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Inacio Medeiros
May 27, 2017, 8:05:57 PM5/27/17
to Node-RED
Hi everyone,
I am developing an app for an activity of Distributed Systems college discipline that performs searches on NCBI. Idea is to be an "one-page app".
In the part of the flow, illustrated by image below, It is performed a search on NCBI "E-fetch" system. Until xml node everything is working fine, inclusive I can track progress via debug nodes, but after "switch db" node application gets stucked and doesn't return a response. "Source code" relative to complete flow is given below the image.
How can I solve this problem?
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Remove if using .navbar-static-top. Change if height of navigation changes. */\n}\n\n.portfolio-item {\n margin-bottom: 25px;\n}\n\n.result_box {\n border-radius: 25px;\n border: 2px solid #73AD21;\n padding: 2pt;\n}\n\n.result_text {\n color: #0000FF;\n}\n\n.pub_title, .pub_authors {\n font-weight: bold;\n color: #00FF00;\n}\n\n.abstract {\n color: #00AA00;\n}\n\nfooter {\n margin: 50px 0;\n}","x":3324.2865600585938,"y":199.57144355773926,"wires":[["9e1f4692.93f4f8"]]},{"id":"18055fe.9d593a","type":"http in","z":"8f712d25.103e6","name":"","url":"/biosuitcase/ncbi_search","method":"post","swaggerDoc":"","x":145,"y":55.14282703399658,"wires":[["dfa21026.fb93b"]]},{"id":"3fb96b1c.5915cc","type":"xml","z":"8f712d25.103e6","name":"","attr":"","chr":"","x":1386.4998893737793,"y":57.14270305633545,"wires":[["a114c5e.bed78b8"]]},{"id":"a114c5e.bed78b8","type":"function","z":"8f712d25.103e6","name":"Extract ID List","func":"msg.id_list = msg.payload.eSearchResult.IdList[0].Id;\nreturn msg;","outputs":1,"noerr":0,"x":1575.500144958496,"y":145.14276444911957,"wires":[["2ea17a0.1d53e86"]]},{"id":"1c38721f.59e7b6","type":"function","z":"8f712d25.103e6","name":"Publications Search","func":"msg.payload = \"db=pubmed&\";\nreturn msg;","outputs":1,"noerr":0,"x":768.0000114440918,"y":20,"wires":[["d74b1aa8.83d71"]]},{"id":"b769692a.62e0f","type":"function","z":"8f712d25.103e6","name":"DNA-Seq Search","func":"msg.payload = \"db=nucleotide&\";\nreturn msg;","outputs":1,"noerr":0,"x":758.0000114440918,"y":56,"wires":[["d74b1aa8.83d71"]]},{"id":"a5788c3e.c40e68","type":"function","z":"8f712d25.103e6","name":"Structure Search","func":"msg.payload = \"db=structure&\";\nreturn msg;","outputs":1,"noerr":0,"x":758.0000839233398,"y":96.00000762939453,"wires":[["d74b1aa8.83d71"]]},{"id":"dec1f4a5.614ec","type":"switch","z":"8f712d25.103e6","name":"","property":"db","propertyType":"msg","rules":[{"t":"eq","v":"pubmed","vt":"str"},{"t":"eq","v":"nucleotide","vt":"str"},{"t":"eq","v":"structure","vt":"str"}],"checkall":"true","outputs":3,"x":549.5000114440918,"y":56,"wires":[["1c38721f.59e7b6"],["b769692a.62e0f"],["a5788c3e.c40e68"]]},{"id":"dfa21026.fb93b","type":"function","z":"8f712d25.103e6","name":"param config","func":"msg.db = msg.payload.db;\nmsg.term = msg.payload.term;\nreturn msg;","outputs":1,"noerr":0,"x":387.50003814697266,"y":56,"wires":[["dec1f4a5.614ec"]]},{"id":"ed3c60a2.7cd1","type":"http request","z":"8f712d25.103e6","name":"NCBI E-Search","method":"GET","ret":"txt","url":"","tls":"","x":1223.2858695983887,"y":56.71429443359375,"wires":[["3fb96b1c.5915cc"]]},{"id":"96c8005.f62928","type":"http request","z":"8f712d25.103e6","name":"NCBI E-Summary","method":"GET","ret":"txt","url":"","tls":"","x":2049.250534057617,"y":198.75011730194092,"wires":[["70692f4.8670dd"]]},{"id":"d44455da.1157b8","type":"switch","z":"8f712d25.103e6","name":"switch db","property":"db","propertyType":"msg","rules":[{"t":"eq","v":"pubmed","vt":"str"},{"t":"eq","v":"nucleotide","vt":"str"},{"t":"eq","v":"structure","vt":"str"}],"checkall":"true","outputs":3,"x":2373.0003662109375,"y":198.75012266635895,"wires":[["f649dcef.7b4b68"],["dd2bc388.b125a8"],["e339317c.c971a8"]]},{"id":"f649dcef.7b4b68","type":"function","z":"8f712d25.103e6","name":"Parse Pubmed Results","func":"var publications = [];\n\nvar publication = null;\nvar pub_it = null;\nvar author_list = null;\n\nvar e_summary_results = msg.payload.eSummaryResult.DocSum;\n\nconst TITLE_INDEX = 5;\nconst AUTHOR_LIST_INDEX = 3;\nconst PUB_DATE_INDEX = 1;\n\nfor(var pub = 0; pub < e_summary_results.length; pub++){\n publication = {};\n pub_it = e_summary_results[pub];\n \n publication.id = pub_it.Id[0];\n publication.title = pub_it.Item[TITLE_INDEX]._;\n publication.pub_date = pub_it.Item[PUB_DATE_INDEX]._;\n \n publication.authors = [];\n \n author_list = pub_it.Item[AUTHOR_LIST_INDEX].Item;\n for(var i_author = 0; i_author < author_list.length; i_author++){\n publication.authors.push(author_list[i_author]._);\n }\n\n publications.push(publication);\n}\n\nmsg.pub_ids = [];\nmsg.pub_titles = [];\nmsg.pub_authors = [];\nmsg.pub_dates = [];\n\nfor(var pub = 0; pub < publications.length; pub++){\n msg.pub_ids.push(publications[pub].id);\n msg.pub_titles.push(publications[pub].title.replace(/[^a-zA-Z ]/g, \"\"));\n msg.pub_dates.push(publications[pub].pub_date);\n msg.pub_authors.push(publications[pub].authors[0]);\n}\n\nreturn msg;","outputs":1,"noerr":0,"x":2598.0004806518555,"y":155.5001484155655,"wires":[["60c8a7de.fce128"]]},{"id":"dd2bc388.b125a8","type":"function","z":"8f712d25.103e6","name":"Parse Nucleotide Results","func":"var gene = null;\nvar gene_it = null;\nvar author_list = null;\n\nmsg.gene_ids = [];\nmsg.gene_names = [];\nmsg.gene_bps = [];\n\nvar e_summary_results = msg.payload.eSummaryResult.DocSum;\n\nconst NAME_INDEX = 1;\nconst BP_INDEX = 8;\n\nfor(var gen = 0; gen < e_summary_results.length; gen++){\n gene = {};\n gene_it = e_summary_results[gen];\n \n msg.gene_ids.push(gene_it.Id[0]);\n msg.gene_names.push(gene_it.Item[NAME_INDEX]._.replace(/[^a-zA-Z ]/g, \"\"));\n msg.gene_bps.push(gene_it.Item[BP_INDEX]._);\n}\n\nreturn msg;","outputs":1,"noerr":0,"x":2608.0005416870117,"y":198.50010359287262,"wires":[["d83da379.80172"]]},{"id":"e339317c.c971a8","type":"function","z":"8f712d25.103e6","name":"Parse Structure Results","func":"var structure = null;\nvar structure_it = null;\nvar author_list = null;\n\nvar e_summary_results = msg.payload.eSummaryResult.DocSum;\n\nconst PDB_INDEX = 0;\nconst DESCRIPTION_INDEX = 1;\nconst CLASS_INDEX = 5;\n\nmsg.struct_ids = [];\nmsg.struct_pdbs = [];\nmsg.struct_descrs = [];\nmsg.struct_classes = [];\n\nfor(var struct = 0; struct < e_summary_results.length; struct++){\n structure = {};\n structure_it = e_summary_results[struct];\n \n msg.struct_ids.push(structure_it.Id[0]);\n msg.struct_pdbs.push(structure_it.Item[PDB_INDEX]._);\n msg.struct_descrs.push(structure_it.Item[DESCRIPTION_INDEX]._.replace(/[^a-zA-Z ]/g, \"\"));\n msg.struct_classes.push(structure_it.Item[CLASS_INDEX]._.replace(/[^a-zA-Z ]/g, \"\"));\n}\n\nreturn msg;","outputs":1,"noerr":0,"x":2607.0005111694336,"y":241.50011885166168,"wires":[["6800a188.5f209"]]},{"id":"d74b1aa8.83d71","type":"function","z":"8f712d25.103e6","name":"NCBI E-Search URL","func":"var base_url = \"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?\";\n\nvar db = msg.payload;\nvar term = \"&term=\" + msg.term;\n\nmsg.payload = base_url + db + term;\n\nmsg.url = msg.payload;\n\nreturn msg;","outputs":1,"noerr":0,"x":1008.5000114440918,"y":56,"wires":[["ed3c60a2.7cd1"]]},{"id":"2ea17a0.1d53e86","type":"function","z":"8f712d25.103e6","name":"NCBI E-Summary URL","func":"var esummary_url = \"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?\";\n\nvar ids = \"id=\";\n\nfor(var i = 0; i < msg.id_list.length-1; i++){\n ids += msg.id_list[i] + \",\";\n}\n\nids += msg.id_list[msg.id_list.length-1];\n\nmsg.url = esummary_url + \"db=\" + msg.db + \"&\" + ids + \"&retmode=xml\";\n\nreturn msg;","outputs":1,"noerr":0,"x":1804.7583465576172,"y":198.88680934906006,"wires":[["96c8005.f62928"]]},{"id":"70692f4.8670dd","type":"xml","z":"8f712d25.103e6","name":"","attr":"","chr":"","x":2227.762233734131,"y":198.8828535079956,"wires":[["d44455da.1157b8"]]},{"id":"3999846f.57f98c","type":"change","z":"8f712d25.103e6","name":"HTML Content-Type","rules":[{"t":"set","p":"headers","pt":"msg","to":"{}","tot":"str"},{"t":"set","p":"headers.content-type","pt":"msg","to":"text/html; charset=utf-8","tot":"str"}],"action":"","property":"","from":"","to":"","reg":false,"x":3109.7664947509766,"y":198.75004386901855,"wires":[["fa7f6c66.48355"]]},{"id":"60c8a7de.fce128","type":"template","z":"8f712d25.103e6","name":"Pubmed Template","field":"payload.results","fieldType":"msg","format":"handlebars","syntax":"mustache","template":"<script>\n var results_html = \"\";\n \n var ids = \"{{{pub_ids}}}\".split(\",\");\n var titles = \"{{{pub_titles}}}\".split(\",\");\n var authors = \"{{{pub_authors}}}\".split(\",\");\n var dates = \"{{{pub_dates}}}\".split(\",\");\n \n var number_of_publications = titles.length;\n\n for (var i = 0; i < number_of_publications; i++) {\n results_html += \"<div class=\\\"result_box\\\">\";\n results_html += \"<h3 class=\\\"result_text\\\"><a href=/biosuitcase/ncbi_search/pubmed/\"+ids[i]+\">\"+titles[i]+\"</a></h3>\";\n results_html += \"<p class=\\\"result_text\\\">First Author: \"+authors[i]+\"</p>\";\n results_html += \"<p class=\\\"result_text\\\">Publication Date: \"+dates[i]+\"</p>\";\n results_html += \"</div>\";\n }\n \n $(\"#results\").html(results_html);\n</script>","x":2852.0078125,"y":155.1328125,"wires":[["3999846f.57f98c"]]},{"id":"d83da379.80172","type":"template","z":"8f712d25.103e6","name":"Nucleotide Template","field":"payload.results","fieldType":"msg","format":"handlebars","syntax":"mustache","template":"<script>\n var results_html = \"\";\n \n var ids = \"{{{gene_ids}}}\".split(\",\");\n var names = \"{{{gene_names}}}\".split(\",\");\n var bps = \"{{{gene_bps}}}\".split(\",\");\n \n var number_of_genes = ids.length;\n\n for (var i = 0; i < number_of_genes; i++) {\n results_html += \"<div class=\\\"result_box\\\">\";\n results_html += \"<h3 class=\\\"result_text\\\"><a href=/biosuitcase/ncbi_search/nucleotide/\"+ids[i]+\">\"+names[i]+\"</a></h3>\";\n results_html += \"<p class=\\\"result_text\\\">\"+bps[i]+\" base pairs</p>\";\n results_html += \"</div>\";\n }\n \n $(\"#results\").html(results_html);\n</script>","x":2862.765884399414,"y":198.75000953674316,"wires":[["3999846f.57f98c"]]},{"id":"6800a188.5f209","type":"template","z":"8f712d25.103e6","name":"Structure Template","field":"payload.results","fieldType":"msg","format":"handlebars","syntax":"mustache","template":"<script>\n var results_html = \"\";\n \n var ids = \"{{{struct_ids}}}\".split(\",\");\n var pdbs = \"{{{struct_pdbs}}}\".split(\",\");\n var descrs = \"{{{struct_descrs}}}\".split(\",\");\n var classes = \"{{{struct_classes}}}\".split(\",\");\n \n var number_of_structs = ids.length;\n\n for (var i = 0; i < number_of_structs; i++) {\n results_html += \"<div class=\\\"result_box\\\">\";\n results_html += \"<h3 class=\\\"result_text\\\"><a href=/biosuitcase/ncbi_search/structure/\"+ids[i]+\">\"+pdbs[i]+\"</a></h3>\";\n results_html += \"<p class=\\\"result_text\\\">\"+descrs[i]+\"</p>\";\n results_html += \"<p class=\\\"result_text\\\"><strong>Class: </strong>\"+classes[i]+\"</p>\";\n results_html += \"</div>\";\n }\n \n $(\"#results\").html(results_html);\n</script>\n\n<!-- \n\nmsg.struct_ids = [];\nmsg.struct_pdbs = [];\nmsg.struct_descrs = [];\nmsg.struct_classes = [];\n\n-->","x":2852.7657012939453,"y":241.75001430511475,"wires":[["3999846f.57f98c"]]},{"id":"cae1f491.7260e8","type":"http request","z":"8f712d25.103e6","name":"NCBI E-Fetch","method":"GET","ret":"txt","url":"","tls":"","x":2518.451675415039,"y":473.8889193534851,"wires":[["e5083011.ebdd"]]},{"id":"242bbad.4cd3446","type":"switch","z":"8f712d25.103e6","name":"switch db","property":"db","propertyType":"msg","rules":[{"t":"eq","v":"pubmed","vt":"str"},{"t":"eq","v":"nucleotide","vt":"str"},{"t":"eq","v":"structure","vt":"str"}],"checkall":"true","outputs":3,"x":2823.2015075683594,"y":473.88892471790314,"wires":[["d0f1c4c8.5c7788"],["7a2d035f.025d1c"],["73a99e62.b01e3"]]},{"id":"d0f1c4c8.5c7788","type":"function","z":"8f712d25.103e6","name":"Parse Pubmed Results","func":"var publication = msg.payload.PubmedArticleSet.PubmedArticle[0].MedlineCitation[0];\nvar pub_details = publication.Article[0];\n\nmsg.pmid = publication.PMID[0]._;\nmsg.pub_journal = pub_details.Journal[0].Title[0];\nmsg.pub_title = pub_details.ArticleTitle[0];\nmsg.abstract = pub_details.Abstract[0].AbstractText;\nmsg.authors = [];\n\nvar authors_list = pub_details.AuthorList[0].Author;\nvar author_name = \"\";\nfor(var i = 0; i < authors_list.length; i++){\n author_name = authors_list[i].ForeName + \" \" + authors_list[i].LastName;\n msg.authors.push(author_name);\n}\n\nreturn msg;","outputs":1,"noerr":0,"x":3048.2016220092773,"y":430.6389504671097,"wires":[["92190818.6a2ba8"]]},{"id":"7a2d035f.025d1c","type":"function","z":"8f712d25.103e6","name":"Parse Nucleotide Results","func":"return msg;","outputs":1,"noerr":0,"x":3058.2016830444336,"y":473.6389056444168,"wires":[["2632512b.7a19de"]]},{"id":"73a99e62.b01e3","type":"function","z":"8f712d25.103e6","name":"Parse Structure Results","func":"return msg;","outputs":1,"noerr":0,"x":3057.2016525268555,"y":516.6389209032059,"wires":[["47f8d556.fdecec"]]},{"id":"5f534156.1daee","type":"function","z":"8f712d25.103e6","name":"NCBI E-Fetch URL","func":"var efetch_url = \"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?\";\n\nmsg.url = efetch_url + \"db=\" + msg.req.params.db + \"&\" + \"id=\" + msg.req.params.id + \"&retmode=xml\";\n\nreturn msg;","outputs":1,"noerr":0,"x":2314.959487915039,"y":474.02561140060425,"wires":[["cae1f491.7260e8"]]},{"id":"e5083011.ebdd","type":"xml","z":"8f712d25.103e6","name":"","attr":"","chr":"","x":2677.9633750915527,"y":474.0216555595398,"wires":[["242bbad.4cd3446"]]},{"id":"92190818.6a2ba8","type":"template","z":"8f712d25.103e6","name":"Pubmed Template","field":"payload.result_details","fieldType":"msg","format":"handlebars","syntax":"mustache","template":"<h1 class=\"pub_title\">{{{pub_title}}}</h1>\n<h2 class=\"pub_authors\">{{{authors}}}</h2>\n<p>Published on: {{{pub_journal}}}. PMID: {{{pmid}}}</p>\n<p class=\"abstract\">{{{abstract}}}</p>","x":3304.000442504883,"y":430.0000433921814,"wires":[["d2670d1f.9e9a3"]]},{"id":"2632512b.7a19de","type":"template","z":"8f712d25.103e6","name":"Nucleotide Template","field":"payload.result_details","fieldType":"msg","format":"handlebars","syntax":"mustache","template":"{{{payload}}} ","x":3314.758514404297,"y":473.61724042892456,"wires":[["d2670d1f.9e9a3"]]},{"id":"47f8d556.fdecec","type":"template","z":"8f712d25.103e6","name":"Structure Template","field":"payload.result_details","fieldType":"msg","format":"handlebars","syntax":"mustache","template":"{{{payload}}} ","x":3304.758331298828,"y":516.6172451972961,"wires":[["d2670d1f.9e9a3"]]},{"id":"d2670d1f.9e9a3","type":"change","z":"8f712d25.103e6","name":"HTML Content-Type","rules":[{"t":"set","p":"headers","pt":"msg","to":"{}","tot":"str"},{"t":"set","p":"headers.content-type","pt":"msg","to":"text/html; charset=utf-8","tot":"str"}],"action":"","property":"","from":"","to":"","reg":false,"x":3628.0078125,"y":474.5234375,"wires":[["fa7f6c66.48355"]]},{"id":"4ccfdb83.1fc9a4","type":"http in","z":"8f712d25.103e6","name":"","url":"/biosuitcase/ncbi_search/:db/:id","method":"get","swaggerDoc":"","x":2022.5,"y":389,"wires":[["5f534156.1daee"]]}]
Inacio Medeiros
May 27, 2017, 8:08:36 PM5/27/17
to Node-RED
For a more organized view of code, follow link below:
Julian Knight
May 28, 2017, 5:24:37 AM5/28/17
to Node-RED
Code is a bit long for me to check right now but I'd put a debug after the XML node to see what output you are getting and then check that against your switch, I'd also add a 4th entry to the switch "otherwise" and add a debug to that so you can see what isn't picked up. I suspect that your switch statement is incorrect.
Inacio Medeiros
May 28, 2017, 4:05:18 PM5/28/17
to Node-RED
In fact, use of debug was worth. In http request for e-fetch, field "db" that was in "msg" before is moved to "msg.req.params", so I've "moved back".
Julian Knight
May 28, 2017, 5:01:38 PM5/28/17
to Node-RED
;-)
Always debug first!
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