{"id":2816,"date":"2016-07-03T05:09:40","date_gmt":"2016-07-03T05:09:40","guid":{"rendered":"https:\/\/notebooks.dataone.org\/?p=2816"},"modified":"2016-07-11T02:33:25","modified_gmt":"2016-07-11T02:33:25","slug":"week-6-blog-reproducibility-of-script-based-workflows-projec","status":"publish","type":"post","link":"https:\/\/notebooks.dataone.org\/workflow-reproducibility\/week-6-blog-reproducibility-of-script-based-workflows-projec\/","title":{"rendered":"Week 6 : Reproducibility of Script-Based Workflows projec"},"content":{"rendered":"<div>\n<p>For this week,\u00a0I spent time on using XSB interactively to debug some conundrum in recursive queries which are applied in LCA, figured out the answer trying to get first by observing\u00a0intermediate outputs &amp; final outputs, also classified inputs such that they have the same lineage. Another bug\u00a0occurred in SQLite and XSB query comparison I found out that\u00a0YW view rules is\u00a0case sensitive so it does not take\u00a0PARAM tag into account that resulted in missing data in\u00a0the YW view rules. The problem traced back to the assumption that YW is outputting the standardized keyword associated with each port, so any capital letters in the actual spelling in the keyword will lead to erroneous results. At this stage, we will move from the exploratory phase to the &#8220;delivery phase&#8221; by discussing and clarifying final deliverables such as creating &#8220;demo site&#8221;similar to the YW-NW demo. So I focused on writing\u00a0a\u00a0script (ReadMe) which\u00a0makes other easy to run\/reproduce and run their query and compare the results. Additionally, \u00a0it should let users get all the things to run and ask interesting question like runtime query, logging.<\/p>\n<\/div>\n<div>Next week, I plan to query the single YW trace along with the entire collection of NW queries. So, YW and NW facts queried together by extending some of the sample queries with clauses on the data dependencies as well as\u00a0the queries operating on a collection of traces, knowing that those traces all come from the same script (one single YW trace). The next task will involve in analyzing the reproducibility of LIGO script on\u00a0Reprozip and\u00a0Docker\u00a0approach. Then I will experiment on feature \u201cURI template\u201d of YW in query by\u00a0using the YW-recon approach to cross-check whether URI-template reconstructed file-names (and folder-names) have been declared accordingly via YW annotations.<\/div>\n","protected":false},"excerpt":{"rendered":"<p>For this week,\u00a0I spent time on using XSB interactively to debug some conundrum in recursive queries which are applied in LCA, figured out the answer trying to get first by observing\u00a0intermediate outputs &amp; final outputs, also classified inputs such that they have the same lineage. Another bug\u00a0occurred in SQLite and <a class=\"more-link\" href=\"https:\/\/notebooks.dataone.org\/workflow-reproducibility\/week-6-blog-reproducibility-of-script-based-workflows-projec\/\">Continue reading <span class=\"screen-reader-text\">  Week 6 : Reproducibility of Script-Based Workflows projec<\/span><span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":104,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[371],"tags":[],"_links":{"self":[{"href":"https:\/\/notebooks.dataone.org\/wp-json\/wp\/v2\/posts\/2816"}],"collection":[{"href":"https:\/\/notebooks.dataone.org\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/notebooks.dataone.org\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/notebooks.dataone.org\/wp-json\/wp\/v2\/users\/104"}],"replies":[{"embeddable":true,"href":"https:\/\/notebooks.dataone.org\/wp-json\/wp\/v2\/comments?post=2816"}],"version-history":[{"count":2,"href":"https:\/\/notebooks.dataone.org\/wp-json\/wp\/v2\/posts\/2816\/revisions"}],"predecessor-version":[{"id":2832,"href":"https:\/\/notebooks.dataone.org\/wp-json\/wp\/v2\/posts\/2816\/revisions\/2832"}],"wp:attachment":[{"href":"https:\/\/notebooks.dataone.org\/wp-json\/wp\/v2\/media?parent=2816"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/notebooks.dataone.org\/wp-json\/wp\/v2\/categories?post=2816"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/notebooks.dataone.org\/wp-json\/wp\/v2\/tags?post=2816"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}