opentreeoflife.github.io/taxobrowse.html at master · OpenTreeOfLife/opentreeoflife.github.io · GitHub

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<html class="">
<head class="">
  <link rel="stylesheet" href="https://opentreeoflife.github.io/css/main.css" />
  <style type="text/css">
    h1 {
        color: #999;
        /* indent multi-line heading (a very long taxon name) */
        padding-left: 55px;
        text-indent: -25px;
        /* maintain pleasing placement of Open Tree logo */
        height: auto;
        padding-top: 0.35em;
        line-height: 1.0em;
        min-height: 32px;
        background: url(https://opentreeoflife.github.io/images/mini-opentree-logo.png) no-repeat left 5px;
    }
    h1 strong {
        color: #000;
    }
    h3 {
        margin-bottom: 0.3em;
    }
    .legend {
        font-style: italic;
    }
    .legend .flag {
        font-style: normal;
    }
    .error {
        color: #933;
    }
    h4,
    p.taxon,
    p.synonyms,
    p.lineage,
    ul.children {
        margin-top: 0.25em;
        margin-left: 2em;
    }
    ul.children {
        padding-left: 0;
    }
    ul.children li {
        list-style: none;
        padding: 0.25em;
        /* align text with other details; pad for bg color and indent second line */
        margin-left: -0.5em;
        padding-left: 2.5em;
        text-indent: -2em;
    }
    li.odd {
        background-color: #fff;
    }
    li.even {
        background-color: #f5f5f5;
    }
    span.name {
        font-weight: bold;
    }
    span.taxname {
        font-weight: bold;
    }
    span.taxsynname {
        font-weight: bold;
    }
    span.ancname {
        font-weight: bold;
    }
    span.sources,
    span.flags {
        padding-left: 1em;
    }
    span.flag {
        font-family: monospace;
        color: #999;
    }
  </style>
</head>
<body class="" onload="postload()">
    <form id="searchform" action="browse">
        <p align="right">
            <input type="text" name="name" placeholder="name or id"/>
        </p>
    </form>
  <span class="error" id="errorpanel"></span>
  <span class="multimatch" id="multimatch"></span>

  <span id="knownidcontainer">
    <h1 class="">Open Tree taxonomy: <strong><span class="taxname"></span></strong></h1>
    <p class="legend">The current taxonomy version is
        <a target="_blank" class="abouttaxon">ott3.7 (click for more information)</a>.
        See the OTT documentation for
        <a href="https://github.com/OpenTreeOfLife/reference-taxonomy/blob/master/doc/taxon-flags.md#taxon-flags">an explanation of the taxon flags used</a> below, e.g.,
        <span class="flag">extinct</span>
    </p>
    <h3>Taxon details</h3>
    <p class="taxon"><span class="taxrank"></span>
        <a class="browsebyid"><span class="taxname"></span></a>
        <br/>
        <span class="legend">OTT ID:</span> <span class="taxonid"></span>
        <br/>
        <span class="legend">Sources:</span>
        <span class="sources" id="taxsrcpar"><span class="taxsrc"></span>
        </span>
        <br />
        <span class="legend">Flags:</span>
        <span class="flags">
        </span>
        <br/>
        <a target="_blank" class="synthtreebyid">View this taxon in the current synthetic tree</a>
    </p>
    <span id="synspan"><h3 id="synheader">Synonym(s)</h3><p class="synonyms" id="synpar"></p></span>
    <h3>Lineage</h3>
    <p class="lineage" id="linepar"></p>

    <h3>Children included in the synthetic tree</h3>
    <ul class="children" id="childpar"></ul>
    <h3>Children suppressed in the synthetic tree</h3>
    <ul class="children" id="exchildpar"></ul>
  </span>

<script type="text/javascript">

var tree_server = "https://tree.opentreeoflife.org";
var api_server = "https://api.opentreeoflife.org";
var taxon_info_url = api_server + "/v3/taxonomy/taxon_info";
var name_match_url = api_server + "/v3/tnrs/match_names";
var about_taxon_url = tree_server + "/about/taxonomy-version/ott3.7";
var page_route = "taxobrowse.html";

var get_link_for_taxsrc = function (taxsrc) {
    var tsurl;
    var link_c = taxsrc;
    if (taxsrc.startsWith("http:") || taxsrc.startsWith("https:")) {
        tsurl = taxsrc;
    } else {
        var tsspl = taxsrc.split(":");
        if (tsspl.length == 2) {
            var tstag = tsspl[0];
            var tsextid = tsspl[1];
            if (tstag == "ncbi") {
                tsurl = "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=" + tsextid;
            } else if (tstag == 'gbif') {
                tsurl = "http://www.gbif.org/species/" + tsextid + "/";
            } else if (tstag == 'irmng') {
                tsurl = "http://www.irmng.org/aphia.php?p=taxdetails&id=" + tsextid;
            } else if (tstag == 'if') {
                tsurl = "http://www.indexfungorum.org/names/NamesRecord.asp?RecordID=" + tsextid;
            } else if (tstag == 'worms') {
                tsurl = "http://www.marinespecies.org/aphia.php?p=taxdetails&id=" + tsextid;
            } else if (tstag == 'silva') {
                tsurl = "http://www.arb-silva.de/browser/ssu/silva/" + tsextid;
            }
        }
    }
    var tax_a;
    if (tsurl) {
        tax_a = document.createElement("a");
        tax_a.textContent = taxsrc;
        tax_a.setAttribute("href", tsurl);

    } else {
        tax_a = document.createElement("span")
        tax_a.textContent = taxsrc;
        ;
    }
    return tax_a;
}

var append_tax_src_links = function(par, tax_sources) {
    for (let tsi in tax_sources) {
        var ts = tax_sources[tsi];
        var nel = document.createElement("span");
        nel.setAttribute("class", "taxsrc");
        if (tsi != 0) {
            nel.textContent = ", ";
        }
        nel.appendChild(get_link_for_taxsrc(ts));
        par.appendChild(nel);
    }
};

var append_flags = function(par, flags) {
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            var flag = flags[fi];
            var nel = document.createElement("span");
            nel.setAttribute("class", "flag");
            if (fi != 0) {
                nel.textContent = ", " + flag;
            } else {
                nel.textContent = flag;
            }
            par.appendChild(nel);
        }
    } else {

    }
};

var fill_with_basic_taxon_info = function(par, taxon) {
    var rank_span = document.createElement("span");
    var r = taxon.rank;
    if (r && ! (r.startsWith("no rank")) ) {
        rank_span.textContent = r + " ";
    }
    par.appendChild(rank_span)
    var nel = document.createElement("a");
    nel.setAttribute("href", page_route + "?id=" + taxon.ott_id);
    var inner_name = document.createElement("span");
    inner_name.setAttribute("class", "name");
    inner_name.textContent = taxon.name;
    nel.appendChild(inner_name);
    par.appendChild(nel);
    var srcs_span = document.createElement("span");
    srcs_span.setAttribute("class", "sources");
    append_tax_src_links(srcs_span, taxon.tax_sources);
    par.appendChild(srcs_span);
    var flags_span = document.createElement("span");
    flags_span.textContent = " ";
    flags_span.setAttribute("class", "cflags");
    append_flags(flags_span, taxon.flags);
    par.appendChild(flags_span);

};

var fill_child_lists = function(par, children, tag) {
    var ccn;
    var inc;
    if (tag == "exposed") {
        continue_on = true;
        ccn = "child exposed ";
    } else {
        continue_on = false;
        ccn = "child suppressed ";
    }
    if (par) {
        tn = document.getElementsByClassName(ccn + "even");
        for (let el of tn) {
            par.removeChild(el);
        }
        tn = document.getElementsByClassName(ccn + "odd");
        for (let el of tn) {
            par.removeChild(el);
        }
        var ceo = "even";
        if (children) {
            for (let si in children) {
                var child = children[si];
                if (child.is_suppressed == continue_on) {
                    continue;
                }
                if (ceo == "even") {
                    ceo = "odd";
                } else {
                    ceo = "even";
                }
                var nel = document.createElement("li");
                nel.setAttribute("class", ccn + ceo);
                var ems = document.createElement("span");
                if (continue_on) {
                    ems.setAttribute("class", "exposedmarker");
                    nel.appendChild(ems);
                }
                fill_with_basic_taxon_info(nel, child)
                par.appendChild(nel);
            }
        } else {
            var nel = document.createElement("li");
            nel.setAttribute("class", ccn + "odd");
            nel.textContent = "(None)";
            par.appendChild(nel);
        }
    }
};

var by_name_response_cb = function(resp_obj, name_param) {
    var res = resp_obj.results[0];
    if (res.matches.length > 0) {
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        multimatch_container.hidden = false;
        tn = document.getElementsByClassName("mmul");
        for (let el of tn) {
            multimatch_container.removeChild(el);
        }
        multimatch_container.textContent = "multiple matches found. Click on your choice to resolve.";
        var mmul = document.createElement("ul");
        mmul.setAttribute("class", "mmul");
        for (let mi in res.matches) {
            var one_match = res.matches[mi];
            var liel = document.createElement("li");
            var link = document.createElement("a");
            var mott_id = one_match.taxon.ott_id;
            link.setAttribute("href", page_route + "?id=" + mott_id);
            link.textContent = one_match.taxon.unique_name;
            liel.appendChild(link);
            mmul.appendChild(liel);
        }
        multimatch_container.appendChild(mmul);

     } else {
        var the_match = res.matches[0];
        error_id_container.textContent = "Match found loading taxon info...";
        error_id_container.hidden = false;
        populate_by_id(the_match.taxon.ott_id);
     }
    } else {
        error_id_container.textContent = "No taxon found matching name \"" + name_param + "\"";
        error_id_container.hidden = false;
    }

};

var by_id_response_cb = function(resp_obj) {
    error_id_container.hidden = true;
    multimatch_container.hidden = true;
    known_id_container.hidden = false;
    var tn = document.getElementsByClassName("taxname");
    for (let el of tn) {
        el.textContent = resp_obj.name;
    }
    var r = resp_obj.rank;
    if (r && ! (r.startsWith("no rank")) ) {
        tn = document.getElementsByClassName("taxrank");
        for (let el of tn) {
            el.textContent = resp_obj.rank;
        }
    }
    tn = document.getElementsByClassName("taxonid");
    var ott_id = resp_obj.ott_id
    for (let el of tn) {
        el.textContent = ott_id;
    }
    tn = document.getElementsByClassName("abouttaxon");
    for (let el of tn) {
        el.setAttribute("href", about_taxon_url);
    }
    var taxon_in_tree_url  = tree_server + "/opentree/argus/ottol@" + ott_id
    tn = document.getElementsByClassName("synthtreebyid");
    for (let el of tn) {
        el.setAttribute("href", taxon_in_tree_url);
    }
    var srcpar = document.getElementById("taxsrcpar");
    if (srcpar) {
        tn = document.getElementsByClassName("taxsrc");
        for (let el of tn) {
            srcpar.removeChild(el);
        }
        append_tax_src_links(srcpar, resp_obj.tax_sources);
    }
    var flagspar = document.getElementById("flags");
    if (flagspar) {
        tn = document.getElementsByClassName("flag");
        for (let el of tn) {
            flagspar.removeChild(el);
        }
        append_flags(flagspar, resp_obj.flags);
    }
    var synpar = document.getElementById("synpar");
    if (synpar) {
        tn = document.getElementsByClassName("taxsynname");
        for (let el of tn) {
            synpar.removeChild(el);
        }
        for (let si in resp_obj.synonyms) {
            var syn = resp_obj.synonyms[si];
            var nel = document.createElement("a");
            nel.setAttribute("href", page_route + "?name=" + syn);
            var inner_name = document.createElement("span");
            inner_name.setAttribute("class", "taxsynname");
            inner_name.textContent = syn;
            if (si != 0) {
                var comma_el = document.createElement("span");
                comma_el.textContent = ", ";
                synpar.appendChild(comma_el);
            }
            nel.appendChild(inner_name);
            synpar.appendChild(nel);
        }
    }
    var linepar = document.getElementById("linepar");
    if (linepar) {
        tn = document.getElementsByClassName("ancname");
        for (let el of tn) {
            linepar.removeChild(el);
        }
        var rllist = resp_obj.lineage.reverse();
        for (let si in rllist) {
            var anc = rllist[si];
            var nel = document.createElement("a");
            nel.setAttribute("href", page_route + "?id=" + anc.ott_id);
            var inner_name = document.createElement("span");
            inner_name.setAttribute("class", "ancname");
            inner_name.textContent = anc.name;
            if (si != 0) {
                var gt_el = document.createElement("span");
                gt_el.textContent = " > ";
                linepar.appendChild(gt_el);
            }
            nel.appendChild(inner_name);
            linepar.appendChild(nel);
        }
    }
    var childpar = document.getElementById("childpar");
    fill_child_lists(childpar, resp_obj.children, "exposed")
    var exchildpar = document.getElementById("exchildpar");
    fill_child_lists(exchildpar, resp_obj.children, "suppressed")
};

var match_by_name = function(name_param) {
    error_id_container.hidden = true;
    multimatch_container.hidden = true;

    var xmlhttp = new XMLHttpRequest();
    var response_obj;
    var args = {"names": [name_param],
                'include_suppressed': true};

    xmlhttp.onreadystatechange = function() {
        if (this.readyState == 4) {
            if (this.status == 200) {
                response_obj = JSON.parse(this.responseText);
                by_name_response_cb(response_obj, name_param);
            } else {
                alert("Call to API to match_name failed");
            }
        }
    }
    xmlhttp.open("POST", name_match_url);
    xmlhttp.setRequestHeader("Content-Type", "application/json;charset=UTF-8");
    xmlhttp.send(JSON.stringify(args));
};

var populate_by_id = function(ott_int) {
    var xmlhttp = new XMLHttpRequest();
    var response_obj;
    var args = {"ott_id": ott_int,
                'include_children': true,
                'include_lineage': true};

    xmlhttp.onreadystatechange = function() {
        if (this.readyState == 4) {
            if (this.status == 200) {
                response_obj = JSON.parse(this.responseText);
                by_id_response_cb(response_obj);
            } else {
                var errmsg = "Call to API to fetch taxon info for " + ott_int + "failed";
                alert(errmsg);
                error_id_container.textContent = errmsg;
                error_id_container.hidden = false;
            }
        }
    }
    xmlhttp.open("POST", taxon_info_url);
    xmlhttp.setRequestHeader("Content-Type", "application/json;charset=UTF-8");
    xmlhttp.send(JSON.stringify(args));
};

var known_id_container = document.getElementById("knownidcontainer");
var error_id_container = document.getElementById("errorpanel");
var multimatch_container = document.getElementById("multimatch");
var postload = function() {
    const urlParams = new URLSearchParams(window.location.search);
    var id_param = urlParams.get('id');
    const name_param = urlParams.get('name');
    known_id_container.hidden = true;
    error_id_container.hidden = true;
    multimatch_container.hidden = true;
    document.getElementById("searchform").setAttribute("action", page_route);
    if ((!id_param) && (!name_param)) {
        id_param = "93302"; // OTT ID for "cellular organisms"
    }
    if (id_param) {
        var ott_int = parseInt(id_param, 10);
        if (isNaN(ott_int) || ott_int < 1) {
            alert("Expected id param to be a positive integer found \"" + id_param + "\"");
        } else {
            populate_by_id(ott_int);
        }
    } else {
        if (name_param) {
            match_by_name(name_param);
        }
    }
};

</script>
</body>
</html>