@iebh/polyglot 4.5.0 → 4.6.0

package/lib/modules/tools.js

@@ -4,46 +4,43 @@ Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports["default"] = void 0;
-
 var _global = _interopRequireDefault(require("./global.js"));
-
 var _lodash = _interopRequireDefault(require("lodash"));
-
 function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { "default": obj }; }
-
-/**
-* Collection of utility functions to apply common behaviour to a compiled tree
-* @var {Object}
+/**
+* Collection of utility functions to apply common behaviour to a compiled tree
+* @var {Object}
 */
 var tools = {
-  /**
-  * Visit the given node types within a deeply nested tree and run a function
-  * This function may mutate the input tree depending on the actions of the callbacks
-  * NOTE: If the return value of the callback is `"DEL"` the node is deleted
-  * @param {array} tree The tree sturcture to operate on
-  * @param {null|array} types Node filter to apply to (if falsy all are used)
-  * @param {function} callback The callback to call with each node. Called as (node, path)
-  * @return {array} The input tree
+  /**
+  * Visit the given node types within a deeply nested tree and run a function
+  * This function may mutate the input tree depending on the actions of the callbacks
+  * NOTE: If the return value of the callback is `"DEL"` the node is deleted
+  * @param {array} tree The tree sturcture to operate on
+  * @param {null|array} types Node filter to apply to (if falsy all are used)
+  * @param {function} callback The callback to call with each node. Called as (node, path)
+  * @return {array} The input tree
   */
   visit: function visit(tree, types, callback) {
     var removals = []; // Stack of removal paths we are performing when done
 
     var treeWalker = function treeWalker(tree, path) {
       tree.forEach(function (branch, branchKey) {
-        var nodePath = path.concat(branchKey); // Fire callback if it matches
+        var nodePath = path.concat(branchKey);
 
+        // Fire callback if it matches
         if (!types || _lodash["default"].includes(types, branch.type)) {
           var result = callback(branch, nodePath);
           if (result === 'DEL') removals.push(nodePath);
-        } // Walk down nodes if its a group
-
+        }
 
+        // Walk down nodes if its a group
         if (branch.type == 'group' || branch.type == 'line') treeWalker(branch.nodes, nodePath.concat(['nodes']));
       });
     };
+    treeWalker(tree, []);
 
-    treeWalker(tree, []); // Crop all items marked as removals
-
+    // Crop all items marked as removals
     removals.reverse() // Walk in reverse order so we don't screw up arrays
     .forEach(function (path) {
       var nodeName = path.pop();
@@ -52,14 +49,13 @@ var tools = {
     });
     return tree;
   },
-
-  /**
-  * Apply a series of text replacements to every matching node object within a tree
-  * This function mutates tree
-  * @param {array} tree The tree sturcture to operate on
-  * @param {null|array} types Type filter to apply. If falsy all are used
-  * @param {array} replacements Array of replacements to apply. Each must be of the form `{subject: STRING|REGEXP, value: STRING|FUNCTION}`
-  * @return {array} The input tree element with the replacements applied
+  /**
+  * Apply a series of text replacements to every matching node object within a tree
+  * This function mutates tree
+  * @param {array} tree The tree sturcture to operate on
+  * @param {null|array} types Type filter to apply. If falsy all are used
+  * @param {array} replacements Array of replacements to apply. Each must be of the form `{subject: STRING|REGEXP, value: STRING|FUNCTION}`
+  * @return {array} The input tree element with the replacements applied
   */
   replaceContent: function replaceContent(tree, types, replacements) {
     this.visit(tree, types, function (branch) {
@@ -74,10 +70,10 @@ var tools = {
   escapeRegExp: function escapeRegExp(string) {
     return string.replace(/[.*+?^${}()[\]\\]/g, '\\$&'); // $& means the whole matched string
   },
+
   // Replace multiple terms at once
   multiReplace: function multiReplace(text, replaceObj) {
     var template = tools.escapeRegExp(Object.keys(replaceObj).join("|"));
-
     if (template.length > 0) {
       var regex = new RegExp(template, "g");
       return text.replace(regex, function (match) {
@@ -87,13 +83,12 @@ var tools = {
       return text;
     }
   },
-
-  /**
-  * Retrieve the contents of a template by its ID
-  * NOTE: If the specific engine definition is not found 'default' is used (and it will be pre-parsed via .translate())
-  * @param {string} template The template to resolve
-  * @param {string} engine The current engine (used to get the correct sub-templating string)
-  * @return {string} The resolved template
+  /**
+  * Retrieve the contents of a template by its ID
+  * NOTE: If the specific engine definition is not found 'default' is used (and it will be pre-parsed via .translate())
+  * @param {string} template The template to resolve
+  * @param {string} engine The current engine (used to get the correct sub-templating string)
+  * @return {string} The resolved template
   */
   resolveTemplate: function resolveTemplate(template, engine) {
     if (!_global["default"].templates[template]) return 'UNKNOWN-TEMPLATE:' + template;
@@ -102,68 +97,59 @@ var tools = {
     if (!_global["default"].templates[template].engines[engine]) return "Template: \"".concat(template, "\" not found for engine: \"").concat(engine, "\"");
     return '';
   },
-
-  /**
-   * Structure the wild cards correctly for cochrane to ensure no wildcards appear inside quotation marks
-   * @param {string} text The text to parse
-   * @param {Boolean} highlighting Whether to assign custom fonts
-   * @return {string} The parsed string seperated by NEXT
+  /**
+   * Structure the wild cards correctly for cochrane to ensure no wildcards appear inside quotation marks
+   * @param {string} text The text to parse
+   * @param {Boolean} highlighting Whether to assign custom fonts
+   * @return {string} The parsed string seperated by NEXT
    */
   wildCardCochrane: function wildCardCochrane(text, highlighting) {
     var wildcards = ["?", "$", "*"];
     var words = text.split(" ");
     var lastMatch = -1;
     var foundMatch = false;
-
     var _loop = function _loop(i) {
       if (wildcards.some(function (wildcard) {
         return words[i].includes(wildcard);
       })) {
-        foundMatch = true; // Add quotation marks to previous word/s if the previous word was not a match
-
+        foundMatch = true;
+        // Add quotation marks to previous word/s if the previous word was not a match
         if (i - 1 > lastMatch) {
           words[lastMatch + 1] = highlighting ? '<font color="DarkBlue">"' + words[lastMatch + 1] : '"' + words[lastMatch + 1];
           words[i - 1] = highlighting ? words[i - 1] + '"</font>' : words[i - 1] + '"';
         }
-
-        lastMatch = i; // Check that there is a word before and it is not a wildcard word
-
+        lastMatch = i;
+        // Check that there is a word before and it is not a wildcard word
         if (i > 0 && !wildcards.some(function (wildcard) {
           return words[i - 1].includes(wildcard);
         })) {
           words[i] = highlighting ? '<font color="purple">NEXT</font> ' + words[i] : 'NEXT ' + words[i];
-        } // Check that there is a word after
-
-
+        }
+        // Check that there is a word after
         if (i < words.length - 1) {
           words[i] = highlighting ? words[i] + ' <font color="purple">NEXT</font>' : words[i] + " NEXT";
         }
       }
     };
-
     for (var i = 0; i < words.length; i++) {
       _loop(i);
-    } // Add quotation marks to word/s after the final match
-
-
+    }
+    // Add quotation marks to word/s after the final match
     if (lastMatch + 1 < words.length) {
       words[lastMatch + 1] = highlighting ? '<font color="DarkBlue">"' + words[lastMatch + 1] : '"' + words[lastMatch + 1];
       words[words.length - 1] = highlighting ? words[words.length - 1] + '"</font>' : words[words.length - 1] + '"';
     }
-
     return foundMatch ? "(".concat(words.join(" "), ")") : words.join(" ");
   },
-
-  /**
-   * Print number in format defined by engine
-   * @param {string} engine Engine to use
-   * @param {string} ref Branch ref (e.g. 1)
-   * @return {string} Formatted number
+  /**
+   * Print number in format defined by engine
+   * @param {string} engine Engine to use
+   * @param {string} ref Branch ref (e.g. 1)
+   * @return {string} Formatted number
    */
   printNumber: function printNumber(engine, ref) {
     // Get line number format for engine
     var number = ref;
-
     switch (engine) {
       case 'PubMed full':
       case 'PubMed abbreviation':
@@ -173,41 +159,37 @@ var tools = {
       case 'WoS Advanced':
       case 'Scopus (basic search)':
       case 'Scopus (advanced search)':
+      //HTA
+      case 'International HTA Database':
         number = "#" + ref;
         break;
-
       case 'Ovid MEDLINE':
       case 'PsycInfo (Ovid)':
       case 'ProQuest Health and Medical':
         number = ref;
         break;
-
       case 'CINAHL (Ebsco)':
       case 'SPORTDiscus':
         number = "S" + ref;
         break;
-
       default:
     }
-
     return number;
   },
-
-  /**
-  * Determine if a phrase needs to be enclosed within speachmarks and return the result
-  * @param {Object} branch Phrase branch to examine
-  * @param {string} engine Optional engine ID to examine for other enclose methods
-  * @param {boolean} highlighting Optional bool to determine if html color styling is added
-  * @return {string} The phrase enclosed as needed
+  /**
+  * Determine if a phrase needs to be enclosed within speachmarks and return the result
+  * @param {Object} branch Phrase branch to examine
+  * @param {string} engine Optional engine ID to examine for other enclose methods
+  * @param {boolean} highlighting Optional bool to determine if html color styling is added
+  * @return {string} The phrase enclosed as needed
   */
   quotePhrase: function quotePhrase(branch, engine, settings) {
     var text = _lodash["default"].trimEnd(branch.content);
+    var space = /\s/.test(text);
 
-    var space = /\s/.test(text); // Apply wildcard replacements
-
+    // Apply wildcard replacements
     if (settings.replaceWildcards) {
       var replaceObj = {};
-
       switch (engine) {
         case 'PubMed full':
         case 'PubMed abbreviation':
@@ -217,23 +199,19 @@ var tools = {
             '#': settings.highlighting ? tools.createTooltip("*", "As PubMed does not single character wildcards a wildcard is used here", "highlight") : '*'
           };
           break;
-
         case 'Ovid MEDLINE':
           break;
         // Nothing needed
-
         case 'Cochrane Library':
           if (space) {
             text = tools.wildCardCochrane(text, settings.highlighting);
           }
-
           replaceObj = {
             '$': settings.highlighting ? tools.createTooltip("?", "As Cochrane does not support single character truncation, the 0 or 1 character truncation is used here.", "highlight") : '?',
             '#': '?'
           };
           return tools.multiReplace(text, replaceObj);
         // Return here to prevent duplicate quotes
-
         case 'Embase (Elsevier)':
         case 'Web of Science':
         case 'WoS Advanced':
@@ -243,7 +221,6 @@ var tools = {
             '#': '?'
           };
           break;
-
         case 'CINAHL (Ebsco)':
           replaceObj = {
             '$': '?',
@@ -251,7 +228,6 @@ var tools = {
             '#': '?'
           };
           break;
-
         case 'Scopus (basic search)':
         case 'Scopus (advanced search)':
           // space = true; //Always include quotes with scopus to make phrase a "loose phrase"
@@ -261,20 +237,17 @@ var tools = {
             '#': '?'
           };
           break;
-
         case 'PsycInfo (Ovid)':
           replaceObj = {
             '$': '#'
           };
           break;
-
         case 'ProQuest Health and Medical':
           replaceObj = {
             '$': '?',
             '#': '?'
           };
           break;
-
         case 'SPORTDiscus':
           if (!settings.testing) {
             space = true; //Always include quotes with SPORTDiscus
@@ -285,85 +258,82 @@ var tools = {
             '?': '#'
           };
           break;
-
         case 'Informit Health Collection':
           replaceObj = {
             '$': '?',
             '?': '*1'
           };
           break;
+        //HTA
+        case 'International HTA Database':
+          replaceObj = {
+            '$': settings.highlighting ? tools.createTooltip("*", "As INAHTA does not support single character truncation a wildcard is used here", "highlight") : '*',
+            '?': settings.highlighting ? tools.createTooltip("*", "As INAHTA does not support single character truncation a wildcard is used here", "highlight") : '*',
+            '#': settings.highlighting ? tools.createTooltip("*", "As INAHTA does not support single character truncation a wildcard is used here", "highlight") : '*'
+          };
+          break;
       }
-
       text = tools.multiReplace(text, replaceObj);
     }
-
     return engine == 'Embase (Elsevier)' ? space ? settings.highlighting ? "<font color='DarkBlue'>'" + text + "'</font>" : "'" + text + "'" : text : space ? settings.highlighting ? '<font color="DarkBlue">"' + text + '"</font>' : '"' + text + '"' : text;
   },
-
-  /**
-  * Convert the '$or' / '$and' nodes within a tree into a nested structure
-  * This function will also flatten identical branches (i.e. run-on multiple $and / $or into one array)
-  * @param {Object} tree The object tree to recombine
-  * @returns {Object} The recombined tree
+  /**
+  * Convert the '$or' / '$and' nodes within a tree into a nested structure
+  * This function will also flatten identical branches (i.e. run-on multiple $and / $or into one array)
+  * @param {Object} tree The object tree to recombine
+  * @returns {Object} The recombined tree
   */
   renestConditions: function renestConditions(tree) {
     if (!_lodash["default"].isArray(tree)) return tree; // Not an array - skip
-    // Transform arrays of the form: [X1, $or/$and, X2] => {$or/$and: [X1, X2]}
 
+    // Transform arrays of the form: [X1, $or/$and, X2] => {$or/$and: [X1, X2]}
     return tree.reduce(function (res, branch, index, arr) {
       var firstKey = (0, _lodash["default"])(branch).keys().first();
-
       if (firstKey == '$or' || firstKey == '$and') {
         // Is a combinator
         var expression = {};
-        expression[firstKey] = [res.pop(), // Right side is the last thing we added to the buffer
+        expression[firstKey] = [res.pop(),
+        // Right side is the last thing we added to the buffer
         arr.splice(index + 1, 1)[0] // Left side is the next thing we're going to look at in the array
         ];
+
         res.push(expression);
       } else {
         // Unknown - just push to array and carry on processing
         res.push(branch);
       }
-
       return res;
     }, []);
   },
-
-  /**
-  * Combine multiple run-on $and / $or conditional branches into one branch
-  * This function is a companion function to renestConditions and should be called directly afterwards if needed
-  * @param {Object} tree The tree to traverse
-  * @param {Object} [options] Additional options to accept
-  * @param {number} [options.depth=10] The maximum depth to traverse before giving up, set to 0 to infinitely recurse
-  * @return {Object} The collapsed tree
-  * @example
-  * {left, joinAnd, right} => {joinAnd: [left, right]}
-  * @example
-  * {foo, joinOr, bar, joinOr, baz} => {joinOr: [foo, bar, baz]}
+  /**
+  * Combine multiple run-on $and / $or conditional branches into one branch
+  * This function is a companion function to renestConditions and should be called directly afterwards if needed
+  * @param {Object} tree The tree to traverse
+  * @param {Object} [options] Additional options to accept
+  * @param {number} [options.depth=10] The maximum depth to traverse before giving up, set to 0 to infinitely recurse
+  * @return {Object} The collapsed tree
+  * @example
+  * {left, joinAnd, right} => {joinAnd: [left, right]}
+  * @example
+  * {foo, joinOr, bar, joinOr, baz} => {joinOr: [foo, bar, baz]}
   */
   combineConditions: function combineConditions(tree, options) {
     var settings = _lodash["default"].defaults(options, {
       depth: 10
     });
-
     var collapses = [];
-
     var traverseTree = function traverseTree(branch) {
       var path = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : [];
-
       // Recurse into each tree node and make a bottom-up list of nodes we need to collapse
       _lodash["default"].forEach(branch, function (v, k) {
         // Use _.map if its an array and _.mapValues if we're examining an object
         if (_lodash["default"].isObject(v)) {
           var firstKey = (0, _lodash["default"])(branch).keys().first();
-
           if (path.length > 1 && (firstKey == '$or' || firstKey == '$and')) {
             // Mark for cleanup later (when we can do a bottom-up traversal)
             var lastKey = _lodash["default"].findLast(collapses, function (i) {
               return i.key == '$and' || i.key == '$or';
             }); // Collapse only identical keys
-
-
             if (!lastKey || lastKey.key == firstKey) {
               collapses.push({
                 key: firstKey,
@@ -371,48 +341,43 @@ var tools = {
               });
             }
           }
-
           if (settings.depth && path.length > settings.depth) return; // Stop recursing after depth has been reached
-
           traverseTree(v, path.concat([k]));
         }
       });
     };
-
     traverseTree(tree);
     collapses.forEach(function (collapse) {
       var parent = _lodash["default"].get(tree, collapse.path.slice(0, -1));
-
       var child = _lodash["default"].get(tree, collapse.path.concat([collapse.key]));
-
       if (!child || !parent || !parent.length) return;
       var child2 = parent[1];
-      if (child2) child.push(child2); // Wrap $or conditions (that have an '$and' parent) in an object {{{
+      if (child2) child.push(child2);
 
+      // Wrap $or conditions (that have an '$and' parent) in an object {{{
       var lastParent = (0, _lodash["default"])(collapse.path).slice(0, -1).findLast(_lodash["default"].isString);
       if (lastParent && lastParent == '$and' && collapse.key == '$or') child = {
         $or: child
-      }; // }}}
+      };
+      // }}}
 
       _lodash["default"].set(tree, collapse.path.slice(0, -1), child);
     });
     return tree;
   },
-
-  /**
-  * Create a tooltip with a specified message
-  * @param {string} content Content to append tooltip to
-  * @param {string} message Message to contain inside tooltip
-  * @param {string} css CSS class to use
+  /**
+  * Create a tooltip with a specified message
+  * @param {string} content Content to append tooltip to
+  * @param {string} message Message to contain inside tooltip
+  * @param {string} css CSS class to use
   */
   createTooltip: function createTooltip(content, message, css) {
     css = typeof css !== 'undefined' ? css : "black-underline";
     return "<span class=\"" + css + '" v-tooltip="`' + message + '`">' + content + '</span>';
   },
-
-  /**
-  * Create a popover with options to replace empty field tags with specified field tag
-  * @param {string} content Content to append popover to
+  /**
+  * Create a popover with options to replace empty field tags with specified field tag
+  * @param {string} content Content to append popover to
   */
   createPopover: function createPopover(content, offset) {
     return '<v-popover offset="8" placement="right">' + '<span class="blue-underline">' + content + '</span>' + '<template slot="popover">' + '<h3 class="popover-header">Add Field Tag</h3>' + '<input class="tooltip-content" v-model="customField" placeholder="Field tag" />' + '<div class="replace-all">' + '<input type="checkbox" id="checkbox" v-model="replaceAll">' + '<label for="checkbox">Replace All</label>' + '</div>' + '<div class="replace-buttons">' + '<button v-on:click="replaceFields(customField, replaceAll, ' + offset + ')" type="button" class="btn btn-primary">Replace</button>' + '<button v-close-popover type="button" class="btn btn-dark">Close</button>' + '</div>' + '</template>' + '</v-popover>';

package/package.json

@@ -1,54 +1,59 @@
-{
-  "name": "@iebh/polyglot",
-  "version": "4.5.0",
-  "description": "IEBH-SRA tool to convert between different medical database search formats",
-  "main": "lib/index.js",
-  "scripts": {
-    "test": "npm run prepare && mocha",
-    "test:old": "npm run prepare && mocha './test/**/!(v4).js'",
-    "test:new": "npm run prepare && mocha test/v4",
-    "prepare": "babel src --out-dir lib",
-    "preprocess": "cd ./data && node ./preprocess"
-  },
-  "babel": {
-    "presets": [
-      "@babel/preset-env"
-    ]
-  },
-  "repository": {
-    "type": "git",
-    "url": "git+https://github.com/IEBH/sra-polyglot.git"
-  },
-  "keywords": [
-    "iebh",
-    "sra",
-    "search",
-    "translation",
-    "syntax",
-    "conversion",
-    "polyglot",
-    "medical",
-    "research"
-  ],
-  "author": "Matt Carter <m@ttcarter.com> (https://github.com/hash-bang), Connor Forbes <cforbes.software@gmail.com> (https://github.com/connorf25)",
-  "license": "MIT",
-  "bugs": {
-    "url": "https://github.com/IEBH/sra-polyglot/issues"
-  },
-  "homepage": "https://github.com/IEBH/sra-polyglot#readme",
-  "devDependencies": {
-    "@babel/cli": "^7.0.0",
-    "@babel/core": "^7.0.0",
-    "@babel/plugin-syntax-dynamic-import": "^7.2.0",
-    "@babel/preset-env": "^7.0.0",
-    "chai": "^4.2.0",
-    "mocha": "^8.2.1",
-    "xlsx": "^0.16.9"
-  },
-  "dependencies": {
-    "lodash": "^4.17.15"
-  },
-  "engines": {
-    "node": ">=14.0.0"
-  }
-}
+{
+  "name": "@iebh/polyglot",
+  "version": "4.6.0",
+  "description": "IEBH-SRA tool to convert between different medical database search formats",
+  "main": "lib/index.js",
+  "scripts": {
+    "test": "npm run prepare && mocha",
+    "test:old": "npm run prepare && mocha './test/**/!(v4).js'",
+    "test:new": "npm run prepare && mocha test/v4",
+    "prepare": "babel src --out-dir lib",
+    "preprocess": "cd ./data && node ./preprocess"
+  },
+  "babel": {
+    "presets": [
+      "@babel/preset-env"
+    ]
+  },
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/IEBH/sra-polyglot.git"
+  },
+  "keywords": [
+    "iebh",
+    "sra",
+    "search",
+    "translation",
+    "syntax",
+    "conversion",
+    "polyglot",
+    "medical",
+    "research"
+  ],
+  "author": [
+    "Matt Carter <m@ttcarter.com> (https://github.com/hash-bang)",
+    "Connor Forbes <cforbes.software@gmail.com> (https://github.com/connorf25)",
+    "Justin Cark <jclark@bond.edu.au> (https://github.com/Justin-Clarc)",
+    "Tian Liang <amethystoct2012@gmail.com> (https://github.com/Octian)"
+  ],
+  "license": "MIT",
+  "bugs": {
+    "url": "https://github.com/IEBH/sra-polyglot/issues"
+  },
+  "homepage": "https://github.com/IEBH/sra-polyglot#readme",
+  "devDependencies": {
+    "@babel/cli": "^7.0.0",
+    "@babel/core": "^7.0.0",
+    "@babel/plugin-syntax-dynamic-import": "^7.2.0",
+    "@babel/preset-env": "^7.0.0",
+    "chai": "^4.2.0",
+    "mocha": "^8.4.0",
+    "xlsx": "^0.16.9"
+  },
+  "dependencies": {
+    "lodash": "^4.17.15"
+  },
+  "engines": {
+    "node": ">=14.0.0"
+  }
+}