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clinicaltrials
Commit 8593b1cb authored by Romain Loth's avatar Romain Loth
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Merge branch 'new_db_json_specifies_type'

parents 231c96f6 54ed16c2
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Showing with 107 additions and 91 deletions
db.json
View file @ 8593b1cb
{
"data/gargistex": {
"first" : "shale_and_ice.gexf",
"gexfs": {
"graphs":{
"shale_and_ice.gexf": {
"dbtype": "csv",
"semantic":["title","keywords","abstract"],
"social":["authors"],
"dbfile": "shale_and_ice.csv"
"dbfile": "shale_and_ice.csv",
"node0": { "name": "terms" }
},
"model_calibration.gexf": {
"dbtype": "csv",
"semantic":["title","keywords","abstract"],
"social":["authors"],
"dbfile": "model_calibration.csv",
"node0": { "name": "terms" }
}
}
},
"data/test": {
"first" : "mini_for_csv.gexf",
"gexfs": {
"graphs": {
"mini_for_csv.gexf": {
"_comment": "NB: underspecified for csv and for db.json !! so this is a prototype structure",
"_comment": "POSS: weighted columns for matching importance",
"dbtype": "csv",
"semantic":["title","keywords","text"],
"social":["author"],
"dbfile": "mini_for_csv.csv"
"dbfile": "mini_for_csv.csv",
"node0": { "name": "term" },
"node1": { "name": "person" }
},
"test_with_various_atts.gexf": {}
}
......@@ -30,12 +40,14 @@
"date":"2017",
"abstract":"",
"first" : "ProgrammeDesCandidats.enrichi.gexf",
"gexfs": {
"graphs": {
"ProgrammeDesCandidats.enrichi.gexf": {
"node0": { "name": "terms" },
"social": {},
"semantic": {}
},
"ProgrammeDesCandidats.gexf": {
"node0": { "name": "terms" },
"social": {},
"semantic": {}
}
......@@ -46,8 +58,9 @@
"title":"ISITITLE",
"date":"ISIpubdate",
"abstract":"ISIABSTRACT",
"gexfs": {
"graphs": {
"Maps_S_800.gexf": {
"node0": { "name": "ISItermsWhitelistV2Oct_5 & ISItermsWhitelistV2Oct_5" },
"social": { "table":"ISIAUTHOR" , "textCol":"data","forkeyCol":"id"},
"semantic": { "table":"ISItermsWhitelistV2Oct_5" , "textCol":"data","forkeyCol":"id"}
}
......@@ -55,8 +68,11 @@
},
"data/comexjsons": {
"first" : "graph_example.json",
"gexfs": {
"graph_example.json": {}
"graphs": {
"graph_example.json": {
"node0": { "name": "NGram" },
"node1": { "name": "Document" }
}
}
}
}
settings_explorerjs.js
View file @ 8593b1cb
......@@ -157,8 +157,9 @@ TW.conf = (function(TW){
// Node typology: categories (resp. 0 and 1) will get these default labels
TWConf.catSem = "NGram";
TWConf.catSoc = "Document";
// NB: these labels may be superseded by the input data's node types values
// cf. sortNodeTypes()
// NB: these labels may be superseded by:
// - the input data's node types values cf. sortNodeTypes()
// - in servermenu mode, by the node0 & node1 properties
// Modules path
// ------------
......
twbackends/phpAPI/README.md
View file @ 8593b1cb
......@@ -64,7 +64,7 @@ Finally, to match the correct DB with the correct graph file:
"title":"yourDocumentTitlesTable",
"date":"yourDocumentPubDatesTable",
"abstract":"yourDocumentContentsTable",
"gexfs": {
"graphs": {
"your.graph.gexf": {
"semantic": { "table":"yourTableWithTerms"},
"social": { "table":"yourTableWithSocialNodes"}
......
twmain/Tinaweb.js
View file @ 8593b1cb
......@@ -643,31 +643,22 @@ var TinaWebJS = function ( sigmacanvas ) {
});
$("#changetype").click(function(){
console.log("")
console.log(" ############ changeTYPE click");
console.log("changeTYPE click");
if (TW.partialGraph.isForceAtlas2Running())
sigma_utils.ourStopFA2();
console.log("DBG before changeType SystemState:", TW.SystemState())
changeType();
setTimeout(function(){
$('.etabs a[href="#tabs1"]').trigger('click');
},500)
console.log(" ############ / changeTYPE click");
console.log("")
});
$("#changelevel").click(function(){
console.log("")
console.log(" ############ changeLEVEL click");
console.log("changeLEVEL click");
if (TW.partialGraph.isForceAtlas2Running())
sigma_utils.ourStopFA2();
changeLevel();
console.log(" ############ / changeLEVEL click");
console.log("")
});
// sidepanel folding
......
twmain/enviroment.js
View file @ 8593b1cb
......@@ -1040,8 +1040,8 @@ function createWaitIcon(idname, width) {
}
function jsActionOnGexfSelector(gexfBasename){
let gexfPath = TW.gexfPaths[gexfBasename] || gexfBasename+".gexf"
function jsActionOnGexfSelector(graphBasename){
let graphPath = TW.gmenuPaths[graphBasename] || graphBasename+".gexf"
let serverPrefix = ''
var pathcomponents = window.location.pathname.split('/')
for (var i in pathcomponents) {
......@@ -1049,13 +1049,19 @@ function jsActionOnGexfSelector(gexfBasename){
serverPrefix += '/'+pathcomponents[i]
}
var newDataRes = AjaxSync({ "url": window.location.origin+serverPrefix+'/'+gexfPath });
var newDataRes = AjaxSync({ "url": window.location.origin+serverPrefix+'/'+graphPath });
// remove any previous instance and flags
TW.resetGraph()
// override default categories with the ones from db.json
if (TW.gmenuInfos[graphPath].nodetypes) {
TW.conf.catSem = TW.gmenuInfos[graphPath].nodetypes.node0
TW.conf.catSoc = TW.gmenuInfos[graphPath].nodetypes.node1
}
mainStartGraph(newDataRes["format"], newDataRes["data"], TW.instance)
writeLabel(gexfBasename)
TW.File = gexfPath
writeLabel(graphBasename)
TW.File = graphPath
}
//============================= </OTHER ACTIONS > =============================//
twmain/extras_explorerjs.js
View file @ 8593b1cb
......@@ -449,8 +449,8 @@ function topPapersFetcher(swType, qWords, priorHtml, cbNext){
});
}
else if (TW.conf.relatedDocsType == "wosLocalDB") {
let gexfinfos = TW.relDocsInfos[TW.File]
if (!gexfinfos || !gexfinfos[swType]) {
let thisRelDocsConf = TW.gmenuInfos[TW.File].relDocsConf
if (!thisRelDocsConf || !thisRelDocsConf[swType]) {
resHTML =
`<p>Your settings for relatedDocsType are set on a local wos database,
but your servermenu file does not provide any information about
......@@ -460,7 +460,6 @@ function topPapersFetcher(swType, qWords, priorHtml, cbNext){
return
}
else {
// /!\ documentation and specification needed for the php use cases /!\
let joinedQ = JSON.stringify(qWords).split('&').join('__and__');
// cf. the php code for these url args:
......@@ -469,20 +468,20 @@ function topPapersFetcher(swType, qWords, priorHtml, cbNext){
// or 'csv' (like gargantext exports)
// POSS object + join.map(join)
let urlParams = "type="+swType+"&query="+joinedQ+"&gexf="+TW.File+"&n="+TW.conf.relatedDocsMax+"&dbtype="+gexfinfos.dbtype
let urlParams = "type="+swType+"&query="+joinedQ+"&gexf="+TW.File+"&n="+TW.conf.relatedDocsMax+"&dbtype="+thisRelDocsConf.dbtype
if (gexfinfos.dbtype == "sql") {
var qIndex = gexfinfos[swType] // a table
if (thisRelDocsConf.dbtype == "sql") {
var qIndex = thisRelDocsConf[swType] // a table
urlParams += `&index=${qIndex}`
}
else {
// a list of csv columns to search in
// ex: for semantic nodes matching we look in 'title', 'keywords' cols
// for social nodes matching we look in 'authors' col... etc.
let joinedSearchCols = JSON.stringify(gexfinfos[swType])
let joinedSearchCols = JSON.stringify(thisRelDocsConf[swType])
urlParams += `&searchin=${joinedSearchCols}`
let joinedAllCols = JSON.stringify(gexfinfos)
let joinedAllCols = JSON.stringify(thisRelDocsConf)
urlParams += `&toindex=${joinedAllCols}`
// POSS use a direct access from php to db.json to avoid toindex
// POSS make it a REST array like: index[]=title&index[]=keywords
......@@ -502,12 +501,6 @@ function topPapersFetcher(swType, qWords, priorHtml, cbNext){
cbNext(priorHtml + stockErrMsg)
}
});
}
}
}
......
twmain/main.js
View file @ 8593b1cb
......@@ -12,15 +12,15 @@ TW.File = "" // remember the currently opened file
TW.partialGraph = null // will contain the sigma visible graph instance
TW.labels=[]; // fulltext search list
TW.gexfPaths={}; // for file selectors iff servermenu
TW.relDocsInfos={}; // map [graphsource => relatedDocs db fields or tables names]
// TODO requires specifications !!
// (iff servermenu && relatedDocsType == 'wosLocalDB')
TW.categories = []; // possible node types and their inverted map
TW.catDict = {};
// used iff servermenu
TW.gmenuPaths={}; // map [graphname => graphsource] for file selectors
TW.gmenuInfos={}; // map [graphsource => { node0/1 categories
// + relatedDocs db fields names}]
// a system state is the summary of tina situation
TW.initialSystemState = {
activetypes: [], // <== filled from TW.categories
......@@ -259,58 +259,67 @@ function syncRemoteGraphData () {
var files_selector = '<select onchange="jsActionOnGexfSelector(this.value);">'
for( var path in preRES.data ) {
var theGexfs = preRES.data[path]["gexfs"]
var theGraphs = preRES.data[path]["graphs"]
for(var aGexf in theGexfs) {
var gexfBasename = aGexf.replace(/\.gexf$/, "") // more human-readable in the menu
TW.gexfPaths[gexfBasename] = path+"/"+aGexf
for(var aGraph in theGraphs) {
var graphBasename = aGraph.replace(/\.gexf$/, "") // more human-readable in the menu
TW.gmenuPaths[graphBasename] = path+"/"+aGraph
// ex : "RiskV2PageRank1000.gexf":data/AXA/RiskV2PageRank1000.gexf
// (we assume there's no duplicate basenames)
if (TW.conf.debug.logFetchers)
console.log("\t\t\t"+gexfBasename)
console.log("\t\t\t"+graphBasename)
// for associated wosLocalDBs sql queries
if (theGexfs[aGexf]) {
if (theGraphs[aGraph]) {
let gSrcEntry = theGraphs[aGraph]
TW.gmenuInfos[path+"/"+aGraph] = {
"nodetypes": {"node0":'', "node1":''},
"relDocsConf": {
"semantic":null, "social":null, "dbtype": null
}
}
let gSrcEntry = theGexfs[aGexf]
// shortcut
let thisInfos = TW.gmenuInfos[path+"/"+aGraph]
TW.relDocsInfos[path+"/"+aGexf] = {"semantic":null, "social":null, "dbtype": null}
// db.json flat => 2 level structure: nodetype infos and relDocsConf
// POSS have this type attribute in db.json *for all the entries*
// node types (no fallback here)
thisInfos.nodetypes.node0 = gSrcEntry.node0 ? gSrcEntry.node0.name : ''
thisInfos.nodetypes.node1 = gSrcEntry.node1 ? gSrcEntry.node1.name : ''
// TODO here settings + templates by type as per new specifications
// ----------------------------------------------------------------------------------
// choice: we'll keep a flat structure by source unless some use cases need otherwise
// ----------------------------------------------------------------------------------
// csv LocalDB ~ gargantext
if(gSrcEntry["dbtype"] && gSrcEntry["dbtype"] == "csv") {
TW.relDocsInfos[path+"/"+aGexf]['dbtype'] = "csv"
thisInfos.relDocsConf.dbtype = "csv"
// it's CSV columns here
TW.relDocsInfos[path+"/"+aGexf]['semantic'] = gSrcEntry["semantic"]
TW.relDocsInfos[path+"/"+aGexf]['social'] = gSrcEntry["social"]
thisInfos.relDocsConf.semantic = gSrcEntry["semantic"]
thisInfos.relDocsConf.social = gSrcEntry["social"]
}
// sqlite LocalDB ~ wos
else {
TW.relDocsInfos[path+"/"+aGexf]['dbtype'] = "sql"
if (theGexfs[aGexf]["semantic"] && theGexfs[aGexf]["semantic"]["table"]) {
TW.relDocsInfos[path+"/"+aGexf]['semantic'] = theGexfs[aGexf]["semantic"]["table"]
thisInfos.dbtype = "sql"
if (theGraphs[aGraph]["semantic"] && theGraphs[aGraph]["semantic"]["table"]) {
thisInfos.relDocsConf.semantic = theGraphs[aGraph]["semantic"]["table"]
}
if (theGexfs[aGexf]["social"] && theGexfs[aGexf]["social"]["table"]) {
TW.relDocsInfos[path+"/"+aGexf]['social'] = theGexfs[aGexf]["social"]["table"]
if (theGraphs[aGraph]["social"] && theGraphs[aGraph]["social"]["table"]) {
thisInfos.relDocsConf.social = theGraphs[aGraph]["social"]["table"]
}
}
}
else {
TW.relDocsInfos[path+"/"+aGexf] = null
TW.gmenuInfos[path+"/"+aGraph] = null
}
// ^^^^^^ FIXME see if we got the expected behavior right
// (? specifications ?)
// ^^^^^^ FIXME finish implementing new specifications
let cssFileSelected = (TW.File==(path+"/"+aGexf))?"selected":""
files_selector += '<option '+cssFileSelected+'>'+gexfBasename+'</option>'
let cssFileSelected = (TW.File==(path+"/"+aGraph))?"selected":""
files_selector += '<option '+cssFileSelected+'>'+graphBasename+'</option>'
}
// console.log( files_selector )
}
......
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