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Merge pull request #1300 from VirtualFlyBrain/feature/1298
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Feature/1298 testing
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@Robbie1977
Robbie1977 authored Mar 10, 2022
2 parents 8cc6a3f + 1e1c91d commit fc1614a
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Showing 39 changed files with 1,615 additions and 421 deletions.
3 changes: 2 additions & 1 deletion Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ ARG geppettoSimulationRelease=vfb_20200604_a
ARG geppettoDatasourceRelease=vfb_20200604_a
ARG geppettoModelSwcRelease=v1.0.1
ARG geppettoFrontendRelease=development
ARG geppettoClientRelease=VFBv2.2.0.7
ARG geppettoClientRelease=VFBv2.2.2
ARG ukAcVfbGeppettoRelease=download

ARG mvnOpt="-Dhttps.protocols=TLSv1.2 -DskipTests --quiet -Pmaster"
Expand All @@ -38,6 +38,7 @@ ENV VFB_OWL_SERVER=${VFB_OWL_SERVER_ARG}
ENV VFB_R_SERVER=${VFB_R_SERVER_ARG}
ENV SOLR_SERVER=${SOLR_SERVER_ARG}
ENV googleAnalyticsSiteCode=${googleAnalyticsSiteCode_ARG}
ENV LOG4J_FORMAT_MSG_NO_LOOKUPS=true

RUN /bin/echo -e "\e[1;35mORIGIN BRANCH ------------ $originBranch\e[0m" &&\
/bin/echo -e "\e[1;35mTARGET BRANCH ------------ $targetBranch\e[0m" &&\
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79 changes: 20 additions & 59 deletions components/VFBMain.js
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@ import VFBTermInfoWidget from './interface/VFBTermInfo/VFBTermInfo';
import Logo from '@geppettoengine/geppetto-client/components/interface/logo/Logo';
import Canvas from '@geppettoengine/geppetto-client/components/interface/3dCanvas/Canvas';
import QueryBuilder from '@geppettoengine/geppetto-client/components/interface/query/queryBuilder';
import VFBDownloadContents from './interface/VFBDownloadContents/VFBDownloadContents';
import VFBUploader from './interface/VFBUploader/VFBUploader';
import HTMLViewer from '@geppettoengine/geppetto-ui/html-viewer/HTMLViewer';
import VFBListViewer from './interface/VFBListViewer/VFBListViewer';
Expand Down Expand Up @@ -52,6 +53,7 @@ class VFBMain extends React.Component {
quickHelpVisible: undefined,
UIUpdated: true,
wireframeVisible: false,
downloadContentsVisible : true,
uploaderContentsVisible : true
};

Expand Down Expand Up @@ -488,6 +490,12 @@ class VFBMain extends React.Component {
[buttonState]: !this.state[buttonState]
});
break;
case 'downloadContentsVisible':
this.refs.downloadContentsRef?.openDialog();
break;
case 'uploaderContentsVisible':
this.refs.uploaderContentsRef?.openDialog();
break;
case 'quickHelpVisible':
if (this.state[buttonState] === undefined) {
this.setState({
Expand Down Expand Up @@ -527,6 +535,9 @@ class VFBMain extends React.Component {
case 'triggerSetTermInfo':
this.handlerInstanceUpdate(click.value[0]);
break;
case 'downloadContentsVisible':
this.refs.downloadContentsRef?.openDialog();
break;
case 'uploaderContentsVisible':
this.refs.uploaderContentsRef?.openDialog();
break;
Expand Down Expand Up @@ -1286,63 +1297,6 @@ class VFBMain extends React.Component {
idsList += ",";
}
idsList += this.idFromURL;
// populate page meta for this term for indexing
try {
window.ga('vfb.send', 'pageview', window.location.href );
if ( window.XMLHttpRequest ) {
var xhr = new XMLHttpRequest();
xhr.onload = function () {
try {
if (this.responseXML.title.indexOf("404 Not Found") < 0) {
document.title = 'Virtual Fly Brain (' + this.responseXML.title + ')';
document.body.style.font = "x-large";
document.querySelector('meta[property="og:title"]').setAttribute("content",this.responseXML.title);
document.querySelector('meta[name="description"]').setAttribute("content",this.responseXML.getElementById('json').innerText.substring(0, 4900));
document.querySelector('meta[property="og:description"]').setAttribute("content",this.responseXML.getElementById('json').innerText.substring(0, 4900));
if (document.getElementById('metaDesc') != null) {
if (this.responseXML.head != undefined && this.responseXML.head.getElementsByTagName('script') != undefined && this.responseXML.head.getElementsByTagName('script') != null && this.responseXML.head.getElementsByTagName('script')[1] != undefined) {
document.getElementById('metaDesc').innerHTML = this.responseXML.head.getElementsByTagName('script')[1].innerHTML;
}
} else {
if (this.responseXML.head != undefined && this.responseXML.head.getElementsByTagName('script') != undefined && this.responseXML.head.getElementsByTagName('script') != null && this.responseXML.head.getElementsByTagName('script')[1] != undefined) {
var script = document.createElement('script');
script.type = 'application/ld+json';
script.id = 'metaDesc';
script.innerHTML = this.responseXML.head.getElementsByTagName('script')[1].innerHTML;
document.getElementsByTagName('head')[0].appendChild(script);
}
}
var viewport = !!document.querySelector("meta[name='viewport']");
viewport = viewport ? document.querySelector("meta[name='viewport']") : document.createElement('meta');
viewport.setAttribute('name', 'viewport');
viewport.setAttribute('content', 'width=device-width, initial-scale=1');
document.head.appendChild(viewport);
}
} catch (err) {
console.log(err);
}
}
xhr.open( 'GET', 'https://virtualflybrain.org/data/VFB/json/' + this.idFromURL + '.html')
xhr.responseType = 'document';
xhr.send();
}
} catch (err) {
console.error(err);
}
try {
var link = !!document.querySelector("link[rel='amphtml']");
link = link ? document.querySelector("link[rel='amphtml']") : document.createElement('link');
link.setAttribute('rel', 'amphtml');
link.setAttribute('href', 'https://virtualflybrain.org/data/VFB/json/' + this.idFromURL + '.html');
document.head.appendChild(link);
var conlink = !!document.querySelector("link[rel='canonical']");
conlink = conlink ? document.querySelector("link[rel='canonical']") : document.createElement('link');
conlink.setAttribute('rel', 'canonical');
conlink.setAttribute('href', 'https://virtualflybrain.org/reports/' + this.idFromURL);
document.head.appendChild(conlink);
} catch (err) {
console.error(err);
}
} else if (idList[list].indexOf("i=") > -1) {
if (idsList.length > 0) {
idsList = "," + idsList;
Expand All @@ -1351,7 +1305,7 @@ class VFBMain extends React.Component {
} else if (idList[list].indexOf("q=") > -1) {
const multipleQueries = idList[list].replace("q=","").replace("%20", " ").split(";");
let that = this;
multipleQueries?.forEach( query => {
multipleQueries?.forEach( query => {
const querySplit = query.split(",");
that.urlQueryLoader.push({ id : querySplit[0].trim(), selection : querySplit[1].trim() });
});
Expand Down Expand Up @@ -1392,7 +1346,7 @@ class VFBMain extends React.Component {
GEPPETTO.on(GEPPETTO.Events.Instance_added, function (instance) {
that.props.instanceAdded(instance);
});

GEPPETTO.on(GEPPETTO.Events.Instances_created, function (instances) {
// Set template Instance to be not clickable in 3D viewer
if ( instances[0]?.id?.includes(window.templateID) ) {
Expand Down Expand Up @@ -1529,6 +1483,10 @@ class VFBMain extends React.Component {

GEPPETTO.on(GEPPETTO.Events.Websocket_disconnected, function () {
window.ga('vfb.send', 'event', 'disconnected', 'websocket-disconnect', (window.location.pathname + window.location.search));
if (GEPPETTO.MessageSocket.protocol == 'wss://' && location.protocol !== 'https:') {
console.log("%c Unsecure connection used reloading with HTTPS connection... ", 'background: #444; color: #bada55');
location.replace(`https:${location.href.substring(location.protocol.length)}`);
}
if (GEPPETTO.MessageSocket.socketStatus == GEPPETTO.Resources.SocketStatus.CLOSE) {
if (GEPPETTO.MessageSocket.attempts < 10) {
window.ga('vfb.send', 'event', 'reconnect-attempt:' + GEPPETTO.MessageSocket.attempts, 'websocket-disconnect', (window.location.pathname + window.location.search));
Expand Down Expand Up @@ -1752,7 +1710,10 @@ class VFBMain extends React.Component {
searchConfiguration={this.searchConfiguration}
datasourceConfiguration={this.datasourceConfiguration} />

<VFBDownloadContents ref="downloadContentsRef" open={false} />

<VFBUploader ref="uploaderContentsRef" open={false} />

{this.htmlToolbarRender}
</div>
);
Expand Down
71 changes: 39 additions & 32 deletions components/configuration/VFBCircuitBrowser/circuitBrowserConfiguration.js
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Original file line number Diff line number Diff line change
Expand Up @@ -19,11 +19,20 @@ var locationCypherQuery = ( instances, paths, weight ) => ({
+ " WITH * ORDER BY index DESC"
+ " UNWIND relationships(path) as sr"
+ " OPTIONAL MATCH cp=(x:Neuron:has_neuron_connectivity)-[:synapsed_to]-(y:Neuron:has_neuron_connectivity) WHERE x=apoc.rel.startNode(sr) AND y=apoc.rel.endNode(sr) OPTIONAL MATCH fp=(x)-[r:synapsed_to]->(y) WHERE r.weight[0] >= " + weight?.toString()
+ " RETURN distinct a as root, collect(distinct fp) as pp, collect(distinct cp) as p, collect(distinct id(r)) as fr, sourceNode as source, targetNode as target, max(length(path)) as maxHops, collect(distinct toString(id(r))+':'+toString(index)) as relationshipY ",
+ " OPTIONAL MATCH (x)-[xio:INSTANCEOF]->(xpc:Class) OPTIONAL MATCH (y)-[yio:INSTANCEOF]->(ypc:Class) WITH *,'\"'+ x.short_form+'\":{\"'+xpc.short_form+'\":\"' + xpc.label + '\"},\"'+ y.short_form+'\":{\"'+ypc.short_form+'\":\"' + ypc.label + '\"}' as Class"
+ " RETURN distinct a as root, collect(distinct fp) as pp, collect(distinct cp) as p, collect(distinct id(r)) as fr, sourceNode as source, targetNode as target, max(length(path)) as maxHops, collect(distinct toString(id(r))+':'+toString(index)) as relationshipY, "
+ " apoc.convert.fromJsonMap('{' + apoc.text.join(collect(Class),',') + '}') as class ",
"resultDataContents": ["row", "graph"]
}
]
});

var Neo4jLabels = {
FAFB : "FAFB",
L1EM : "L1EM",
FlyEM_HB : "FlyEM_HB"
}

// See query explanation on https://github.com/VirtualFlyBrain/graph_queries/blob/main/weighted_path.md

var configuration = {
Expand Down Expand Up @@ -63,46 +72,43 @@ var styling = {
// Color apply to target and source nodes when hovering over a link or a node.
defaultNeighborNodesHoverColor : "orange",
// Font used for text in nodes
defaultNodeFont : "5px sans-serif",
defaultNodeFont : "8px sans-serif",
// Color of font in node's text
defaultNodeFontColor : "black",
// Node border color
defaultBorderColor : "black",
// When hovering over a node, the node's border color changes to create a halo effect
defaultNodeHoverBoderColor : "red",
// Title bar (in node) background color
defaultNodeTitleBackgroundColor : "#11bffe",
defaultNodeTitleBackgroundColor : "grey",
// Description area (in node) background color
defaultNodeDescriptionBackgroundColor : "white",
nodeColorsByLabel : {
"Template" : "#ff6cc8",
"GABAergic" : "#9551ff",
"Dopaminergic" : "#3551ff",
"Cholinergic" : "#95515f",
"Glutamatergic" : "#95f1ff",
"Octopaminergic" : "#f3511f",
"Serotonergic" : "#9501f0",
"Motor_neuron" : "#fffa30",
"Sensory_neuron" : "#ff3a3a",
"Peptidergic_neuron" : "#5f6a3a",
"Glial_cell" : "#ff3a6a",
"Clone" : "#d6007d",
"Synaptic_neuropil" : "#00a2aa",
"License" : "#0164d8",
"Person" : "#023f00",
"Neuron" : "#7f2100",
"Neuron_projection_bundle" : "#d6327d",
"Resource" : "#005f1d",
"Site" : "#005f1d",
"Expression_pattern" : "#534700",
"Split" : "#e012e3",
"DataSet" : "#b700b5",
"Ganglion" : "#d6007d",
"Neuromere" : "#d6507d",
"Cell" : "#ff6a3a",
"Property" : "#005f1d",
"Anatomy" : "#00a2aa",
"_Class" : "#0164d8"
"GABAergic" : "#377eb8",
"Neuron_projection_bundle" : "#ff7f00",
"Nervous_system" : "#4daf4a",
"Dopaminergic" : "#f781bf",
"Motor_neuron" : "#a65628",
"Cholinergic" : "#984ea3",
"Neuromere" : "#999999",
"Expression_pattern_fragment" : "#e41a1c",
"Peptidergic_neuron" : "#dede00",
"Ganglion" : "#377eb8",
"Muscle" : "#ff7f00",
"Glutamatergic" : "#4daf4a",
"Cluster" : "#f781bf",
"Clone" : "#a65628",
"Octopaminergic" : "#984ea3",
"Anatomy" : "#999999",
"Adult" : "#e41a1c",
"Synaptic_neuropil_subdomain" : "#dede00",
"Expression_pattern" : "#377eb8",
"Synaptic_neuropil_block" : "#ff7f00",
"Synaptic_neuropil_domain" : "#4daf4a",
"Serotonergic" : "#f781bf",
"Larva" : "#a65628",
"Neuron" : "#984ea3",
"Sensory_neuron" : "#999999"
},
controlIcons : {
home : "fa fa-home",
Expand All @@ -120,5 +126,6 @@ module.exports = {
configuration,
styling,
restPostConfig,
locationCypherQuery
locationCypherQuery,
Neo4jLabels
};
34 changes: 34 additions & 0 deletions components/configuration/VFBDownloadContents/configuration.json
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@@ -0,0 +1,34 @@
{
"postURL":"https://zip.virtualflybrain.org/download",
"contentType": "application/json",
"zipName" : "VFB Files.zip",
"options" :{
"obj": {
"label" : "OBJ",
"tooltip" : "Download OBJ"
},
"swc": {
"label" : "SWC",
"tooltip" : "Download SWC"
},
"nrrd": {
"label" : "NRRD",
"tooltip" : "Download NRRD"
},
"reference": {
"label" : "References",
"tooltip" : "Download References"
}
},
"text" : {
"title" : "Download Data",
"typesSubtitle" : "Please select the desired types",
"variablesSubtitle" : "Please select Variables:",
"noVariablesSubtitle" : "No loaded variables",
"errorMessage" : "Something went wrong... We were not able to download the data. Please try again.",
"noEntriesFound" : "No entries found for the types and variables selected.",
"cancelButton" : "Cancel",
"downloadButton" : "Download",
"tryAgainButton" : "Try Again"
}
}
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26 changes: 21 additions & 5 deletions components/configuration/VFBMain/searchConfiguration.js
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Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@ var searchStyle = {
singleResult: {
"color": "white",
"fontSize": "18px",

"whiteSpace" : "normal",
":hover": {
"color": "#11bffe",
"background-color": "#252323",
Expand Down Expand Up @@ -91,25 +91,29 @@ var datasourceConfiguration = {
"defType": "edismax",
"qf": "label^100 synonym^100 label_autosuggest_ws label_autosuggest_e label_autosuggest synonym_autosuggest_ws synonym_autosuggest shortform_autosuggest",
"indent": "true",
"fl": "short_form,label,synonym,id,facets_annotation",
"fl": "short_form,label,synonym,id,facets_annotation,unique_facets",
"start": "0",
"pf":"true",
"fq": [
"shortform_autosuggest:VFB* OR shortform_autosuggest:FB* OR facets_annotation:DataSet OR facets_annotation:pub"
],
"rows": "100",
"wt": "json",
"bq": "shortform_autosuggest:VFB*^110.0 shortform_autosuggest:FBbt*^100.0 label_s:\"\"^2 synonym_s:\"\" short_form:FBbt_00003982^2 facets_annotation:Deprecated^0.001"
"bq": "shortform_autosuggest:VFBexp*^10.0 shortform_autosuggest:VFB*^100.0 shortform_autosuggest:FBbt*^100.0 label_s:\"\"^2 synonym_s:\"\" short_form:FBbt_00003982^2 facets_annotation:Deprecated^0.001"
}
};

var searchConfiguration = {
"resultsMapping":
{
"name": "label",
"id": "short_form"
"id": "short_form",
"labels" : "unique_facets"
},
"label_manipulation" : label => label,
"filters_expanded": true,
"filter_positive" : "^100",
"filter_negative" : "^0.001",
"filters": [
{
"key": "facets_annotation",
Expand Down Expand Up @@ -305,6 +309,13 @@ var searchConfiguration = {
if (b.label.toLowerCase().indexOf(InputString.toLowerCase()) > -1 && b.label.toLowerCase().indexOf(InputString.toLowerCase()) < a.label.toLowerCase().indexOf(InputString.toLowerCase())) {
return 1;
}
// move up expression (VFBexp) terms
if (a.id.indexOf("VFBexp") > -1 && b.id.indexOf("VFBexp") < 0) {
return -1;
}
if (b.id.indexOf("VFBexp") > -1 && a.id.indexOf("VFBexp") < 0) {
return 1;
}
// if the match in the id is closer to start then move up
if (a.id.toLowerCase().indexOf(InputString.toLowerCase()) > -1 && a.id.toLowerCase().indexOf(InputString.toLowerCase()) < b.id.toLowerCase().indexOf(InputString.toLowerCase())) {
return -1;
Expand All @@ -323,11 +334,16 @@ var searchConfiguration = {
},
"clickHandler": function (id) {
window.addVfbId(id);
},
"Neo4jLabels" : {
"FAFB" : "FAFB",
"L1EM" : "L1EM",
"FlyEM_HB" : "FlyEM_HB"
}
};

module.exports = {
searchStyle,
searchConfiguration,
datasourceConfiguration,
datasourceConfiguration
};
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