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Start addressing https://github.com/OneZoom/OZtree/issues/183 #185

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Start addressing https://github.com/OneZoom/OZtree/issues/183 #185

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3 changes: 2 additions & 1 deletion OZprivate/rawJS/OZTreeModule/src/factory/data_repo.js
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Original file line number Diff line number Diff line change
Expand Up @@ -257,6 +257,7 @@ function parse_ordered_leaves(data_repo, leaves, node_details) {
leaf_meta_entry[data_repo.mc_key_l["OTTid"]] = ott;
leaf_meta_entry[data_repo.mc_key_l["scientificName"]] =leaves[i][node_details.leaf_cols["name"]];
leaf_meta_entry[data_repo.mc_key_l["popularity"]] = leaves[i][node_details.leaf_cols["popularity"]];
leaf_meta_entry[data_repo.mc_key_l["extinction_date"]] = leaves[i][node_details.leaf_cols["extinction_date"]];
}
}

Expand All @@ -269,7 +270,7 @@ function parse_ordered_nodes(data_repo, nodes, node_details) {
node_meta_entry[data_repo.mc_key_n["OTTid"]] = ott;
node_meta_entry[data_repo.mc_key_n["scientificName"]] = nodes[i][node_details.node_cols["name"]];
node_meta_entry[data_repo.mc_key_n["popularity"]] = nodes[i][node_details.node_cols["popularity"]];
node_meta_entry[data_repo.mc_key_n["lengthbr"]] = Math.abs(nodes[i][node_details.node_cols["age"]]);
node_meta_entry[data_repo.mc_key_n["age_Ma"]] = Math.abs(nodes[i][node_details.node_cols["age"]]);

node_meta_entry[data_repo.mc_key_n["sp1"]] = nodes[i][node_details.node_cols["{pic}1"]];
node_meta_entry[data_repo.mc_key_n["sp2"]] = nodes[i][node_details.node_cols["{pic}2"]];
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38 changes: 26 additions & 12 deletions OZprivate/rawJS/OZTreeModule/src/factory/midnode.js
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Expand Up @@ -25,13 +25,13 @@ class Midnode {
this._sponsor_name = null;
this._sponsor_kind = null;
this._sponsor_extra = null;
this._age = null;
this._age = undefined;
this._spec_num_full = null;
this._picset_len = null;
this._picset_codes = null;
this._signpost_common = false;
this._threatened_branch = null;
this._redlist = null;
this._redlist = undefined;
this._pic_filename = null;
this._picID_credit = null;
this._picID_src = null;
Expand Down Expand Up @@ -90,13 +90,13 @@ class Midnode {
this._sponsor_name = null;
this._sponsor_kind = null;
this._sponsor_extra = null;
this._age = null;
this._age = undefined;
this._spec_num_full = null;
this._picset_len = null;
this._picset_codes = null;
this._signpost_common = false;
this._threatened_branch = null;
this._redlist = null;
this._redlist = undefined;
this._pic_filename = null;
this._picID_credit = null;
this._picID_src = null;
Expand Down Expand Up @@ -239,7 +239,7 @@ class Midnode {


/**
* Get attribute of node by key name. Use this function to fetch metadata of node only.
* Get attribute of node or leaf by key name from the data_repo store.
*/
get_attribute(key_name) {
if (this.detail_fetched && this.is_leaf) {
Expand Down Expand Up @@ -327,14 +327,28 @@ class Midnode {
}
return _sponsor_extra;
}
get lengthbr() {
if (this._age !== null) return this._age;
let age = this.get_attribute("lengthbr");
age = isNaN(age) ? 0 : age;
get age_Ma() {
/* used for internal node dates - if 0 or null, this is unknown */
if (this._age !== undefined) return this._age;
let _age_Ma = this.get_attribute("age_Ma");
_age_Ma = isNaN(_age_Ma) ? 0 : _age_Ma;
if (this.detail_fetched) {
this._age = age;
this._age = _age_Ma;
}
return age;
return _age_Ma;
}
get extinction_Ma() {
/* used for leaf dates. Extant are null, unknown is marked by a large negative value
(-1e4: more Mya than the age of the planet). In this case we simply return `true`.
Zero might mark something very recently extinct, e.g. marked as extinct by IUCN
*/
if (this._age !== undefined) return this._age;
let _extinction_Ma = this.get_attribute("extinction_date");
_extinction_Ma = (_extinction_Ma < -5e3)?true:_extinction_Ma
if (this.detail_fetched) {
this._age = _extinction_Ma;
}
return _extinction_Ma;
}
get spec_num_full() {
if (this._spec_num_full !== null) return this._spec_num_full;
Expand Down Expand Up @@ -396,7 +410,7 @@ class Midnode {
return num_threatened > this.richness_val * 0.5;
}
get redlist() {
if (this._redlist !== null) return this._redlist;
if (this._redlist !== undefined) return this._redlist;
let _redlist = this.get_attribute("IUCN");
if (this.detail_fetched) {
this._redlist = _redlist;
Expand Down
23 changes: 17 additions & 6 deletions OZprivate/rawJS/OZTreeModule/src/factory/utils.js
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Expand Up @@ -58,15 +58,26 @@ export function gpmapper(datein, full) {
}


export function ageAsText(Ma) {
//return e.g. 100 thousand years ago
export function ageAsText(Ma, leaf) {
//return e.g. "100 thousand years ago", or a similar string
let subs_strs = leaf?OZstrings['leaf_date']:OZstrings['node_date'];
if (Ma >10) {
return OZstrings['Mya'].replace(/\{(\w+)\}/g, function (m, c) {return({'mya':(Math.round(Ma*10)/10.0).toString()}[c])});
return subs_strs['Mya'].replace(
/\{(\w+)\}/g,
function (m, c) {return({'mya':(Math.round(Ma*10)/10.0).toString()}[c])});
} else {
if (Ma >1) {
return OZstrings['Mya'].replace(/\{(\w+)\}/g, function (m, c) {return({'mya':(Math.round(Ma*100)/100.0).toString()}[c])});
if (Ma > 1) {
return subs_strs['Mya'].replace(
/\{(\w+)\}/g,
function (m, c) {return({'mya':(Math.round(Ma*100)/100.0).toString()}[c])});
} else if (Ma > 0.001) {
return subs_strs['tya'].replace(
/\{(\w+)\}/g,
function (m, c) {return({'tya':(Math.round(Ma*10000)/10.0).toString()}[c])});
} else {
return OZstrings['tya'].replace(/\{(\w+)\}/g, function (m, c) {return({'tya':(Math.round(Ma*10000)/10.0).toString()}[c])});
return subs_strs['ya'].replace(
/\{(\w+)\}/g,
function (m, c) {return({'ya':(Math.round(Ma*1000000)).toString()}[c])});
}
}
}
Expand Down
10 changes: 5 additions & 5 deletions OZprivate/rawJS/OZTreeModule/src/projection/layout/AT/node_layout.js
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Expand Up @@ -58,16 +58,16 @@ class ATNodeLayout extends NodeLayoutBase {
function get_concestor_interior_header(node) {
let textonly_header;
let concestor_append = "Concestor " + node.concestor + ",";
if (node.lengthbr && node.lengthbr>0) {
if (node.age_Ma && node.age_Ma>0) {
//This is a dated node
if (is_primary_or_secondary_name(node)) {
textonly_header = (["", "", "the most recent common ancestor to today’s",
"the " + gpmapper(node.lengthbr) + " period, lived " + concestor_append,
ageAsText(node.lengthbr) + ", during"]);
"the " + gpmapper(node.age_Ma) + " period, lived " + concestor_append,
ageAsText(node.age_Ma) + ", during"]);
} else {
textonly_header = (["", "common ancestor to species including", "lived " + concestor_append + " the most recent",
"during the " + gpmapper(node.lengthbr) + " period,",
ageAsText(node.lengthbr)])
"during the " + gpmapper(node.age_Ma) + " period,",
ageAsText(node.age_Ma)])
}
} else {
//This is an undated node (shouldn't happen)
Expand Down
28 changes: 18 additions & 10 deletions OZprivate/rawJS/OZTreeModule/src/projection/layout/leaf_layout_helper.js
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Expand Up @@ -13,7 +13,7 @@ import {global_button_action} from '../../button_manager';
import {live_area_config} from '../live_area_config';
import {add_mr} from '../move_restriction';
import {get_image, image_ready} from '../../image_cache';
import {extxt, spec_num_full} from '../../factory/utils';
import {extxt, spec_num_full, ageAsText} from '../../factory/utils';
import config from '../../global_config';

class LeafLayoutBase {
Expand Down Expand Up @@ -156,16 +156,24 @@ class LeafLayoutBase {
}

get_conservation_text(node) {
if (node.redlist === "EX"
||node.redlist === "EW"
||node.redlist === "CR"
||node.redlist === "EN"
||node.redlist === "VU"
||node.redlist === "NT"
||node.redlist === "LC") {
return [OZstrings["Conservation"], OZstrings["IUCN Red List status:"], extxt(node)]
if (node.extinction_Ma !== null) {
if (node.extinction_Ma !== true) {
return ageAsText(node.extinction_Ma, true).split("\n");
} else {
return OZstrings["Fossil species"].split("\n");
};
} else {
return [];
if (node.redlist === "EX"
||node.redlist === "EW"
||node.redlist === "CR"
||node.redlist === "EN"
||node.redlist === "VU"
||node.redlist === "NT"
||node.redlist === "LC") {
return [OZstrings["Conservation"], OZstrings["IUCN Red List status:"], extxt(node)]
} else {
return [];
}
}
}

Expand Down
20 changes: 10 additions & 10 deletions OZprivate/rawJS/OZTreeModule/src/projection/layout/node_layout_helper.js
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Expand Up @@ -601,12 +601,12 @@ class NodeLayoutBase {

get_date_str(node) {
let date_str;
if (node.lengthbr > 10) {
date_str = (Math.round((node.lengthbr)*10)/10.0).toString() + " Ma";
} else if (node.lengthbr > 1) {
date_str = (Math.round((node.lengthbr)*100)/100.0).toString() + " Ma";
} else if (node.lengthbr > 0) {
date_str = (Math.round((node.lengthbr)*10000)/10.0).toString() + " Ka";
if (node.age_Ma > 10) {
date_str = (Math.round((node.age_Ma)*10)/10.0).toString() + " Ma";
} else if (node.age_Ma > 1) {
date_str = (Math.round((node.age_Ma)*100)/100.0).toString() + " Ma";
} else if (node.age_Ma > 0) {
date_str = (Math.round((node.age_Ma)*10000)/10.0).toString() + " Ka";
} else {
date_str = "";
}
Expand All @@ -616,8 +616,8 @@ class NodeLayoutBase {
get_textonly_header(node) {
let ntxt = OZstrings['node_labels']['text_only']
let textonly_header;
if (node.lengthbr && node.lengthbr>0) {
let vars = {'date_with_units':ageAsText(node.lengthbr), 'geo_time':gpmapper(node.lengthbr, true)};
if (node.age_Ma && node.age_Ma>0) {
let vars = {'date_with_units':ageAsText(node.age_Ma), 'geo_time':gpmapper(node.age_Ma, true)};
if (is_primary_or_secondary_name(node)) {
textonly_header = substitute_variables(ntxt['dated']['named'], vars).split("\n").reverse();
} else {
Expand All @@ -637,8 +637,8 @@ class NodeLayoutBase {
let ntxt = OZstrings['node_labels']['with_pic']
let pic_header_text;
//NB - these are in reverse order, as we often don't use the top two lines
if (node.lengthbr && (node.lengthbr>0)) {
let vars = {'date_with_units':ageAsText(node.lengthbr), 'geo_time':gpmapper(node.lengthbr, true)};
if (node.age_Ma && (node.age_Ma>0)) {
let vars = {'date_with_units':ageAsText(node.age_Ma), 'geo_time':gpmapper(node.age_Ma, true)};
if (is_primary_or_secondary_name(node)) {
pic_header_text = substitute_variables(ntxt['dated']['named'], vars).split("\n").reverse();
} else {
Expand Down
62 changes: 41 additions & 21 deletions OZprivate/rawJS/OZTreeModule/src/themes/natural_theme.js
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Expand Up @@ -22,6 +22,13 @@ let iucnDD = green1;
let iucnNE = green1;
let iucnDefault = green1;

function is_fossil(leaf) {
// fossils have extinction_Ma > 0 (if known) or true
// extant (or recently extinct) leaves should all have extinction_Ma===null
// we use == not === to also treat undefined (data not yet filled out) as not fossil
return (leaf.extinction_Ma == null)?false:true;
}

function outline_highlight(node) {
if (node.richness_val > 1) {
return 'rgb(0,0,0)';
Expand All @@ -33,25 +40,29 @@ function outline_highlight(node) {
function leafcolor2b(node) {
switch(node.redlist) {
case "EX":
return ('rgb(50,50,50)');
return ('rgb(50,50,50)');
case "EW":
return ('rgb(50,50,50)');
return ('rgb(50,50,50)');
case "CR":
return ('rgb(80,00,00)');
return ('rgb(80,00,00)');
case "EN":
return ('rgb(80,00,00)');
return ('rgb(80,00,00)');
case "VU":
return ('rgb(80,00,00)');
return ('rgb(80,00,00)');
case "NT":
return ('rgb(20,80,00)');
return ('rgb(20,80,00)');
case "LC":
return ('rgb(20,80,00)');
return ('rgb(20,80,00)');
case "DD":
return ('rgb(20,80,00)');
return ('rgb(20,80,00)');
case "NE":
return ('rgb(20,80,00)');
return ('rgb(20,80,00)');
default:
return ('rgb(20,80,00)');
if (is_fossil(node)) {
return ('rgb(50,50,50)');
} else {
return ('rgb(20,80,00)');
}
}
}

Expand All @@ -69,42 +80,47 @@ function get_redlist_color(node) {
switch(node.redlist) {
case "EX":
//return ('rgb(150,175,215)'); // new blue
return iucnEX;
return iucnEX;
case "EW":
//return ('rgb(150,175,215)'); // new blue
return iucnEW;
return iucnEW;
//return ('rgb(80,80,80)');
case "CR":
return iucnCR;
return iucnCR;
//////////return (red1);
//'rgb(215,175,150)' = dinah pink
case "EN":
//return ('rgb(225,185,130)');
//return ('rgb(210,170,145)');
return iucnEN;
return iucnEN;
//////////return (red1);

case "VU":
return iucnVU;
return iucnVU;
//return (red1);
//return ('rgb(210,170,145)');
//return ('rgb(220,220,220)');
case "NT":
return iucnNT;
return iucnNT;
//return ('rgb(170,195,96)');
//return ('rgb(180,208,90)');
//return ('rgb(200,220,180)');
//return ('rgb(190,200,80)');
case "LC":
return iucnLC;
return iucnLC;
case "DD":
return iucnDD;
return iucnDD;
//return ('rgb(60,50,135)');
case "NE":
return iucnNE;
return iucnNE;
//return ('rgb(0,0,190)');
default:
return iucnDefault;
if (is_fossil(node)) {
return iucnEX;
} else {
// extant leaves should all have age==null or age==0
return iucnDefault;
}
}
}

Expand Down Expand Up @@ -146,7 +162,11 @@ function get_redlist_color2(node) {
return green2;
//return ('rgb(0,0,190)');
default:
return green2;
if (is_fossil(node)) {
return ('rgb(110,110,110)');
} else {
return green2;
}
}
}

Expand Down
13 changes: 11 additions & 2 deletions views/treeviewer/js_strings.json
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Expand Up @@ -22,8 +22,17 @@ OZstrings = {
},
'sp': T("species## singular"),
'spp': T("species## plural"),
'Mya': T("{mya} million years ago"),
'tya': T("{tya} thousand years ago"),
'Fossil species':T("Fossil species"),
'leaf_date':{
'Mya':T("This fossil species\nwent extinct {mya}\nmillion years ago"),
'tya':T("This fossil species\nwent extinct {tya}\nthousand years ago"),
'ya':T("This fossil species\nwent extinct {ya}\nyears ago")
},
'node_date':{
'Mya': T("{mya} million years ago"),
'tya': T("{tya} thousand years ago"),
'ya': T("{ya} years ago")
},
'sciname': T("Scientific name: "),
'sponsor_text':{
'node':{
Expand Down