{"action":"created","issue":{"url":"https://api.github.com/repos/NCEAS/arcticdatautils/issues/51","repository_url":"https://api.github.com/repos/NCEAS/arcticdatautils","labels_url":"https://api.github.com/repos/NCEAS/arcticdatautils/issues/51/labels{/name}","comments_url":"https://api.github.com/repos/NCEAS/arcticdatautils/issues/51/comments","events_url":"https://api.github.com/repos/NCEAS/arcticdatautils/issues/51/events","html_url":"https://github.com/NCEAS/arcticdatautils/issues/51","id":275040601,"number":51,"title":"generation of resource maps with invalid characters ","user":{"login":"jeanetteclark","id":24237074,"avatar_url":"https://avatars0.githubusercontent.com/u/24237074?v=4","gravatar_id":"","url":"https://api.github.com/users/jeanetteclark","html_url":"https://github.com/jeanetteclark","followers_url":"https://api.github.com/users/jeanetteclark/followers","following_url":"https://api.github.com/users/jeanetteclark/following{/other_user}","gists_url":"https://api.github.com/users/jeanetteclark/gists{/gist_id}","starred_url":"https://api.github.com/users/jeanetteclark/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jeanetteclark/subscriptions","organizations_url":"https://api.github.com/users/jeanetteclark/orgs","repos_url":"https://api.github.com/users/jeanetteclark/repos","events_url":"https://api.github.com/users/jeanetteclark/events{/privacy}","received_events_url":"https://api.github.com/users/jeanetteclark/received_events","type":"User","site_admin":false},"labels":[{"id":378707482,"url":"https://api.github.com/repos/NCEAS/arcticdatautils/labels/bug","name":"bug","color":"ee0701","default":true},{"id":378707485,"url":"https://api.github.com/repos/NCEAS/arcticdatautils/labels/help%20wanted","name":"help wanted","color":"128A0C","default":true}],"state":"open","locked":false,"assignee":{"login":"amoeba","id":563,"avatar_url":"https://avatars2.githubusercontent.com/u/563?v=4","gravatar_id":"","url":"https://api.github.com/users/amoeba","html_url":"https://github.com/amoeba","followers_url":"https://api.github.com/users/amoeba/followers","following_url":"https://api.github.com/users/amoeba/following{/other_user}","gists_url":"https://api.github.com/users/amoeba/gists{/gist_id}","starred_url":"https://api.github.com/users/amoeba/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/amoeba/subscriptions","organizations_url":"https://api.github.com/users/amoeba/orgs","repos_url":"https://api.github.com/users/amoeba/repos","events_url":"https://api.github.com/users/amoeba/events{/privacy}","received_events_url":"https://api.github.com/users/amoeba/received_events","type":"User","site_admin":false},"assignees":[{"login":"amoeba","id":563,"avatar_url":"https://avatars2.githubusercontent.com/u/563?v=4","gravatar_id":"","url":"https://api.github.com/users/amoeba","html_url":"https://github.com/amoeba","followers_url":"https://api.github.com/users/amoeba/followers","following_url":"https://api.github.com/users/amoeba/following{/other_user}","gists_url":"https://api.github.com/users/amoeba/gists{/gist_id}","starred_url":"https://api.github.com/users/amoeba/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/amoeba/subscriptions","organizations_url":"https://api.github.com/users/amoeba/orgs","repos_url":"https://api.github.com/users/amoeba/repos","events_url":"https://api.github.com/users/amoeba/events{/privacy}","received_events_url":"https://api.github.com/users/amoeba/received_events","type":"User","site_admin":false}],"milestone":null,"comments":12,"created_at":"2017-11-18T01:17:04Z","updated_at":"2017-11-21T01:14:26Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"@amoeba Edit: An MRE for this is:\r\n\r\n```r\r\nlibrary(arcticdatautils)\r\nlibrary(dataone)\r\n\r\nmn <- MNode(\"https://dev.nceas.ucsb.edu/knb/d1/mn/v2\")\r\npkg <- create_dummy_package(mn)\r\nnew_pkg <- publish_update(mn, pkg$metadata, pkg$resource_map, pkg$data)\r\ncat(rawToChar(getObject(mn, new_pkg$resource_map)))\r\n```\r\n\r\nNoting the output:\r\n\r\n```xml\r\n<rdf:Description rdf:about=\"_:r1511139237r13053r1\">\r\n    <foaf:name rdf:resource=\"&quot;DataONE R Client&quot;^^&lt;http://www.w3.org/2001/XMLSchema#string\"/>\r\n</rdf:Description>\r\n```\r\n\r\n[original issue below]\r\n\r\n```\r\nlibrary(dataone)\r\nlibrary(datapack)\r\nlibrary(arcticdatautils)\r\nlibrary(EML)\r\n\r\ncn <- CNode('STAGING2')\r\nmn <- getMNode(cn,\"urn:node:mnTestKNB\")\r\n\r\n#write metadata and attach a data file in registry on dev.nceas.ucsb.edu\r\nid <- 'knb.109096.1'\r\n\r\n#read in registry EML\r\noutpath <- '~/example.xml'\r\nwriteBin(getObject(mn, id), outpath)\r\n\r\n#make edits and save EML\r\neml <- read_eml(outpath)\r\neml@dataset@abstract@para@.Data[[2]] <- new('para', .Data = 'and edited using R') #this does not actually change anything, annoyingly\r\nwrite_eml(eml, outpath)\r\n\r\n#get ids from initial submission\r\nids <- get_package(mn, id)\r\n#update EML with new version using publish_update\r\nid_new <- publish_update(mn, metadata_pid = ids$metadata, resource_map_pid = ids$resource_map, data_pids = ids$data, metadata_path = outpath)\r\n```\r\n\r\nThese steps generate a resource map with this, evidently problematic line:\r\n```  \r\n  <rdf:Description rdf:about=\"https://cn-stage-2.test.dataone.org/cn/v1/resolve/knb.109095.1\">\r\n    <dcterms:identifier rdf:resource=\"&quot;knb.109095.1&quot;^^&lt;http://www.w3.org/2001/XMLSchema#string\"/>\r\n  </rdf:Description>\r\n```\r\n\r\nLink to package: https://dev.nceas.ucsb.edu/#view/urn:uuid:0c720fed-bbe9-4076-9e59-7636730b3d5a\r\n\r\n\r\nAttached is a list of the 854 resource maps with this problem on the ADC. There are likely some on the KNB as well\r\n\r\n[bad_rms_ADC.txt](https://github.com/NCEAS/arcticdatautils/files/1484241/bad_rms_ADC.txt)\r\n"},"comment":{"url":"https://api.github.com/repos/NCEAS/arcticdatautils/issues/comments/345884290","html_url":"https://github.com/NCEAS/arcticdatautils/issues/51#issuecomment-345884290","issue_url":"https://api.github.com/repos/NCEAS/arcticdatautils/issues/51","id":345884290,"user":{"login":"jagoldstein","id":18270215,"avatar_url":"https://avatars2.githubusercontent.com/u/18270215?v=4","gravatar_id":"","url":"https://api.github.com/users/jagoldstein","html_url":"https://github.com/jagoldstein","followers_url":"https://api.github.com/users/jagoldstein/followers","following_url":"https://api.github.com/users/jagoldstein/following{/other_user}","gists_url":"https://api.github.com/users/jagoldstein/gists{/gist_id}","starred_url":"https://api.github.com/users/jagoldstein/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jagoldstein/subscriptions","organizations_url":"https://api.github.com/users/jagoldstein/orgs","repos_url":"https://api.github.com/users/jagoldstein/repos","events_url":"https://api.github.com/users/jagoldstein/events{/privacy}","received_events_url":"https://api.github.com/users/jagoldstein/received_events","type":"User","site_admin":false},"created_at":"2017-11-21T01:14:26Z","updated_at":"2017-11-21T01:14:26Z","author_association":"NONE","body":"https://arcticdata.io/catalog/#view/doi:10.18739/A2136S\r\nI was able to add prov to the package found here ^ even though the first version was submitted via the registry and I later updated it w arcticdatautils. Peter speculates that this worked because the RDF update was performed prior to June 2017 "}}
{"actor":{"display_login":"jagoldstein"}}