Add nanobot

src/ontology/.gitignore

@@ -12,3 +12,7 @@ candidate*
 modules/*.omn
 modules/*.pro
 status/
+
+# Generated by Nanobot
+.nanobot.db*
+/nanobot

src/ontology/Makefile

@@ -5,9 +5,21 @@
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use ecto.Makefile instead
 
-
-# ----------------------------------------
-# More information: https://github.com/INCATools/ontology-development-kit/
+### Workflow
+#
+# Tasks to update templates.
+#
+# #### Template
+#
+# 1. View and edit templates in `./_nanobot` and save in the tab Actions
+# 2. Check the `git diff`
+# 3. [Rebuild ecto.owl](prepare_release_fast)
+# 4. Check the `git diff` again
+# 5. `git commit` then `git push` your changes
+# 
+##### Maintenance
+#
+# [Clean nanobot](clean_nanobot) when necessary
 
 
 # ----------------------------------------

src/ontology/_nanobot

@@ -0,0 +1,11 @@
+#!/bin/sh
+NANOBOT_URL="https://github.com/ontodev/nanobot.rs/releases/download/v2024-02-16/nanobot-v20240216-x86_64-linux"
+if [ ! -f nanobot ]; then
+  curl -L -o nanobot $NANOBOT_URL
+  chmod +x nanobot
+fi
+if [ ! -f .nanobot.db ] || [ ! -s .nanobot.db ]; then
+  GATEWAY_INTERFACE=NONE ./nanobot init > /tmp/null 2>&1
+fi
+
+./nanobot $@

src/ontology/ecto-odk.yaml

@@ -42,3 +42,19 @@ robot_report:
   use_labels : False
   report_on :
     - ecto-base.owl
+custom_makefile_header: |
+  ### Workflow
+  #
+  # Tasks to update templates.
+  #
+  # #### Template
+  #
+  # 1. View and edit templates in `./_nanobot` and save in the tab Actions
+  # 2. Check the `git diff`
+  # 3. [Rebuild ecto.owl](prepare_release_fast)
+  # 4. Check the `git diff` again
+  # 5. `git commit` then `git push` your changes
+  # 
+  ##### Maintenance
+  #
+  # [Clean nanobot](clean_nanobot) when necessary

src/ontology/ecto.Makefile

@@ -153,4 +153,22 @@ tmp/mre_seed.txt:
 
 
 mre: tmp/mre_seed.txt
-	$(ROBOT) filter -i $(SRC) -T tmp/mre_seed.txt -o $@
+	$(ROBOT) filter -i $(SRC) -T tmp/mre_seed.txt -o $@
+
+
+# ----------------------------------------
+# NANOBOT
+# ----------------------------------------
+
+.PHONY: executable_nanobot
+executable_nanobot:
+	chmod +x _nanobot
+
+NANOBOT := ./nanobot
+
+### Databases
+
+.PHONY: clean
+clean_nanobot:
+	rm -f .nanobot.db nanobot
+	make executable_nanobot

src/ontology/nanobot.toml

@@ -0,0 +1,14 @@
+[nanobot]
+config_version = 1
+
+[logging]
+level = "DEBUG"
+
+[valve]
+path = "src/schema/table.tsv"
+
+[assets]
+path = "src/assets/"
+
+[templates]
+path = "src/resources/"

src/ontology/src/assets/ols-autocomplete.css

@@ -0,0 +1,36 @@
+.ontology-source{
+    background-color: #5FBDCE;
+    padding:2px;
+    padding-right:4px;
+    color: white;
+    /*font-size: larger;*/
+    border-radius: 3px;
+    display: inline-block;
+    margin-right: 4px;
+    vertical-align: middle;
+  }
+
+  a .ontology-source {
+    background-color: #5FBDCE;
+    padding:2px;
+    padding-right:4px;
+    color: white;
+    /*font-size: larger;*/
+    border-radius: 3px;
+    display: inline-block;
+    margin-right: 4px;
+    vertical-align: middle;
+    border-bottom: none;
+  }
+
+  .term-source{
+    background-color: #ffac1b;
+    padding:2px;
+    padding-right:4px;
+    color: white;
+    /*font-size: larger;*/
+    border-radius: 3px;
+    display: inline-block;
+    margin-right: 4px;
+    vertical-align: middle;
+  }

src/ontology/src/assets/ols-autocomplete.js

@@ -0,0 +1,175 @@
+require = function t(e, o, i) {
+    function a(r, s) {
+        if (!o[r]) {
+            if (!e[r]) {
+                var l = "function" == typeof require && require;
+                if (!s && l) return l(r, !0);
+                if (n) return n(r, !0);
+                var u = new Error("Cannot find module '" + r + "'");
+                throw u.code = "MODULE_NOT_FOUND", u
+            }
+            var d = o[r] = {
+                exports: {}
+            };
+            e[r][0].call(d.exports, function(t) {
+                var o = e[r][1][t];
+                return a(o ? o : t)
+            }, d, d.exports, t, e, o, i)
+        }
+        return o[r].exports
+    }
+    for (var n = "function" == typeof require && require, r = 0; r < i.length; r++) a(i[r]);
+    return a
+}({
+    "ols-autocomplete": [function(t, e, o) {
+        e.exports = autocomplete = function() {
+            function t(t) {
+                var e = "terms";
+                return "property" == t ? e = "properties" : "individual" == t ? e = "individuals" : "ontology" == t && (e = "ontology"), e
+            }
+
+            function e(t, e, o, i, a) {
+                if (void 0 != o && void 0 != i) {
+                    var n = encodeURIComponent(i);
+                    window.location.href = t + "ontologies/" + e + "/" + o + "?iri=" + n
+                } else window.location.href = t + "ontologies/" + suggestion_ontoloy
+            }
+
+            function o(e, o, i, a) {
+                e.bind("typeahead:select", function(e, i) {
+                    if (void 0 != i.data) {
+                        var a = t(i.data.type);
+                        "ontology" == a ? options.action.call(this, o, i.data.ontology, a, i.data.iri, i.data, i.value) : options.action.call(this, o, i.data.ontology, a, i.data.iri, i.data, i.value)
+                        // autocomplete selection done
+                        // now automatically fill ID field based on the selection
+                        autocomplete_input_name = e.currentTarget.name;
+                        // get the matching 'id' input field's name
+                        // classifying_ontology_term_label -> classifying_ontology_term
+                        target_input_name = autocomplete_input_name.replace("_label", "");
+                        if ($('input[name="' + target_input_name + '"]').length > 0) {
+                            $('input[name="' + target_input_name + '"]')[0].value = i.data.shortForm;
+                        }
+                    } else e.target.form.submit()
+                }).typeahead({
+                    hint: !1,
+                    highlight: !0,
+                    minLength: 2,
+                    limit: 4,
+                    async: !0
+                }, i)
+            }
+
+            function i(e) {
+                return {
+                    header: '<hr/><h5 style="text-align: center">' + e + "</h5>",
+                    suggestion: function(e) {
+                        var o = e.data.label,
+                            i = "";
+                        "" != e.data.synonym && (o = e.data.synonym, i = "<div class='sub-text'>synonym for " + e.value + "</div>");
+                        var a = "<div class='ontology-source'>" + e.data.prefix + "</div>",
+                            n = t(e.data.type);
+                        return "ontology" != n && (a += "&nbsp;<div class='term-source'>" + e.data.shortForm + "</div>"), "<div style='width: 100%; display: table;'> <div style='display: table-row'><div  style='display: table-cell;' class='ontology-suggest'><div class='suggestion-value'>" + o + "</div>" + i + "</div><div style='vertical-align:middle; text-align: right; width:60px; display: table-cell;'>" + a + "</div></div></div>"
+                    },
+                    footer: Handlebars.compile('<hr/><div onclick="jQuery(this).closest(\'form\').submit()" style="text-align: right;" class="tt-suggestion tt-selectable">Search EBI APIs</div>')
+                }
+            }
+
+            function a(t, e, o) {
+                var i = "";
+                return e && (i = "&ontology=" + e), o && (i += "&type=" + o), new Bloodhound({
+                    datumTokenizer: Bloodhound.tokenizers.whitespace,
+                    queryTokenizer: Bloodhound.tokenizers.whitespace,
+                    identify: function(t) {
+                        return t.id
+                    },
+                    remote: {
+                        url: t + "api/select?q=%QUERY" + i,
+                        wildcard: "%QUERY",
+                        transform: function(t) {
+                            return r(t)
+                        }
+                    }
+                })
+            }
+
+            function n(t, e) {
+                var o = "";
+                return e && (o = "&ontology=" + e), new Bloodhound({
+                    datumTokenizer: Bloodhound.tokenizers.whitespace,
+                    queryTokenizer: Bloodhound.tokenizers.whitespace,
+                    remote: {
+                        url: t + "api/suggest?q=%QUERY" + o,
+                        wildcard: "%QUERY",
+                        transform: function(t) {
+                            return jQuery.map(t.response.docs, function(t) {
+                                return {
+                                    value: t.autosuggest
+                                }
+                            })
+                        }
+                    }
+                })
+            }
+
+            function r(t) {
+                var e = t.responseHeader.params.q;
+                return jQuery.map(t.response.docs, function(o) {
+                    var i = o.id,
+                        a = o.label,
+                        n = "",
+                        r = !0;
+                    void 0 != t.highlighting[i].label_autosuggest ? (a = t.highlighting[i].label_autosuggest[0], r = !1) : void 0 != t.highlighting[i].label && (a = t.highlighting[i].label[0], r = !1), r && (void 0 != t.highlighting[i].synonym_autosuggest ? n = t.highlighting[i].synonym_autosuggest[0] : void 0 != t.highlighting[i].synonym && (n = t.highlighting[i].synonym[0]));
+                    var s = o.obo_id;
+                    return void 0 == s && (s = o.short_form), {
+                        id: i,
+                       // display label of the selected element
+                        value: o.label,
+                        data: {
+                            ontology: o.ontology_name,
+                            prefix: o.ontology_prefix,
+                            iri: o.iri,
+                            label: a,
+                            synonym: n,
+                            shortForm: s,
+                            type: o.type
+                        },
+                        query: e
+                    }
+                })
+            }
+            options = {
+                action: e
+            }, autocomplete.prototype.start = function(t) {
+                options = jQuery.extend(!0, {}, options, t), jQuery("input[data-olswidget='multisearch']").each(function() {
+                    var t = jQuery(this).data("selectpath") ? jQuery(this).data("selectpath") : "",
+                        e = jQuery(this).data("olsontology") ? jQuery(this).data("olsontology") : "",
+                        r = jQuery(this).data("olstype") ? jQuery(this).data("olstype") : "",
+                        s = jQuery(this).data("suggest-header") ? jQuery(this).data("suggest-header") : "",
+                        l = [{
+                            name: "suggestion",
+                            source: n(t, e),
+                            display: "value"
+                        }, {
+                            name: "selection",
+                            source: a(t, e, r),
+                            display: "value",
+                            templates: i(s)
+                        }];
+                    o(jQuery(this), t, l)
+                }), jQuery("input[data-olswidget='select']").each(function() {
+                    var t = jQuery(this).data("selectpath") ? jQuery(this).data("selectpath") : "",
+                        e = jQuery(this).data("olsontology") ? jQuery(this).data("olsontology") : "",
+                        n = jQuery(this).data("olstype") ? jQuery(this).data("olstype") : "",
+                        r = jQuery(this).data("suggest-header") ? jQuery(this).data("suggest-header") : "",
+                        s = [{
+                            name: "selection",
+                            source: a(t, e, n),
+                            display: "value",
+                            templates: i(r)
+                        }];
+                    o(jQuery(this), t, s)
+                })
+            }
+        }
+    }, {}]
+}, {}, []);