{"id":16750666,"url":"https://github.com/egonw/knime-wikipathways","last_synced_at":"2025-10-10T12:10:02.827Z","repository":{"id":66514074,"uuid":"122479362","full_name":"egonw/knime-wikipathways","owner":"egonw","description":"KNIME nodes for WikiPathways.","archived":false,"fork":false,"pushed_at":"2018-03-21T13:22:44.000Z","size":48,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-01-22T17:11:33.596Z","etag":null,"topics":["biological-data-analysis","knime","pathway-analysis","wikipathways","workflow"],"latest_commit_sha":null,"homepage":null,"language":"Java","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/egonw.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2018-02-22T13:03:57.000Z","updated_at":"2018-03-21T13:22:45.000Z","dependencies_parsed_at":"2023-03-07T16:45:39.125Z","dependency_job_id":null,"html_url":"https://github.com/egonw/knime-wikipathways","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/egonw%2Fknime-wikipathways","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/egonw%2Fknime-wikipathways/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/egonw%2Fknime-wikipathways/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/egonw%2Fknime-wikipathways/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/egonw","download_url":"https://codeload.github.com/egonw/knime-wikipathways/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243826243,"owners_count":20354220,"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","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":["biological-data-analysis","knime","pathway-analysis","wikipathways","workflow"],"created_at":"2024-10-13T02:28:56.735Z","updated_at":"2025-10-10T12:09:57.753Z","avatar_url":"https://github.com/egonw.png","language":"Java","funding_links":[],"categories":[],"sub_categories":[],"readme":"# WikiPathways KNIME Nodes\n\nThese nodes are based on the KNIME node skeleton with sample code as described [here](https://tech.knime.org/developer-guide).\n\n[![Build Status](https://travis-ci.org/egonw/knime-wikipathways.svg?branch=master)](https://travis-ci.org/egonw/knime-wikipathways)\n[![SonarCloud Gate](https://sonarcloud.io/api/badges/gate?key=org.wikipathways:org.wikipathways.knime)](https://sonarcloud.io/dashboard?id=org.wikipathways:org.wikipathways.knime)\n[![SonarCloud Coverage](https://sonarcloud.io/api/badges/measure?key=org.wikipathways:org.wikipathways.knime\u0026metric=coverage)](https://sonarcloud.io/component_measures/domain/Coverage?id=org.wikipathways:org.wikipathways.knime)\n\nThis project uses [Eclipse Tycho](https://www.eclipse.org/tycho/) to perform build steps.\n\n# Installation\n\nRequirements:\n\n* KNIME, https://www.knime.org, version 3.5 or higher\n\nSteps to get the WikiPathwaysNode KNIME node inside KNIME:\n\n1. Goto Help \u003e Install new software ... menu\n2. Press add button\n3. Fill text fields with url of update site which contains this node.\n4. Select --all sites-- in `work with` pulldown\n5. Select the node\n6. Install software\n7. Restart KNIME\n\n# Usage\n\n1. Create a new KNIME workflow.\n2. Find node in Node navigator panel.\n3. Drag node to workflow canvas.\n\n# Build\n\nTo build the node extension and verify the tests run with the following command:\n```\nmvn verify\n```\n\nMake sure all code is commited as the snapshot version is determined by git commit timestamp.\n\nAn Eclipse update site will be made in `p2/target/repository` directory.\nThe update site can be used to perform a local installation.\n\n## Continuous Integration\n\nConfiguration files to run Continuous Integration builds on Linux (Travis-CI), OS X (Travis-CI) and Windows (AppVeyor) are present.\n\nSee `./.travis.yml` file how to trigger a Travis-CI build for every push or pull request.\nAlso see `./.travis.yml` file how to perform a [SonarCloud](https://sonarcloud.io/) analysis and code coverage.\n\nSee `./appveyor.yml` file how to run on https://www.appveyor.com .\n\n# Development\n\nSteps to get development environment setup:\n\n1. Download KNIME SDK from https://www.knime.org/downloads/overview\n2. Install/extract KNIME SDK\n3. Start KNIME SDK\n4. Install m2e (Maven integration for Eclipse) + Test workflows in JUnit\n\n    1. Goto Window -\u003e Preferences -\u003e Install/Update -\u003e Available Software Sites\n    2. Make sure the following Software Sites (or a version of them) are present otherwise add them:\n\n      * http://update.knime.org/analytics-platform/3.5\n      * http://download.eclipse.org/eclipse/updates/4.6\n      * http://download.eclipse.org/releases/neon\n      * https://3d-e-chem.github.io/updates (only required for 3D-e-Chem node)\n\n    3. Goto Help -\u003e Check for updates\n    4. Install any updates found \u0026 restart\n    5. Goto Help \u003e Install new software ...\n    6. Select --All Available sites-- in work with pulldown\n    7. Wait for list to be filled, `Pending...` should disappear\n    8. Select the following items:\n\n      * m2e - Maven integration for Eclipse (includes Incubating components)\n      * Test KNIME workflows from a Junit test\n      * Splash \u0026 node category for 3D-e-Chem KNIME nodes (only required for 3D-e-Chem node)\n\n    9. Install software \u0026 restart\n\n5. Import this repo as an Existing Maven project\n\nDuring import the Tycho Eclipse providers must be installed, Eclipse will ask for your permission.\n\n## Tests\n\nTests for the node are in `tests/src` directory.\nTests can be executed with `mvn verify`, they will be run in a separate KNIME environment.\nTest results will be written to `test/target/surefire-reports` directory.\nCode coverage reports (html+xml) can be found in the `tests/target/jacoco/report/` directory.\n\nThe tests can be run against a different KNIME version using `mvn verify -Dknime.version=3.5` where `3.5` is the major.minor version of KNIME.\n\n### Unit tests\n\nUnit tests written in Junit4 format can be put in `tests/src/java`.\n\n### Workflow tests\n\nSee https://github.com/3D-e-Chem/knime-testflow#3-add-test-workflow\n\n## Speed up builds\n\nRunning mvn commands can take a long time as Tycho fetches indices of all p2 update sites.\nThis can be skipped by running maven offline using `mvn -o`.\n\n# New release\n\n1. Update versions in pom files with `mvn org.eclipse.tycho:tycho-versions-plugin:set-version -DnewVersion=\u003cversion\u003e-SNAPSHOT` command.\n2. Create package with `mvn package`, will create update site in `p2/target/repository`\n3. Run tests with `mvn verify`\n4. Optionally, test node by installing it in KNIME from a local update site\n5. Append new release to an update site\n  1. Make clone of an update site repo\n  2. Append release to the update site with `mvn install -Dtarget.update.site=\u003cpath to update site\u003e`\n6. Commit and push changes in this repo and update site repo.\n7. Create a Github release\n8. Update Zenodo entry\n  1. Correct authors\n  2. Correct license\n9. Make nodes available to 3D-e-Chem KNIME feature by following steps at https://github.com/3D-e-Chem/knime-node-collection#new-release\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fegonw%2Fknime-wikipathways","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fegonw%2Fknime-wikipathways","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fegonw%2Fknime-wikipathways/lists"}