{"action":"created","issue":{"url":"https://api.github.com/repos/ISA-tools/isa-api/issues/146","repository_url":"https://api.github.com/repos/ISA-tools/isa-api","labels_url":"https://api.github.com/repos/ISA-tools/isa-api/issues/146/labels{/name}","comments_url":"https://api.github.com/repos/ISA-tools/isa-api/issues/146/comments","events_url":"https://api.github.com/repos/ISA-tools/isa-api/issues/146/events","html_url":"https://github.com/ISA-tools/isa-api/issues/146","id":179746009,"number":146,"title":"Unexpected pooling on MS process in JSON output using isatab2json","user":{"login":"djcomlab","id":3604134,"avatar_url":"https://avatars.githubusercontent.com/u/3604134?v=3","gravatar_id":"","url":"https://api.github.com/users/djcomlab","html_url":"https://github.com/djcomlab","followers_url":"https://api.github.com/users/djcomlab/followers","following_url":"https://api.github.com/users/djcomlab/following{/other_user}","gists_url":"https://api.github.com/users/djcomlab/gists{/gist_id}","starred_url":"https://api.github.com/users/djcomlab/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/djcomlab/subscriptions","organizations_url":"https://api.github.com/users/djcomlab/orgs","repos_url":"https://api.github.com/users/djcomlab/repos","events_url":"https://api.github.com/users/djcomlab/events{/privacy}","received_events_url":"https://api.github.com/users/djcomlab/received_events","type":"User","site_admin":false},"labels":[{"id":186112818,"url":"https://api.github.com/repos/ISA-tools/isa-api/labels/bug","name":"bug","color":"eb6420","default":true}],"state":"open","locked":false,"assignee":{"login":"djcomlab","id":3604134,"avatar_url":"https://avatars.githubusercontent.com/u/3604134?v=3","gravatar_id":"","url":"https://api.github.com/users/djcomlab","html_url":"https://github.com/djcomlab","followers_url":"https://api.github.com/users/djcomlab/followers","following_url":"https://api.github.com/users/djcomlab/following{/other_user}","gists_url":"https://api.github.com/users/djcomlab/gists{/gist_id}","starred_url":"https://api.github.com/users/djcomlab/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/djcomlab/subscriptions","organizations_url":"https://api.github.com/users/djcomlab/orgs","repos_url":"https://api.github.com/users/djcomlab/repos","events_url":"https://api.github.com/users/djcomlab/events{/privacy}","received_events_url":"https://api.github.com/users/djcomlab/received_events","type":"User","site_admin":false},"assignees":[{"login":"djcomlab","id":3604134,"avatar_url":"https://avatars.githubusercontent.com/u/3604134?v=3","gravatar_id":"","url":"https://api.github.com/users/djcomlab","html_url":"https://github.com/djcomlab","followers_url":"https://api.github.com/users/djcomlab/followers","following_url":"https://api.github.com/users/djcomlab/following{/other_user}","gists_url":"https://api.github.com/users/djcomlab/gists{/gist_id}","starred_url":"https://api.github.com/users/djcomlab/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/djcomlab/subscriptions","organizations_url":"https://api.github.com/users/djcomlab/orgs","repos_url":"https://api.github.com/users/djcomlab/repos","events_url":"https://api.github.com/users/djcomlab/events{/privacy}","received_events_url":"https://api.github.com/users/djcomlab/received_events","type":"User","site_admin":false}],"milestone":{"url":"https://api.github.com/repos/ISA-tools/isa-api/milestones/4","html_url":"https://github.com/ISA-tools/isa-api/milestones/Release%200.4","labels_url":"https://api.github.com/repos/ISA-tools/isa-api/milestones/4/labels","id":2059314,"number":4,"title":"Release 0.4","description":"Goal - firm up creation functionality using Python objects for writing to ISA-Tab (priority); implement exports to MAGE-TAB and SampleTab.","creator":{"login":"djcomlab","id":3604134,"avatar_url":"https://avatars.githubusercontent.com/u/3604134?v=3","gravatar_id":"","url":"https://api.github.com/users/djcomlab","html_url":"https://github.com/djcomlab","followers_url":"https://api.github.com/users/djcomlab/followers","following_url":"https://api.github.com/users/djcomlab/following{/other_user}","gists_url":"https://api.github.com/users/djcomlab/gists{/gist_id}","starred_url":"https://api.github.com/users/djcomlab/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/djcomlab/subscriptions","organizations_url":"https://api.github.com/users/djcomlab/orgs","repos_url":"https://api.github.com/users/djcomlab/repos","events_url":"https://api.github.com/users/djcomlab/events{/privacy}","received_events_url":"https://api.github.com/users/djcomlab/received_events","type":"User","site_admin":false},"open_issues":7,"closed_issues":3,"state":"open","created_at":"2016-10-10T13:46:21Z","updated_at":"2016-11-23T14:55:18Z","due_on":"2016-11-11T00:00:00Z","closed_at":null},"comments":5,"created_at":"2016-09-28T11:21:42Z","updated_at":"2016-11-24T11:46:26Z","closed_at":null,"body":"When converting the ISA-Tab of MTBLS2 (http://www.ebi.ac.uk/metabolights/MTBLS2), I noticed that the JSON produced only has one Mass Spectrometry process in the assay process sequence (`Mass_Spectrometry1`) with no `name`, and it lists all of the assay data files in the `outputs` from this single process.\n\nIn this case there is supposed to be one MS process per sample (as the assay file shows MS processes uniquely named in the MS Assay Name column, on each line), with one data file each as output.\n"},"comment":{"url":"https://api.github.com/repos/ISA-tools/isa-api/issues/comments/262757972","html_url":"https://github.com/ISA-tools/isa-api/issues/146#issuecomment-262757972","issue_url":"https://api.github.com/repos/ISA-tools/isa-api/issues/146","id":262757972,"user":{"login":"djcomlab","id":3604134,"avatar_url":"https://avatars.githubusercontent.com/u/3604134?v=3","gravatar_id":"","url":"https://api.github.com/users/djcomlab","html_url":"https://github.com/djcomlab","followers_url":"https://api.github.com/users/djcomlab/followers","following_url":"https://api.github.com/users/djcomlab/following{/other_user}","gists_url":"https://api.github.com/users/djcomlab/gists{/gist_id}","starred_url":"https://api.github.com/users/djcomlab/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/djcomlab/subscriptions","organizations_url":"https://api.github.com/users/djcomlab/orgs","repos_url":"https://api.github.com/users/djcomlab/repos","events_url":"https://api.github.com/users/djcomlab/events{/privacy}","received_events_url":"https://api.github.com/users/djcomlab/received_events","type":"User","site_admin":false},"created_at":"2016-11-24T11:46:26Z","updated_at":"2016-11-24T11:46:26Z","body":"Further testing confirms that the way to encode the ISA-Tab so it does not split on ``Chromatography`` is to put unique values in the ``Labeled Extract Name`` column.\r\n\r\nI tried both adding a ``Parameter Value[curation run order]`` column and also using the ``Label`` with unique values and in both these cases the pooling still occurs in the JSON on a single process ``#process/Chromatography1``."}}
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