[{"_1":2,"_173":-5,"_174":-5},"loaderData",{"_3":4,"_13":14,"_20":21,"_152":153},"root",{"_5":-5,"_6":-7,"_7":8,"_9":-7,"_10":11,"_12":-7},"currentUser","primaryEmail","siteVerification","6LeIxAcTAAAAAJcZVRqyHh71UMIEGNQ_MXjiZKhI","toast","enableDev",false,"incidentStatus","routes/_layout",{"_15":-5,"_16":17,"_18":17,"_19":11},"username","isAskGordonEnabled",true,"isUsingNewTemplate","showMinimalLanding","routes/_layout.r.$namespace.$reponame",{"_22":23,"_24":-5,"_25":11,"_26":11,"_27":28,"_29":30,"_31":-5,"_32":11,"_33":34,"_83":84,"_106":107,"_145":-5,"_146":11,"_147":17,"_148":11,"_149":-5,"_150":151},"canonicalUrl","https://hub.docker.com/r/bioconductor/experimenthub_docker/tags","mcpServer","canSeeDockerfile","canSeeAutobuilds","namespace","bioconductor","reponame","experimenthub_docker","cloudBuildSource","isAutobuildsAvailable","repo",{"_35":36,"_37":38,"_40":41,"_42":43,"_44":11,"_45":46,"_47":48,"_49":50,"_52":30,"_27":28,"_53":54,"_55":39,"_56":57,"_58":57,"_59":60,"_61":-5,"_62":63,"_64":65,"_66":11,"_67":28,"_68":69,"_74":17,"_75":76,"_80":28,"_81":82},"categories",[],"content_types",[39],"image","date_registered","2016-01-12T22:30:35.598212Z","description","Experiment Hub","is_private","last_updated","2020-03-03T17:56:39.664365Z","last_modified","2024-10-16T13:48:34.145251Z","media_types",[51],"application/vnd.docker.container.image.v1+json","name","pull_count",1419,"repository_type","star_count",1,"status","status_description","active","source","collaborator_count",0,"full_description","# Docker Container for ExperimentHub Server\n\n## Table of Contents\n\n- [Overview](#overview)\n- [Setting up the docker container](#setup)\n\t- [Prerequisites](#prerequisites)\n - [Run the continer](#run)\n\t- [Determine URL of server](#url)\n- [Using the container](#use)\n- [Testing the changes](#test)\n- [Pushing changes to production](#push)\n\n## Overview\n\nThis Docker Container provides an isolated environment for modifying the\nmetadata records in the ExperimentHub database. It can be used for testing only\nor the modified database can be dumped and used to replace the production db.\n\nThe docker can be used by anyone who has the password for the 'read only' user\non the production server. With these credentials, a copy of the mysql\nproduction database is downloaded locally to the docker container. From within\nan R session, global options are set to point code from ExperimentHubData and\nExperimentHub to the local db. Changes to the metadata (inserts, modifications\nor extractions) are made to the docker db instead of production.\n\n\n\n## Setting up the docker container\n\n\n### Prerequisites\n\nSet the environment variable `MYSQL_REMOTE_PASSWORD` to the password found in\nthe \"ExperimentHub production server\" section of the Google Doc \"Credentials\nFor Bioconductor Cloud resources\".\n\nThe container will not work properly unless this is set.\n\nYou can set it by doing:\n\n export MYSQL_REMOTE_PASSWORD=XXX\n\nwhere XXX is replaced with the correct password. This password should also be \nadded to 'MYSQL_REMOTE_PASSWORD:' in the docker-compose.yml file.\n\nYou may also need to export the database type for mysql or sqlite:\n\n export HUBSERVER_DATABASE_TYPE=mysql\n\nIf you are on Linux, install docker using\n[Docker Engine](https://docs.docker.com/installation/). Also install\n[Docker Compose](https://docs.docker.com/compose/install/).\nIf you are on Mac or Windows, install Docker Desktop instead. You will not need \nto install Docker Compose because it is included in Docker Desktop.\n[Docker Desktop for Mac](https://docs.docker.com/docker-for-mac/install/),\n[Docker Desktop for Windows](https://docks.docker.com/docker-for-windows/install/).\n\nClone the HubServer code to the same directory as this README:\n\n git clone https://github.com/Bioconductor/HubServer.git\n\nOr if you already have this repository checked out elsewhere\non your system, make a symbolic link to it in the current directory\n(the same directory as this README).\n\nCreate a directory called \"data\" in the same directory as\nthis README.\n\n\n### Run The Container\n\nOpen a terminal window (a Docker Quickstart Terminal if\nyou are on Mac or windows) and change to the same\ndirectory where this README is. Issue the command:\n\n docker-compose up\n\nThis command will *pull down the database contents\nfrom the production ExperimentHub server* and then\nstart a local server.\n\nWhen you see a line like this:\n\n experimenthub_1 | == Shotgun/WEBrick on http://0.0.0.0:3000/\n\n...the ExperimentHub server is running in the container.\n\nTo verify that it is running, you can determine its URL\n(in the next section).\n\n\n### Determining URL of server\n\nIf you are on linux, the URL of the server is likely\n[http://localhost:4000/resource](http://localhost:4000/resource).\n\nIf you are in the cloud you need to use the public DNS name of your instance\nas your IP address.\n\nIf you are using boot2docker (deprecated by Docker Toolbox),\nyou can determine your Docker host's IP address with the command\n`boot2docker ip`. If this returns `1.2.3.4`, your URL\nwould be `http://1.2.3.4:4000/resource`. \n\nIf you are using Docker Toolbox, the command to determine\nyour Docker host's IP address is \n\n docker-machine ip default\n\nIf this returns `1.2.3.4`, your URL would be\n`http://1.2.3.4:4000/resource`.\n\n\n## Using the container\n\nStart a new R session in a new terminal window. Assuming your server URL is\n`http://1.2.3.4:4000/resource`, enter the following at the R prompt:\n\n ## used by ExperimentHubData to insert metadata\n options(EXPERIMENT_HUB_SERVER_POST_URL=\"http://1.2.3.4:4000/resource\")\n ## used by ExperimentHub to get metadata\n options(EXPERIMENT_HUB_URL=\"http://1.2.3.4:4000/resource\")\n\nReplace the URL with your actual URL, of course. These options must be set \nbefore loading `ExperimentHub` and `ExperimentHubData`.\n\n\tlibrary(ExperimentHub)\n\tlibrary(ExperimentHubData)\n\nNow you can run recipes, etc. and the insertions will happen inside the docker\ncontainer, not in the production database.\n\n\n## Testing the changes\n\nYou can interact with the docker db with R or mysql.\n\n#### R session\n\nTo view the docker db from R you must first convert the mysql db to sqlite. From another terminal window do\n\n\tdocker exec -ti experimenthubdocker_experimenthub_1 bash\n\nThat will log you in to the experimenthub server container. Then do the following:\n\n\tcd /HubServer/\n\truby convert_db.rb \n\nThat will convert the mysql database to sqlite. You can then type\n\n\texit\n\t\nto exit the container, start R and set the variables as described in [Using the container](#use). ExperimentHub should recognize that there are changes and download the new sqlite database, but if not you can remove the old one from your cache to trigger a copy.\n\n#### mysql session\n\nmysql is not exposed to the host, so you need to do this from the mysql machine. Run\n\n\tdocker ps\n\t\nto see a list of containers that are running. One will have the string 'db' in it. Let's say the full name is 'db1'. Connect to the container with:\n\n\tdocker exec -ti db_1 bash\n\nFrom within the resulting prompt start mysql and query the db as usual:\n\n\tmysql -p -u hubuser\n\t\nWhen you are satisfied that the changes you have made are \ncorrect, you can update the production database (see next\nsection). If you have messed up and you don't want to\npush your changes to production, you can just exit\nthe container (press Control-C in the window where it is\nrunning) and start over again.\n\n\n## Pushing changes to production\n\nYou need to back up the database inside the docker \ncontainer. You can do it like this:\n\n docker exec experimenthubdocker_experimenthub_1 bash /bin/backup_db.sh\n\nNote that `experimenthub_experimenthub_1` is the name of the\ndocker container that has the experiment hub server on it; this\nname may vary, the `docker ps` command will give you the\naccurate container name.\n\nNow in the `data` directory on your local machine, \nthere is a file called `experimenthub.sql.gz`. Upload this to the production machine.\n\nLog into the production machine and make a backup of production db:\n\n mysqldump -p -u hubuser experimenthub | gzip > dbdump_YYYY_MM_DD_fromProd.sql.gz\n\nDrop the old db and create an empty one:\n\n mysql -p -u root\n drop database experimenthub;\n create database experimenthub;\n quit;\n\nFill the empty with the modified db:\n\n zcat dbdump_YYYY_MM_DD_fromDocker.sql.gz | mysql -p -u root experimenthub\n\n","has_starred","hub_user","immutable_tags_settings",{"_70":11,"_71":72},"enabled","rules",[73],".*","is_automated","permissions",{"_77":17,"_78":11,"_79":11},"read","write","admin","user","storage_size",4505079869,"orgData",{"_85":86,"_87":88,"_89":90,"_91":28,"_92":93,"_94":95,"_96":97,"_98":99,"_100":101,"_102":93,"_103":93,"_104":93,"_105":17},"id","2c5bb01674c011e4bea40242ac11001b","uuid","2c5bb016-74c0-11e4-bea4-0242ac11001b","type","organization","orgname","full_name","","location","Boston, MA, USA","company","Bioconductor","profile_url","http://bioconductor.org/","date_joined","2014-11-19T21:44:32.734936Z","gravatar_url","gravatar_email","badge","is_active","recentTags",[108],{"_109":39,"_110":111,"_112":113,"_85":114,"_115":116,"_45":133,"_134":135,"_136":28,"_137":51,"_52":138,"_139":140,"_141":124,"_142":133,"_143":60,"_144":17},"content_type","creator",585267,"full_size",276269751,1835360,"images",[117],{"_118":119,"_120":121,"_122":93,"_123":124,"_125":126,"_127":128,"_129":93,"_130":-5,"_131":113,"_58":60,"_132":-5},"architecture","amd64","digest","sha256:768e2ccfcd9bfce49e82da7d1863972f5959e5b4e25eeb4462207ea8572040b2","features","last_pulled","2026-09-09T21:00:07.770071819Z","last_pushed","2020-03-03T17:27:15Z","os","linux","os_features","os_version","size","variant","2020-03-03T17:27:15.049618Z","last_updater",150968,"last_updater_username","media_type","latest","repository",479128,"tag_last_pulled","tag_last_pushed","tag_status","v2","sbxKitMetadata","isPotentialSpam","isHubSbxKitsEnabled","displaySecurityMetadata","tagAttestations","tagsHaveAttestations",[],"routes/_layout.r.$namespace.$reponame.tags",{"_33":154,"_161":162,"_150":171,"_172":11},{"_35":155,"_37":156,"_40":41,"_42":43,"_44":11,"_45":46,"_47":48,"_49":157,"_52":30,"_27":28,"_53":54,"_55":39,"_56":57,"_58":57,"_59":60,"_61":-5,"_62":63,"_64":65,"_66":11,"_67":28,"_68":158,"_74":17,"_75":160,"_80":28,"_81":82},[],[39],[51],{"_70":11,"_71":159},[73],{"_77":17,"_78":11,"_79":11},"tags",{"_163":57,"_164":-5,"_165":-5,"_166":167},"count","next","previous","results",[168],{"_109":39,"_110":111,"_112":113,"_85":114,"_115":169,"_45":133,"_134":135,"_136":28,"_137":51,"_52":138,"_139":140,"_141":124,"_142":133,"_143":60,"_144":17},[170],{"_118":119,"_120":121,"_122":93,"_123":124,"_125":126,"_127":128,"_129":93,"_130":-5,"_131":113,"_58":60,"_132":-5},[],"canDeleteTags","actionData","errors"]

bioconductor/experimenthub_docker

Tags for bioconductor/experimenthub_docker