{"action":"created","comment":{"url":"https://api.github.com/repos/reactome/data-release-pipeline/pulls/comments/228161273","pull_request_review_id":168366135,"id":228161273,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDIyODE2MTI3Mw==","diff_hunk":"@@ -0,0 +1,81 @@\n+package org.reactome.release.downloadDirectory;\n+\n+import java.io.BufferedReader;\n+import java.io.FileInputStream;\n+import java.io.FileNotFoundException;\n+import java.io.FileOutputStream;\n+import java.io.FileReader;\n+import java.io.IOException;\n+import java.util.ArrayList;\n+import java.util.zip.ZipEntry;\n+import java.util.zip.ZipOutputStream;\n+\n+import org.apache.logging.log4j.LogManager;\n+import org.apache.logging.log4j.Logger;\n+import org.reactome.gsea.ReactomeToMsigDBExport;\n+\n+public class GSEAOutput {\n+\tprivate static final Logger logger = LogManager.getLogger();\n+\t\n+\tpublic static void execute(String username, String password, String host, int port, String database, int releaseNumber) {\n+\t\tlogger.info(\"Running GSEAOutput...\");\n+\t\tString outFilename = \"ReactomePathways.gmt\";\n+\t\tReactomeToMsigDBExport.main(new String[] {host, database, username, password, Integer.toString(port), outFilename});","path":"downloadDirectory/src/main/java/org/reactome/release/downloadDirectory/GSEAOutput.java","position":23,"original_position":23,"commit_id":"8b11ef9b1877913a502bd0a0a8677dab0cd414f3","original_commit_id":"8b11ef9b1877913a502bd0a0a8677dab0cd414f3","user":{"login":"cookersjs","id":19961210,"node_id":"MDQ6VXNlcjE5OTYxMjEw","avatar_url":"https://avatars0.githubusercontent.com/u/19961210?v=4","gravatar_id":"","url":"https://api.github.com/users/cookersjs","html_url":"https://github.com/cookersjs","followers_url":"https://api.github.com/users/cookersjs/followers","following_url":"https://api.github.com/users/cookersjs/following{/other_user}","gists_url":"https://api.github.com/users/cookersjs/gists{/gist_id}","starred_url":"https://api.github.com/users/cookersjs/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cookersjs/subscriptions","organizations_url":"https://api.github.com/users/cookersjs/orgs","repos_url":"https://api.github.com/users/cookersjs/repos","events_url":"https://api.github.com/users/cookersjs/events{/privacy}","received_events_url":"https://api.github.com/users/cookersjs/received_events","type":"User","site_admin":false},"body":"Right, it a reactome dependency. I'll make a comment about it","created_at":"2018-10-25T12:57:26Z","updated_at":"2018-10-25T12:57:26Z","html_url":"https://github.com/reactome/data-release-pipeline/pull/11#discussion_r228161273","pull_request_url":"https://api.github.com/repos/reactome/data-release-pipeline/pulls/11","author_association":"CONTRIBUTOR","_links":{"self":{"href":"https://api.github.com/repos/reactome/data-release-pipeline/pulls/comments/228161273"},"html":{"href":"https://github.com/reactome/data-release-pipeline/pull/11#discussion_r228161273"},"pull_request":{"href":"https://api.github.com/repos/reactome/data-release-pipeline/pulls/11"}},"in_reply_to_id":227965855},"pull_request":{"url":"https://api.github.com/repos/reactome/data-release-pipeline/pulls/11","id":225485040,"node_id":"MDExOlB1bGxSZXF1ZXN0MjI1NDg1MDQw","html_url":"https://github.com/reactome/data-release-pipeline/pull/11","diff_url":"https://github.com/reactome/data-release-pipeline/pull/11.diff","patch_url":"https://github.com/reactome/data-release-pipeline/pull/11.patch","issue_url":"https://api.github.com/repos/reactome/data-release-pipeline/issues/11","number":11,"state":"open","locked":false,"title":"Feature/download directory","user":{"login":"cookersjs","id":19961210,"node_id":"MDQ6VXNlcjE5OTYxMjEw","avatar_url":"https://avatars0.githubusercontent.com/u/19961210?v=4","gravatar_id":"","url":"https://api.github.com/users/cookersjs","html_url":"https://github.com/cookersjs","followers_url":"https://api.github.com/users/cookersjs/followers","following_url":"https://api.github.com/users/cookersjs/following{/other_user}","gists_url":"https://api.github.com/users/cookersjs/gists{/gist_id}","starred_url":"https://api.github.com/users/cookersjs/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cookersjs/subscriptions","organizations_url":"https://api.github.com/users/cookersjs/orgs","repos_url":"https://api.github.com/users/cookersjs/repos","events_url":"https://api.github.com/users/cookersjs/events{/privacy}","received_events_url":"https://api.github.com/users/cookersjs/received_events","type":"User","site_admin":false},"body":"Code for the download directory steps. It currently works in a docker container, but it's not been tested on any of the servers. A few notes:\r\n\r\n- Unit testing hasn't been done yet\r\n- The wrapper script that will call this on Release (and allow you to specify which steps to run) will be done after review\r\n- Parallelization of the sub-steps will be done in the near future\r\n- SBMLDumper and OutputCuratedComplexInstances can be ignored. These were finished before we found out what needed to be kept and what needed to be dropped\r\n\r\nRight now the script finishes by moving all files to the download-directory/ folder, under the folder corresponding to the release number. The parent Perl script will still handle moving all files to the static website directory. This is so that downloadDirectory doesn't interfere with any files EBI places in that folder. 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