{"id":30670516,"url":"https://github.com/bridgedb/bridgedb","last_synced_at":"2026-01-05T21:17:59.661Z","repository":{"id":11460294,"uuid":"13923694","full_name":"bridgedb/BridgeDb","owner":"bridgedb","description":"The BridgeDb Library source code","archived":false,"fork":false,"pushed_at":"2025-07-26T23:03:32.000Z","size":34226,"stargazers_count":29,"open_issues_count":36,"forks_count":21,"subscribers_count":11,"default_branch":"main","last_synced_at":"2025-07-27T02:45:55.739Z","etag":null,"topics":["bioinformatics","bridgedb","database","hacktoberfest","identifier-mapping","java","mysql-backend","uri"],"latest_commit_sha":null,"homepage":"https://bridgedb.org/","language":"Java","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/bridgedb.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2013-10-28T11:15:16.000Z","updated_at":"2025-05-18T18:11:29.000Z","dependencies_parsed_at":"2023-01-13T16:31:27.335Z","dependency_job_id":"1f792c1e-c640-4bb3-bdd7-8da22ff44ac4","html_url":"https://github.com/bridgedb/BridgeDb","commit_stats":{"total_commits":2087,"total_committers":37,"mean_commits":56.4054054054054,"dds":0.7589841878294202,"last_synced_commit":"0e0ad85c88a67c0c8e65e7707b74c7394effc8d4"},"previous_names":[],"tags_count":84,"template":false,"template_full_name":null,"purl":"pkg:github/bridgedb/BridgeDb","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bridgedb%2FBridgeDb","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bridgedb%2FBridgeDb/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bridgedb%2FBridgeDb/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bridgedb%2FBridgeDb/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bridgedb","download_url":"https://codeload.github.com/bridgedb/BridgeDb/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bridgedb%2FBridgeDb/sbom","scorecard":{"id":253632,"data":{"date":"2025-08-11","repo":{"name":"github.com/bridgedb/BridgeDb","commit":"73479d92cdfddc702cd8f720f6a617d6ac3a6c6e"},"scorecard":{"version":"v5.2.1-40-gf6ed084d","commit":"f6ed084d17c9236477efd66e5b258b9d4cc7b389"},"score":3.3,"checks":[{"name":"Maintained","score":10,"reason":"16 commit(s) and 1 issue activity found in the last 90 days -- score normalized to 10","details":null,"documentation":{"short":"Determines if the project is \"actively maintained\".","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#maintained"}},{"name":"Dangerous-Workflow","score":10,"reason":"no dangerous workflow patterns detected","details":null,"documentation":{"short":"Determines if the project's GitHub Action workflows avoid dangerous patterns.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#dangerous-workflow"}},{"name":"Token-Permissions","score":0,"reason":"detected GitHub workflow tokens with excessive permissions","details":["Warn: no topLevel permission defined: .github/workflows/build.yml:1","Info: no jobLevel write permissions found"],"documentation":{"short":"Determines if the project's workflows follow the principle of least privilege.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#token-permissions"}},{"name":"Packaging","score":-1,"reason":"packaging workflow not detected","details":["Warn: no GitHub/GitLab publishing workflow detected."],"documentation":{"short":"Determines if the project is published as a package that others can easily download, install, easily update, and uninstall.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#packaging"}},{"name":"Code-Review","score":0,"reason":"Found 0/18 approved changesets -- score normalized to 0","details":null,"documentation":{"short":"Determines if the project requires human code review before pull requests (aka merge requests) are merged.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#code-review"}},{"name":"CII-Best-Practices","score":0,"reason":"no effort to earn an OpenSSF best practices badge detected","details":null,"documentation":{"short":"Determines if the project has an OpenSSF (formerly CII) Best Practices Badge.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#cii-best-practices"}},{"name":"Binary-Artifacts","score":3,"reason":"binaries present in source code","details":["Warn: binary detected: org.bridgedb.gui/lib/org.pathvisio.jgoodies.forms-1.2.0.jar:1","Warn: binary detected: org.bridgedb.rdf/lib/openrdf-sesame-2.6.5-onejar.jar:1","Warn: binary detected: org.bridgedb.uri.ws.server/lib/jsr311-api-1.1.1.jar:1","Warn: binary detected: org.bridgedb.ws.client/lib/jersey-client-1.10.jar:1","Warn: binary detected: org.bridgedb.ws.client/lib/jersey-core-1.10.jar:1","Warn: binary detected: org.bridgedb.ws.client/lib/jsr311-api-1.1.1.jar:1","Warn: binary detected: org.bridgedb.ws.server/lib/jsr311-api-1.1.1.jar:1"],"documentation":{"short":"Determines if the project has generated executable (binary) artifacts in the source repository.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#binary-artifacts"}},{"name":"Security-Policy","score":0,"reason":"security policy file not detected","details":["Warn: no security policy file detected","Warn: no security file to analyze","Warn: no security file to analyze","Warn: no security file to analyze"],"documentation":{"short":"Determines if the project has published a security policy.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#security-policy"}},{"name":"License","score":10,"reason":"license file detected","details":["Info: project has a license file: LICENSE:0","Info: FSF or OSI recognized license: Apache License 2.0: LICENSE:0"],"documentation":{"short":"Determines if the project has defined a license.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#license"}},{"name":"Fuzzing","score":0,"reason":"project is not fuzzed","details":["Warn: no fuzzer integrations found"],"documentation":{"short":"Determines if the project uses fuzzing.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#fuzzing"}},{"name":"Pinned-Dependencies","score":0,"reason":"dependency not pinned by hash detected -- score normalized to 0","details":["Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/build.yml:14: update your workflow using https://app.stepsecurity.io/secureworkflow/bridgedb/BridgeDb/build.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/build.yml:16: update your workflow using https://app.stepsecurity.io/secureworkflow/bridgedb/BridgeDb/build.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/build.yml:29: update your workflow using https://app.stepsecurity.io/secureworkflow/bridgedb/BridgeDb/build.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/build.yml:31: update your workflow using https://app.stepsecurity.io/secureworkflow/bridgedb/BridgeDb/build.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/build.yml:39: update your workflow using https://app.stepsecurity.io/secureworkflow/bridgedb/BridgeDb/build.yml/main?enable=pin","Info:   0 out of   4 GitHub-owned GitHubAction dependencies pinned","Info:   0 out of   1 third-party GitHubAction dependencies pinned"],"documentation":{"short":"Determines if the project has declared and pinned the dependencies of its build process.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#pinned-dependencies"}},{"name":"Signed-Releases","score":-1,"reason":"no releases found","details":null,"documentation":{"short":"Determines if the project cryptographically signs release artifacts.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#signed-releases"}},{"name":"Branch-Protection","score":-1,"reason":"internal error: error during branchesHandler.setup: internal error: githubv4.Query: Resource not accessible by integration","details":null,"documentation":{"short":"Determines if the default and release branches are protected with GitHub's branch protection settings.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#branch-protection"}},{"name":"SAST","score":0,"reason":"SAST tool is not run on all commits -- score normalized to 0","details":["Warn: 0 commits out of 13 are checked with a SAST tool"],"documentation":{"short":"Determines if the project uses static code analysis.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#sast"}},{"name":"Vulnerabilities","score":2,"reason":"8 existing vulnerabilities detected","details":["Warn: Project is vulnerable to: GHSA-735f-pc8j-v9w8","Warn: Project is vulnerable to: GHSA-rcjc-c4pj-xxrp","Warn: Project is vulnerable to: GHSA-h46c-h94j-95f3","Warn: Project is vulnerable to: GHSA-78wr-2p64-hpwj","Warn: Project is vulnerable to: GHSA-j288-q9x7-2f5v","Warn: Project is vulnerable to: GHSA-5m48-vr54-vmh3","Warn: Project is vulnerable to: GHSA-36wv-v2qp-v4g4","Warn: Project is vulnerable to: GHSA-fh5r-crhr-qrrq"],"documentation":{"short":"Determines if the project has open, known unfixed vulnerabilities.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#vulnerabilities"}}]},"last_synced_at":"2025-08-17T09:04:11.481Z","repository_id":11460294,"created_at":"2025-08-17T09:04:11.482Z","updated_at":"2025-08-17T09:04:11.482Z"},"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273064983,"owners_count":25039267,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-09-01T02:00:09.058Z","response_time":120,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","bridgedb","database","hacktoberfest","identifier-mapping","java","mysql-backend","uri"],"created_at":"2025-09-01T02:06:59.892Z","updated_at":"2026-01-05T21:17:59.655Z","avatar_url":"https://github.com/bridgedb.png","language":"Java","funding_links":[],"categories":[],"sub_categories":[],"readme":"BridgeDb\n========\n\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.593034.svg)](https://doi.org/10.5281/zenodo.593034)\n[![Actions Status](https://github.com/bridgedb/BridgeDb/workflows/build/badge.svg)](https://github.com/bridgedb/BridgeDb/actions)\n[![Maven Central](https://maven-badges.herokuapp.com/maven-central/org.bridgedb/bridgedb-bundle/badge.svg)](https://maven-badges.herokuapp.com/maven-central/org.bridgedb/bridgedb-bundle)\n[![codecov](https://codecov.io/gh/bridgedb/BridgeDb/branch/master/graph/badge.svg?token=F0kJdoEt0x)](https://codecov.io/gh/bridgedb/BridgeDb)\n[![NWO](https://img.shields.io/badge/NWO%20Open%20Science-203.001.121-orange)](https://www.nwo.nl/en/projects/203001121)\n\nBridgeDb is currently tested with Java 11 and higher (3.0.x releases and master branch).\n\nUsing BridgeDb dependencies\n---------------------------\n\nThe [BridgeDb releases](https://github.com/bridgedb/BridgeDb/releases) are published to \n[Maven Central](https://search.maven.org/artifact/org.bridgedb/bridgedb-bundle), which means you can use the BridgeDb JARs without needing to compile BridgeDb.\n\nUsage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `3.0.30`:\n\nFor [Maven](https://maven.apache.org/):\n\n```xml\n\u003cdependencies\u003e\n    \u003cdependency\u003e\n        \u003cgroupId\u003eorg.bridgedb\u003c/groupId\u003e\n        \u003cartifactId\u003eorg.bridgedb.bio\u003c/artifactId\u003e\n        \u003cversion\u003e3.0.30\u003c/version\u003e\n    \u003c/dependency\u003e\n\u003c/dependencies\u003e\n```\n\nFor [Gradle](https://gradle.org/):\n\n```gradle\ncompile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.30'\n```\n\nFor [Ivy](http://ant.apache.org/ivy/):\n\n```xml\n\u003cdependency org=\"org.bridgedb\" name=\"org.bridgedb.bio\" rev=\"3.0.30\"/\u003e\n```\n\nFor [Buildr](https://buildr.apache.org/):\n\n```buildr\n'org.bridgedb:org.bridgedb.bio:jar:3.0.30'\n```\n\n\nCompilation\n-----------\n\nIf you've obtained the source code of BridgeDb, you should be\nable to compile with a simple:\n\n```shell\nmvn clean install -Dgpg.skip\n```\n\nWhen compiling the Java8-compatible components, use the `pom-java8.xml` file instead, with `mvn -f pom-java8.xml`.\n\nYou can find the libraries in the folder called \"target\", in each sublibrary folder (used to be called \"dist\" in ant).\n\nIf you want to ignore failing tests, e.g. because you are not online,\nadd this option: -Dmaven.test.failure.ignore=true. Furthermore,\nnote that 'mvn clean compile' fails.\n\nCommand line tools\n------------------\n\nThe BridgeDb distribution comes with a few command line tools. You\ncan try:\n\n```shell\nbash info.sh \u003cdatabase.bridge\u003e\nbash qc.sh \u003cdatabase.bridge\u003e \u003cdatabase2.bridge\u003e\nbash voidtool.sh \u003cdatabase.bridge\u003e \u003cfileName.void\u003e\n```\n\nChecking for regressions\n------------------------\n\nYou may want to run the following commands to detect regressions,\nwhich is particularly important before starting to make a release:\n\n```shell\nmvn clean test\n```\n\nNote that the first call may fail a number of unit tests, like for those\nof `IDMapperCapabilitiesTest`. For that one, this is because it is an\nabstract class that should not actually be run by JUnit as test suite.\n\nNote also that the second one may fail because BridgeDb module dependencies\nmay not be resolved yet.\n\nSeveral tests also depend on a running MySQL backend or running BridgeDb\nwebservice. You can exclude these tests in Maven with:\n\n```shell\nmvn clean test -Djunit5.excludeGroups=webservice,mysql\n```\n\nThe JUnit5 tagging also allows to specifically test the MySQL-backend tests,\nfor example with:\n\n```shell\nmvn clean test junit5.groups=mysql\n```\n\nUpdating the datasources\n------------------------\n\nThe `datasources.tsv` and `organisms.tsv` files were separated from this\nrepository, and this BridgeDb library is regularly updated for releases\nfrom [https://github.com/bridgedb/datasources](https://github.com/bridgedb/datasources).\n\n```shell\nwget -O ./org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv https://bridgedb.github.io/datasources/datasources.tsv\nwget -O ./org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources_headers.tsv https://bridgedb.github.io/datasources/datasources_headers.tsv\nwget -O ./org.bridgedb.bio/src/main/resources/org/bridgedb/bio/organisms.tsv https://bridgedb.github.io/datasources/organisms.tsv\ncp ./org.bridgedb.bio/src/main/resources/org/bridgedb/bio/*.tsv ./org.bridgedb.bio/resources/org/bridgedb/bio/.\n```\n\nThe last line makes a copy for backwards compatibility.\n\nMaking releases\n---------------\n\nIf it is time for a release, first, update `org.bridgedb/src/main/resources/version.props` (for BridgeDb),\nthis `README.md` and `CITATION.cff` (for Zenodo).\n\nTo make the release, run the following commands. Mind you, this requires you\nto have an approved Sonatype (http://oss.sonatype.org/) account with push rights:\n\n```shell\nmvn versions:set -DnewVersion=3.0.30\nmvn clean deploy\n```\n\nThe second command will make the actual push. These commands will update the version\nand everything.\n\nTo make a development (SNAPSHOT) release, use:\n\n```shell\nmvn versions:set -DnewVersion=3.0.31-SNAPSHOT\nmvn clean deploy\n```\n\nLibrary dependencies\n--------------------\n\nIf you do not use all mappers, you do not need to include all\nlibraries in the dist directory in your project.\n\nHere is a brief overview that will help you to find out\nwhich ones you need. For questions, you can always contact our mailing list.\n\n * org.bridgedb.jar - always needed. This includes the tab-delimited file driver.\n * org.bridgedb.bio.jar - includes the BioDataSource enum, often needed\n * org.bridgedb.webservice.cronos.jar - needed for CRONOS webservice\n * org.bridgedb.webservice.synergizer.jar - needed for Synergizer webservice\n * org.bridgedb.webservice.picr.jar - needed for PICR webservice\n * org.bridgedb.server.jar - the BridgeRest SERVER, not needed if you only want to access BridgeRest or BridgeWebservice as client\n * org.bridgedb.tools.batchmapper.jar - Contains the batchmapper command line tool\n\norg.bridgedb.jar and org.bridgedb.bio.jar do not need any other jar files to work.\nMost of the other jar files in dist/ are part of the SOAP libraries needed only for\nsome of the webservices. Look in the lib directory and build.xml of the \nrespective mappers to find clues which libraries are needed by which service.\n\nAdditional packages added for version 2 (mainly for URI support needed for OpenPHACTS)\norg.bridgedb.utils - adds logging and some utils - Needed for all of modules below\norg.bridgedb.sql - Alternative SQL database optimized for speed not size\n\norg.bridgedb.ws.*  Another version of the Webservice. Runs with and IDMapper\n\norg.bridgedb.rdf   Loads DataSources from rdf and miriam (with URI suppport)\n\norg.bridgedb.uri.sql   Adds support for URIs (requires org.bridgedb.sql)\norg.bridgedb.uri.loader  Loads RDF linksets into org.bridgedb.uri.sql. Also creates transitive linksets\n\norg.bridgedb.uri.ws.*  Extends org.bridgedb.ws.* with URI supports from org.bridgedb.uri.sql \n\nDatabase structure\n------------------\n\nFor further information about the database structure check [the documentation here](docs/database).\n\nContact\n-------\n\n* Website, wiki and bug tracker: http://www.bridgedb.org\n* Mailing list: http://groups.google.com/group/bridgedb-discuss/\n* Source code can be obtained from http://github.com/bridgedb/BridgeDb\n\nAuthors\n-------\n\nBridgeDb and related tools are developed by (alphabetic order):\n\n * Manas Awasthi\n * Christian Brenninkmeijer\n * Jianjiong Gao\n * Alasdair Gray\n * Isaac Ho\n * Martijn van Iersel\n * Alexander Pico\n * Stian Soiland-Reyes\n * Egon Willighagen\n * Martina Kutmon\n * Jonathan Mélius\n * Anders Riutta\n * Randy Kerber\n\nThe lead teams at this moment are (alphabetic order):\n\n * Gladstone Institutes\n * Maastricht University\n * The University of Manchester\n\nLicense\n-------\n\nBridgeDb is free and open source. It is available under\nthe conditions of the [Apache License, version 2.0](https://www.apache.org/licenses/LICENSE-2.0). \nSee LICENSE-2.0.txt for details.\n\nConfiguration For the URI/OpenPHACTS packages ONLY!\n=============\n\nWhere are configuration files loaded from?\n------------------------------------------\nBridgeDb looks for the configuration files from the following locations with priority given to those at the top of the list (i.e. location 1 is a\nhigher priority than 2 etc). Once it finds a configuration file the other locations are ignored.  \n\n1. Directly in the run directory  (Mainly for java *.jar runs)  \n2. Environment Variable `BRIDGEDB_CONFIG` : can be used to point to any location  \n3. Tomcat configuration folder : `$CATALINA_HOME/conf/BridgeDb`  \n4. conf/BridgeDb : Allows tomcat 7 to pick up `$CATALINA_HOME/conf/BridgeDb` even if it can not get `$CATALINA_HOME`  \n4. ../conf/BridgeDb : Allows tomcat 6 to pick up `$CATALINA_HOME/../conf/BridgeDb` even if it can not get `$CATALINA_HOME`  \n5. Using classLoader getResource : This will pick up the files included in Jars and Wars.  \n\n\nConfiguration files\n-------------------\n\n* local.properties\n* BridgeDB.properties\n* log4j.properties  \n* DataSource.ttl  \n* lens.properties  \n* graph.properties\n\n### local.properties\n(There is no local properties files included)\n\nThis is the recommended place to overwrite individual property values of any other *.properties file.\n\n`local.properties` will overwrite values with the same key in any other properties file.\nProperties not overwritten in local will keep their original values.\n\nTo install local properties you need to.\n\n1. Create a local.properties file  \n2. Store it in a location as described above  \n3. Copy the keys from the original file  \n\n### BridgeDB.properties\n(Default file is included in build and can be found in org.bridgedb.utils/resources)\n\nThis file contains the local setup information which **MUST** be configured correctly for the service to run. It is essential that the\ndatabase user, password and database name are correct.\n\t\t\nYou **MUST** either supply local values matching your local setup or setup your data stores to use the defaults. \nThe recommended way to overwrite properties is to add a property with the exact (case sensitive) key to local.properties\n\nDatabase Dependency   \n-------------------\n(for the org.bridgedb.sql package and its dependencies ONLY)\n\n* MySQL **MUST** be installed and running, otherwise it fails to start. Tested with MySQL up to version 5.5\n* MySQL databases and users **MUST** be created with CREATE, DROP, INDEX, INSERT, ALTER,\nUPDATE, DELETE, and SELECT permissions.\n\nConsult the BridgeDB.properties file for the defaults, or copy and amend the configuration file\nto reflect your own setup.\n\nIf you are using the default MySQL accounts and databases then execute the file \nmysqlConfig.sql from the BridgeDB root directory which will configure your local mysql with the BridgeDb defaults\n\n```shell\nmysql -u root -p \u003c mysqlConfig.sql\n```\n\nNote that the SQL script will fail, without reverting changes made up to the \npoint of failure, if any of the user accounts or databases already exist.\n\nRDF Repository and Transitive Directory Dependency\n-------------------------\n(For org.bridgedb.rdf package and its extensions ONLY)\n\nBridgeDb uses OpenRDF Sesame RDF engine and this is included automatically via Maven.  \n**WARNING**: All directories **MUST** exists and the (linux) user running tomcat **MUST** have READ/WRITE permission set!\nSome of the OpenRDF error message are unclear if this is not the case.\n\nSee BridgeDb.properties and change the appropriate property to point to the correct directory.\nA Sesame SailNativeStore(s) will be created automatically as long as the loader can create/find the directory,\n\nWe recommend changing the relative directories to absolute directories.\nPlease ensure the parent directories exist and have the correct permissions. \n\nThe settings for testing (and therefore compilation) can be left as is as long as the testing user would have permission to create and delete files there.\n\nThe BaseURI variable is no longer used but may be in the future so is worth setting correctly.\n\nOther Configuration files\n-------------------------\n### log4j.properties\n(Default file is included in build and can be found in org.bridgedb.utils/resources)\n\nEdit this to change the logger setup.\nThe default can be found in the Utils Resource directory\nPlease refer to the log4j documentation for more information.\n\n### DataSource.ttl \n(Included in the build and found at org.bridgedb.rdf/resources)\n\nRDF format of all the BridgeDb DataSource(s) and Registered UriPatterns,\nFound in $BRIDGEDB_HOME/org.bridgedb.rdf/resources\n\nThis file defines all the URI patterns that will match every BridgeDb DataSource.\nWarning: As additional UriPatterns are constantly being found and created this file is subject to continuous updates. \nHaving a local DataSource.ttl is therefore highly discouraged as it will block future updates being discovered.\nInstead please push any changes into the version inside the source code. \nThis file is **NOT** effected by local.properties and \nyou cannot change existing or add additional datasource URI patterns through local.properties. \nIf you require local additions that should not become general usage (such as commercial uriPatterns)\nthen the suggested approach is for you to change the code to use multiple dataSource files.\n\n### lens.properties\n(Included in the build and found at org.bridgedb.uri.sql\\resources)\n\nThis file defines the lenses to be used in the system.\nSee [Scientific Lenses over Linked Data](http://ceur-ws.org/Vol-951/paper5.pdf)\nfor more information on what lenses are.\n\nCan and should be added to using local.properties\n\n**WARNING**: As the Lens work is still evolving it is subject to alterations and the format of this file could be changed at any time.\nHaving a local lens.properties is highly discouraged as it will block future updates being discovered.\nInstead please push any changes into the version inside the source code.\n\nLocal additions that should not become general usage (such as commercial lens) can be added to the local.properties file.\n\nNote: the fourth part of the key  \n`lens.lenkey.justification.***`  \nonly serves to keep the keys unique and can have any value.\nIf extending a key we suggest using `local**` as the fourth part of the justification key to ensure not overwriting general additions.\n\n### graph.properties\n(Included in the build and found at org.bridgedb.uri.sql\\resources)\n\nThis file maps RDF Graphs/Context with the UriPatterns found in that graph.\nThis allows Map functions to supply a graph name rather than a list of targetUriPatterns\n\nData in the included file is Open PHACTS specific.\n\nData Loading\n============\nAll tests should load their required data at the start of the tests.\nTo load the test data into the live SQL use the method SetupWithTestData in the URI loader package.\nThe [IMS project](https://github.com/openphacts/IdentityMappingService) also has a data loader which should be used\nif the IMS is the deployed project.\n\nCompilation\n===========\nFor URI/Open PHACTS packages\n\nIf you've obtained the source code of BridgeDb, you should be\nable to compile with a simple: \n\n```shell\nmvn clean install\n```\n\t\nNote that for the maven build to run all tests: \n1. The MySQL database **MUST** be running and configured as above.\n2. (Optional) http://localhost:8080/OPS-IMS to be running the war created by the URI webserver Server module,\n   with test data which can be loaded using the class SetupWithTestData in the URI Loader module.\n   Maven will skip the client tests if the localhost server is not found.\n\t\nOPS Webservice Setup.\n--------------------\n\nMake sure your local.properties file matches:\n* The SQL databases included user names and password\n* The RDF parent directories are setup (and accessible) as above.\n\nor you have set up the default databases etc from BridgeDB.properties\n\nDeploy $BridgeDb/org.bridgedb.uri.ws.service/target/org.bridgedb.uri.ws.server-*.war to something like your local\nTomcat webapps directory\nTo setup databases and add test data run org.bridgedb.uri.loader.SetupLoaderWithTestData. The easiest way is within eclipse since you\ncan set the OPS_IMS_CONFIG environment variable within the run configuration, Netbeans unfortunately does not allow environment variables to be set\nwithin the IDE.\n(Optional) Deploy $BridgeDb/org.bridgedb.ws.service/target/BridgeDb.war\n   Both wars share the same SQL data.\n\n\nNote: If Installing the Open PHACTS IMS and or the Open PHACTS QueryExpander the org.bridgedb.uri.ws.server-*.war should not be deployed but\ninstead the war appropriate to the other project should be deployed. See the readme within the\nother projects for more details.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbridgedb%2Fbridgedb","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbridgedb%2Fbridgedb","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbridgedb%2Fbridgedb/lists"}