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Top level meta #769

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Aug 14, 2019
Merged

Top level meta #769

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ae2e31d
Update example v2 JSON with top level meta layer
joverlee521 Aug 14, 2019
a55f4f4
Update server conversion to top level meta layer
joverlee521 Aug 14, 2019
c3d0205
Update func: createMetadataStateFromJSON
joverlee521 Aug 14, 2019
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15 changes: 8 additions & 7 deletions cli/server/convertJsonSchemas.js
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Original file line number Diff line number Diff line change
Expand Up @@ -88,8 +88,6 @@ const setAuthorInfo = (v2, meta, tree) => {
const setMiscMetaProperties = (v2, meta) => {
// TITLE (required)
v2.title = meta.title;
// VERSION (not required)
v2.version = "2.0-alpha.0";
// UPDATED (required)
v2.updated = meta.updated;
if (!v2.updated) {
Expand Down Expand Up @@ -271,14 +269,17 @@ const storeTreeAsV2 = (v2, tree) => {


const convertFromV1 = ({tree, meta, treeName}) => {
const v2 = {};
setColorings(v2, meta);
setMiscMetaProperties(v2, meta);
setAuthorInfo(v2, meta, tree);
const v2 = {
"version": "2.0",
"meta": {}
};
setColorings(v2["meta"], meta);
setMiscMetaProperties(v2["meta"], meta);
setAuthorInfo(v2["meta"], meta, tree);
setVaccineChoicesOnNodes(meta, tree);
storeTreeAsV2(v2, tree);
if (treeName) {
v2.tree_name = treeName;
v2["meta"].tree_name = treeName;
}
return v2;
};
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216 changes: 109 additions & 107 deletions examples/minimal.json
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Original file line number Diff line number Diff line change
@@ -1,120 +1,122 @@
{
"title": "Minimal (v2) auspice spec based on Zika pipeline",
"updated": "02 Apr 2019",
"version": "2.0",
"maintainers": [
{
"url": "http://bedford.io/team/trevor-bedford/",
"name": "Trevor Bedford"
}
],
"panels": [
"tree",
"map"
],
"filters": [
"country",
"region"
],
"display_defaults": {
"color_by": "country"
},
"geographic_info": {
"country": {
"american_samoa": {
"latitude": -14.27806,
"longitude": -170.7025
},
"brazil": {
"latitude": -10.3333332,
"longitude": -53.1999999
},
"honduras": {
"latitude": 15.0610686,
"longitude": -84.5978533
},
"dominican_republic": {
"latitude": 18.50012,
"longitude": -69.98857
},
"usa": {
"latitude": 39.7837304,
"longitude": -100.4458824
},
"singapore": {
"latitude": 1.2904527,
"longitude": 103.852038
},
"venezuela": {
"latitude": 8,
"longitude": -66
},
"panama": {
"latitude": 8.3096067,
"longitude": -81.3066245
},
"puerto_rico": {
"latitude": 18.2459121,
"longitude": -66.4164147
},
"guatemala": {
"latitude": 15.6356088,
"longitude": -89.8988086
},
"colombia": {
"latitude": 2.893108,
"longitude": -73.7845142
},
"french_polynesia": {
"latitude": -17.6797,
"longitude": -149.4068
},
"thailand": {
"latitude": 14.8971921,
"longitude": 100.83273
},
"nicaragua": {
"latitude": 13,
"longitude": -85
},
"ecuador": {
"latitude": -1.3397667,
"longitude": -79.3666964
"meta":{
"title": "Minimal (v2) auspice spec based on Zika pipeline",
"updated": "02 Apr 2019",
"maintainers": [
{
"url": "http://bedford.io/team/trevor-bedford/",
"name": "Trevor Bedford"
}
],
"panels": [
"tree",
"map"
],
"filters": [
"country",
"region"
],
"display_defaults": {
"color_by": "country"
},
"region": {
"southeast_asia": {
"latitude": 3.020567,
"longitude": 112.390683
"geographic_info": {
"country": {
"american_samoa": {
"latitude": -14.27806,
"longitude": -170.7025
},
"brazil": {
"latitude": -10.3333332,
"longitude": -53.1999999
},
"honduras": {
"latitude": 15.0610686,
"longitude": -84.5978533
},
"dominican_republic": {
"latitude": 18.50012,
"longitude": -69.98857
},
"usa": {
"latitude": 39.7837304,
"longitude": -100.4458824
},
"singapore": {
"latitude": 1.2904527,
"longitude": 103.852038
},
"venezuela": {
"latitude": 8,
"longitude": -66
},
"panama": {
"latitude": 8.3096067,
"longitude": -81.3066245
},
"puerto_rico": {
"latitude": 18.2459121,
"longitude": -66.4164147
},
"guatemala": {
"latitude": 15.6356088,
"longitude": -89.8988086
},
"colombia": {
"latitude": 2.893108,
"longitude": -73.7845142
},
"french_polynesia": {
"latitude": -17.6797,
"longitude": -149.4068
},
"thailand": {
"latitude": 14.8971921,
"longitude": 100.83273
},
"nicaragua": {
"latitude": 13,
"longitude": -85
},
"ecuador": {
"latitude": -1.3397667,
"longitude": -79.3666964
}
},
"oceania": {
"latitude": -25.0562891,
"longitude": 152.008576
"region": {
"southeast_asia": {
"latitude": 3.020567,
"longitude": 112.390683
},
"oceania": {
"latitude": -25.0562891,
"longitude": 152.008576
},
"north_america": {
"latitude": 28.2367447,
"longitude": -97.738017
},
"south_america": {
"latitude": -13.083583,
"longitude": -58.470721
}
}
},
"colorings": {
"country": {
"type": "categorical",
"title": "country"
},
"north_america": {
"latitude": 28.2367447,
"longitude": -97.738017
"region": {
"type": "categorical",
"title": "region"
},
"south_america": {
"latitude": -13.083583,
"longitude": -58.470721
"num_date": {
"type": "continuous",
"title": "Sampling date"
}
}
},
"colorings": {
"country": {
"type": "categorical",
"title": "country"
},
"region": {
"type": "categorical",
"title": "region"
},
"num_date": {
"type": "continuous",
"title": "Sampling date"
}
},
"tree": {
"name": "NODE_0000031",
"div": 0,
Expand Down
32 changes: 16 additions & 16 deletions src/actions/recomputeReduxState.js
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Original file line number Diff line number Diff line change
Expand Up @@ -489,29 +489,29 @@ const modifyControlsViaTreeToo = (controls, name) => {
};

/**
* TODO -- this will change with https://github.com/nextstrain/auspice/issues/755
*
* A lot of this is simply changing augur's snake_case to auspice's camelCase
*/
const createMetadataStateFromJSON = (json) => {
const metadata = {};
if (json.colorings) {
metadata.colorings = json.colorings;
if (json.meta.colorings) {
metadata.colorings = json.meta.colorings;
}
metadata.title = json.title;
metadata.updated = json.updated;
metadata.title = json.meta.title;
metadata.updated = json.meta.updated;
if (json.version) {
metadata.version = json.version;
}
if (json.genome_annotations) {
metadata.genomeAnnotations = json.genome_annotations;
if (json.meta.genome_annotations) {
metadata.genomeAnnotations = json.meta.genome_annotations;
}
if (json.filters) {
metadata.filters = json.filters;
if (json.meta.filters) {
metadata.filters = json.meta.filters;
}
if (json.panels) {
metadata.panels = json.panels;
if (json.meta.panels) {
metadata.panels = json.meta.panels;
}
if (json.display_defaults) {
if (json.meta.display_defaults) {
metadata.displayDefaults = {};
const jsonKeyToAuspiceKey = {
color_by: "colorBy",
Expand All @@ -521,13 +521,13 @@ const createMetadataStateFromJSON = (json) => {
layout: "layout"
};
for (const [jsonKey, auspiceKey] of Object.entries(jsonKeyToAuspiceKey)) {
if (json.display_defaults[jsonKey]) {
metadata.displayDefaults[auspiceKey] = json.display_defaults[jsonKey];
if (json.meta.display_defaults[jsonKey]) {
metadata.displayDefaults[auspiceKey] = json.meta.display_defaults[jsonKey];
}
}
}
if (json.geographic_info) {
metadata.geographicInfo = json.geographic_info;
if (json.meta.geographic_info) {
metadata.geographicInfo = json.meta.geographic_info;
}


Expand Down