[{"_1":2,"_155":-5,"_156":-5},"loaderData",{"_3":4,"_13":14,"_21":22,"_134":135},"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,"_20":11},"username","isAskGordonEnabled",true,"isUsingNewTemplate","showMinimalLanding","showHoneypotTrap","routes/_layout.r.$namespace.$reponame",{"_23":24,"_25":-5,"_26":11,"_27":11,"_28":29,"_30":31,"_32":-5,"_33":11,"_34":35,"_84":-5,"_85":86,"_125":-5,"_126":11,"_127":17,"_128":11,"_129":-5,"_130":11,"_131":-5,"_132":133},"canonicalUrl","https://hub.docker.com/r/artemsokolovdh/synextra/tags","mcpServer","canSeeDockerfile","canSeeAutobuilds","namespace","artemsokolovdh","reponame","synextra","cloudBuildSource","isAutobuildsAvailable","repo",{"_36":37,"_38":39,"_41":42,"_43":44,"_45":11,"_46":47,"_48":49,"_50":51,"_53":31,"_28":29,"_54":55,"_56":40,"_57":58,"_59":60,"_61":62,"_63":-5,"_64":58,"_65":66,"_67":11,"_68":29,"_69":70,"_75":11,"_76":77,"_81":29,"_82":83},"categories",[],"content_types",[40],"image","date_registered","2021-04-05T18:20:27.40659Z","description","Extension of `synapser`, a Synapse R client","is_private","last_updated","2021-04-05T18:35:42.080998Z","last_modified","2024-10-16T13:48:34.145251Z","media_types",[52],"application/vnd.docker.container.image.v1+json","name","pull_count",22911,"repository_type","star_count",0,"status",1,"status_description","active","source","collaborator_count","full_description","# synExtra: Extensions for `synapser`\n\nSage Bionetworks develops and maintains [synapser](https://github.com/Sage-Bionetworks/synapser), an R client for interfacing with [Synapse](https://www.synapse.org/). This package builds on top of `synapser` to streamline its usage in a functional programming (FP) paradigm. The package can be installed directly from GitHub by running the following from R:\n\n``` R\nif( !require(devtools) ) install.packages( \"devtools\" )\ndevtools::install_github( \"ArtemSokolov/synExtra\" )\n```\n\nThe functionality can be loosely grouped into three categories: 1) downloading and uploading of files, 2) traversal of the Synapse directory structure, and 3) miscellaneous inspection of Synapse entities\n\n## 1) Downloading and uploading of files\n\nFile downloading from Synapse is done primarily via `synapser::synGet()`. Since the follow-up action is often to load the downloaded file, a canonical `synGet()` call retrieves the local filename of the downloaded file:\n\n``` R\nfn <- synapser::synGet( \"syn15663039\", downloadLocation = \"/data/myproject\" )$path\nX <- readr::read_csv( fn )\n```\n\nIf multiple files are to be downloaded, the above code would be wrapped inside a `for` loop or a `purrr::map()`-family call:\n\n``` R\n## 1. Downloading multiple files using a for loop\nfns <- c()\nfor( id in c(\"syn1710445\", \"syn1695376\", \"syn1710429\") )\n fns[id] <- synapser::synGet( id, downloadLocation = \"/data/myproject\" )$path\n\n## 2. Downloading multiple files using purrr::map() family of functions\nfns <- purrr::map_chr( c(\"syn1710445\", \"syn1695376\", \"syn1710429\"),\n ~synapser::synGet( .x, downloadLocation = \"/data/myproject\" )$path )\n```\n\nAn alternative solution provided by `synExtra` creates a downloader function that is linked to a specific local path. The downloader returns location of the downloaded file(s), thereby streamlining the process:\n\n``` R\nsyn <- synExtra::synDownloader( \"/data/myproject\" )\n\n# Pass Synapse IDs directly to the downloader\nfns <- syn( \"syn1710445\", \"syn1695376\", \"syn1710429\" )\n\n# Or store them in a vector and pass that vector instead\nids <- c( \"syn1710445\", \"syn1695376\", \"syn1710429\" )\nfns <- syn( ids )\n\n# In either case, fns is now a character vector of local paths\n# [1] \"/data/myproject/PANCAN12.IlluminaGA_miRNASeq.miRNA.tumor_whitelist\" \n# [2] \"/data/myproject/PANCAN12.IlluminaHiSeq_miRNASeq.miRNA.normal_whitelist\"\n# [3] \"/data/myproject/PANCAN12.MDA_RPPA_Core.RPPA.tumor_whitelist\" \n```\n\nAn important feature of the downloader is that it recognizes whether its arguments are valid synapse IDs. Any argument not recognized to be one is assumed to be a local filename already.\n\n``` R\nsyn( \"localFile.csv\" ) ## returns \"localFile.csv\"\n```\n\nThis allows for development of tools that abstract away the distinction of local files and files residing on Synapse. For example, consider a simple `csvpeek.R` script which displays the first 10 lines of a .csv file:\n\n``` R\nsynapser::synLogin()\nsyn <- synExtra::synDownloader( \"./.syn\" )\nfn <- syn( commandArgs( trailingOnly=TRUE )[1] )\nreadr::read_csv( fn, col_types=readr::cols(), n_max = 10 )\n```\n\nSuch a script accepts local filenames as well as synapse IDs; in the latter case, the file is automatically downloaded to the local `.syn` directory. The distinction is completely transparent to the user who would use `csvpeek.R` as follows:\n\n Rscript csvpeek.R localFile.csv\n Rscript csvpeek.R syn15663039\n \n### File uploading\n\nSimilarly, file uploading to Synapse is done primarily via `synapser::synStore()`. However, uploading a large number of files in a complicated directory structure can become tedious. `synExtra` provides a wrapper `synStoreMany()` that functions effectively like the Linux `mv` command. The function takes two arguments: a local path and the synapse ID of the Project/Folder where the files are to be uploaded to.\n\n``` R\nsynExtra::synStoreMany( \"/home/sokolov/devel/synExtra\", \"syn12180284\" )\n\n## The function understands local paths\nsynExtra::synStoreMany( \".\", \"syn12180284\" )\n\n## As well as relative paths\nsynExtra::synStoreMany( \"../myOtherFolder\", \"syn12180284\" )\n```\n\n## 2) Traversal of the Synapse directory structure\n\nSimilarly to a local filesystem, Synapse entities are organized in a hierarchical fashion. `synExtra` provides several functions for traversing this hierarchy. First, there is `synAncestry()`, which takes one or more of synapse IDs and retrieves their full parentId ancestry up to their respective projects:\n\n``` R\nsynAncestry( \"syn15663039\", \"syn1695362\" )\n# $syn15663039\n# [1] \"syn15663039\" \"syn15673834\" \"syn15673837\" \"syn12180284\"\n#\n# $syn1695362\n# [1] \"syn1695362\" \"syn1695324\" \"syn2812925\" \"syn300013\" \n```\n\nIn the example above, `syn12180284` and `syn300013` are the Synapse projects that host the corresponding entities. Note that `synAncestry()` accepts individual IDs, as well as lists and vectors of IDs. All of the following calls are equivalent:\n``` R\nsynAncestry( \"syn15663039\", \"syn1695362\" )\nsynAncestry( c(\"syn15663039\", \"syn1695362\") )\nsynAncestry( list(\"syn15663039\", \"syn1695362\") )\nsynAncestry( list(\"syn15663039\"), list(\"syn1695362\") )\n```\n\nThe second function for traversing the Synapse hierarchy looks in the opposite direction. It's a wrapper around `synGetChildren()` that returns a named vector of synapse IDs, rather than a Python object. As with `synAncestry()`, this second function understands individual IDs, as well as lists and vectors of IDs:\n\n``` R\nsynChildren( \"syn6185321\", \"syn5049679\" )\n# $syn6185321\n# hairpin fasta miRNA mature structure\n# \"syn6185324\" \"syn6185325\"\n#\n# $syn5049679\n# hsa_MTI_6.1.csv\n# \"syn5049680\"\n```\n\nThe last traversal function allows you to identify the synapse ID of an arbitrary descendant, using the names of entities on the traversal path. For example, suppose we want to retrieve the synapse ID of `C4 Raw Data/mRNA/Counts/htseq-count/H9.144.7.7.txt` from the [Progenitor Cell Biology Consortium](https://www.synapse.org/#!Synapse:syn1773109) project. We can do so by calling `synPluck()` with the synapse ID of the project (`syn1773109`) as the first argument:\n\n``` R\nsynPluck(\"syn1773109\", \"C4 Raw Data\", \"mRNA\", \"Counts\", \"htseq-count\", \"H9.144.7.7.txt\")\n# [1] \"syn2822560\"\n\n## Or equivalently\nsynPluck(\"syn1773109\", c(\"C4 Raw Data\", \"mRNA\", \"Counts\", \"htseq-count\", \"H9.144.7.7.txt\"))\nsynPluck(\"syn1773109\", list(\"C4 Raw Data\", \"mRNA\", \"Counts\", \"htseq-count\", \"H9.144.7.7.txt\"))\n```\n\n## 3) Miscellaneous\n\n`synExtra` provides several additional utility functions. These allow you to\n\n``` R\n# determine if something is a valid Synapse ID\nisSynID( \"syn1234\", \"syn\", \"syn123ab\" )\n# [1] TRUE FALSE FALSE\nisSynID( list( mtcars, 123, \"syn123\" ) )\n# [1] FALSE FALSE TRUE\n\n# retrieve the entity name by Synapse ID\nsynName( \"syn1896429\", \"syn1901530\" )\n# syn1896429 syn1901530 \n# \"ESTIMATE_scores_PANCAN11.tsv\" \"ESTIMATE_scores_PANCAN11_RNASeqV2.tsv\"\nsynName( c(\"syn2247543\", \"syn2653626\"), list(\"syn1773111\", \"syn2246520\") )\n# syn2247543 syn2653626 syn1773111 syn2246520 \n# \"mRNA\" \"methylation\" \"BAM\" \"BED\" \n\n# rename an entity identified by its Synapse ID.\n# synRename() returns the provided Synapse ID for easy integration with %>% pipe\nsynRename( \"syn123\", \"newfilename.csv\" )\n# [1] \"syn123\"\n\n# Retrieve the size of a file or all content inside a folder\nsynSize( \"syn1695362\", \"syn1695324\" )\n# syn1695362 syn1695324\n# 1678169935 11682238368\n```\n\n","has_starred","hub_user","immutable_tags_settings",{"_71":11,"_72":73},"enabled","rules",[74],".*","is_automated","permissions",{"_78":17,"_79":11,"_80":11},"read","write","admin","user","storage_size",940112921,"orgData","recentTags",[87],{"_88":40,"_89":90,"_91":92,"_93":94,"_95":96,"_46":114,"_115":90,"_116":29,"_117":52,"_53":118,"_119":120,"_121":105,"_122":114,"_123":62,"_124":17},"content_type","creator",3195541,"full_size",940101702,"id",144291429,"images",[97],{"_98":99,"_100":101,"_102":103,"_104":105,"_106":107,"_108":109,"_110":103,"_111":-5,"_112":92,"_59":62,"_113":-5},"architecture","amd64","digest","sha256:113af34715aba6f2eaed9293af4477a6ac657df6138b843dd1a0296127ba6ec2","features","","last_pulled","2026-09-21T16:18:37.780043271Z","last_pushed","2021-04-05T18:35:42Z","os","linux","os_features","os_version","size","variant","2021-04-05T18:35:41.68288Z","last_updater","last_updater_username","media_type","latest","repository",12091547,"tag_last_pulled","tag_last_pushed","tag_status","v2","sbxKitMetadata","isPotentialSpam","isHubSbxKitsEnabled","showSbxLogoOverride","sbxTrademarkText","displaySecurityMetadata","tagAttestations","tagsHaveAttestations",[],"routes/_layout.r.$namespace.$reponame.tags",{"_34":136,"_143":144,"_132":153,"_154":11},{"_36":137,"_38":138,"_41":42,"_43":44,"_45":11,"_46":47,"_48":49,"_50":139,"_53":31,"_28":29,"_54":55,"_56":40,"_57":58,"_59":60,"_61":62,"_63":-5,"_64":58,"_65":66,"_67":11,"_68":29,"_69":140,"_75":11,"_76":142,"_81":29,"_82":83},[],[40],[52],{"_71":11,"_72":141},[74],{"_78":17,"_79":11,"_80":11},"tags",{"_145":60,"_146":-5,"_147":-5,"_148":149},"count","next","previous","results",[150],{"_88":40,"_89":90,"_91":92,"_93":94,"_95":151,"_46":114,"_115":90,"_116":29,"_117":52,"_53":118,"_119":120,"_121":105,"_122":114,"_123":62,"_124":17},[152],{"_98":99,"_100":101,"_102":103,"_104":105,"_106":107,"_108":109,"_110":103,"_111":-5,"_112":92,"_59":62,"_113":-5},[],"canDeleteTags","actionData","errors"]

artemsokolovdh/synextra

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