {
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IRODSDataObjectInputStream in = (IRODSDataObjectInputStream) (stream);
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in.close();
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} else if (stream instanceof IRODSDataObjectOutputStream) {
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IRODSDataObjectOutputStream out = (IRODSDataObjectOutputStream) (stream);
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out.close();
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}
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}
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}

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