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search.js 257.53 KiB
window.pdocSearch = (function(){
/** elasticlunr - http://weixsong.github.io * Copyright (C) 2017 Oliver Nightingale * Copyright (C) 2017 Wei Song * MIT Licensed */!function(){function e(e){if(null===e||"object"!=typeof e)return e;var t=e.constructor();for(var n in e)e.hasOwnProperty(n)&&(t[n]=e[n]);return t}var t=function(e){var n=new t.Index;return n.pipeline.add(t.trimmer,t.stopWordFilter,t.stemmer),e&&e.call(n,n),n};t.version="0.9.5",lunr=t,t.utils={},t.utils.warn=function(e){return function(t){e.console&&console.warn&&console.warn(t)}}(this),t.utils.toString=function(e){return void 0===e||null===e?"":e.toString()},t.EventEmitter=function(){this.events={}},t.EventEmitter.prototype.addListener=function(){var e=Array.prototype.slice.call(arguments),t=e.pop(),n=e;if("function"!=typeof t)throw new TypeError("last argument must be a function");n.forEach(function(e){this.hasHandler(e)||(this.events[e]=[]),this.events[e].push(t)},this)},t.EventEmitter.prototype.removeListener=function(e,t){if(this.hasHandler(e)){var n=this.events[e].indexOf(t);-1!==n&&(this.events[e].splice(n,1),0==this.events[e].length&&delete this.events[e])}},t.EventEmitter.prototype.emit=function(e){if(this.hasHandler(e)){var t=Array.prototype.slice.call(arguments,1);this.events[e].forEach(function(e){e.apply(void 0,t)},this)}},t.EventEmitter.prototype.hasHandler=function(e){return e in this.events},t.tokenizer=function(e){if(!arguments.length||null===e||void 0===e)return[];if(Array.isArray(e)){var n=e.filter(function(e){return null===e||void 0===e?!1:!0});n=n.map(function(e){return t.utils.toString(e).toLowerCase()});var i=[];return n.forEach(function(e){var n=e.split(t.tokenizer.seperator);i=i.concat(n)},this),i}return e.toString().trim().toLowerCase().split(t.tokenizer.seperator)},t.tokenizer.defaultSeperator=/[\s\-]+/,t.tokenizer.seperator=t.tokenizer.defaultSeperator,t.tokenizer.setSeperator=function(e){null!==e&&void 0!==e&&"object"==typeof e&&(t.tokenizer.seperator=e)},t.tokenizer.resetSeperator=function(){t.tokenizer.seperator=t.tokenizer.defaultSeperator},t.tokenizer.getSeperator=function(){return t.tokenizer.seperator},t.Pipeline=function(){this._queue=[]},t.Pipeline.registeredFunctions={},t.Pipeline.registerFunction=function(e,n){n in t.Pipeline.registeredFunctions&&t.utils.warn("Overwriting existing registered function: "+n),e.label=n,t.Pipeline.registeredFunctions[n]=e},t.Pipeline.getRegisteredFunction=function(e){return e in t.Pipeline.registeredFunctions!=!0?null:t.Pipeline.registeredFunctions[e]},t.Pipeline.warnIfFunctionNotRegistered=function(e){var n=e.label&&e.label in this.registeredFunctions;n||t.utils.warn("Function is not registered with pipeline. This may cause problems when serialising the index.\n",e)},t.Pipeline.load=function(e){var n=new t.Pipeline;return e.forEach(function(e){var i=t.Pipeline.getRegisteredFunction(e);if(!i)throw new Error("Cannot load un-registered function: "+e);n.add(i)}),n},t.Pipeline.prototype.add=function(){var e=Array.prototype.slice.call(arguments);e.forEach(function(e){t.Pipeline.warnIfFunctionNotRegistered(e),this._queue.push(e)},this)},t.Pipeline.prototype.after=function(e,n){t.Pipeline.warnIfFunctionNotRegistered(n);var i=this._queue.indexOf(e);if(-1===i)throw new Error("Cannot find existingFn");this._queue.splice(i+1,0,n)},t.Pipeline.prototype.before=function(e,n){t.Pipeline.warnIfFunctionNotRegistered(n);var i=this._queue.indexOf(e);if(-1===i)throw new Error("Cannot find existingFn");this._queue.splice(i,0,n)},t.Pipeline.prototype.remove=function(e){var t=this._queue.indexOf(e);-1!==t&&this._queue.splice(t,1)},t.Pipeline.prototype.run=function(e){for(var t=[],n=e.length,i=this._queue.length,o=0;n>o;o++){for(var r=e[o],s=0;i>s&&(r=this._queue[s](r,o,e),void 0!==r&&null!==r);s++);void 0!==r&&null!==r&&t.push(r)}return t},t.Pipeline.prototype.reset=function(){this._queue=[]},t.Pipeline.prototype.get=function(){return this._queue},t.Pipeline.prototype.toJSON=function(){return this._queue.map(function(e){return t.Pipeline.warnIfFunctionNotRegistered(e),e.label})},t.Index=function(){this._fields=[],this._ref="id",this.pipeline=new t.Pipeline,this.documentStore=new t.DocumentStore,this.index={},this.eventEmitter=new t.EventEmitter,this._idfCache={},this.on("add","remove","update",function(){this._idfCache={}}.bind(this))},t.Index.prototype.on=function(){var e=Array.prototype.slice.call(arguments);return this.eventEmitter.addListener.apply(this.eventEmitter,e)},t.Index.prototype.off=function(e,t){return this.eventEmitter.removeListener(e,t)},t.Index.load=function(e){e.version!==t.version&&t.utils.warn("version mismatch: current "+t.version+" importing "+e.version);var n=new this;n._fields=e.fields,n._ref=e.ref,n.documentStore=t.DocumentStore.load(e.documentStore),n.pipeline=t.Pipeline.load(e.pipeline),n.index={};for(var i in e.index)n.index[i]=t.InvertedIndex.load(e.index[i]);return n},t.Index.prototype.addField=function(e){return this._fields.push(e),this.index[e]=new t.InvertedIndex,this},t.Index.prototype.setRef=function(e){return this._ref=e,this},t.Index.prototype.saveDocument=function(e){return this.documentStore=new t.DocumentStore(e),this},t.Index.prototype.addDoc=function(e,n){if(e){var n=void 0===n?!0:n,i=e[this._ref];this.documentStore.addDoc(i,e),this._fields.forEach(function(n){var o=this.pipeline.run(t.tokenizer(e[n]));this.documentStore.addFieldLength(i,n,o.length);var r={};o.forEach(function(e){e in r?r[e]+=1:r[e]=1},this);for(var s in r){var u=r[s];u=Math.sqrt(u),this.index[n].addToken(s,{ref:i,tf:u})}},this),n&&this.eventEmitter.emit("add",e,this)}},t.Index.prototype.removeDocByRef=function(e){if(e&&this.documentStore.isDocStored()!==!1&&this.documentStore.hasDoc(e)){var t=this.documentStore.getDoc(e);this.removeDoc(t,!1)}},t.Index.prototype.removeDoc=function(e,n){if(e){var n=void 0===n?!0:n,i=e[this._ref];this.documentStore.hasDoc(i)&&(this.documentStore.removeDoc(i),this._fields.forEach(function(n){var o=this.pipeline.run(t.tokenizer(e[n]));o.forEach(function(e){this.index[n].removeToken(e,i)},this)},this),n&&this.eventEmitter.emit("remove",e,this))}},t.Index.prototype.updateDoc=function(e,t){var t=void 0===t?!0:t;this.removeDocByRef(e[this._ref],!1),this.addDoc(e,!1),t&&this.eventEmitter.emit("update",e,this)},t.Index.prototype.idf=function(e,t){var n="@"+t+"/"+e;if(Object.prototype.hasOwnProperty.call(this._idfCache,n))return this._idfCache[n];var i=this.index[t].getDocFreq(e),o=1+Math.log(this.documentStore.length/(i+1));return this._idfCache[n]=o,o},t.Index.prototype.getFields=function(){return this._fields.slice()},t.Index.prototype.search=function(e,n){if(!e)return[];e="string"==typeof e?{any:e}:JSON.parse(JSON.stringify(e));var i=null;null!=n&&(i=JSON.stringify(n));for(var o=new t.Configuration(i,this.getFields()).get(),r={},s=Object.keys(e),u=0;u<s.length;u++){var a=s[u];r[a]=this.pipeline.run(t.tokenizer(e[a]))}var l={};for(var c in o){var d=r[c]||r.any;if(d){var f=this.fieldSearch(d,c,o),h=o[c].boost;for(var p in f)f[p]=f[p]*h;for(var p in f)p in l?l[p]+=f[p]:l[p]=f[p]}}var v,g=[];for(var p in l)v={ref:p,score:l[p]},this.documentStore.hasDoc(p)&&(v.doc=this.documentStore.getDoc(p)),g.push(v);return g.sort(function(e,t){return t.score-e.score}),g},t.Index.prototype.fieldSearch=function(e,t,n){var i=n[t].bool,o=n[t].expand,r=n[t].boost,s=null,u={};return 0!==r?(e.forEach(function(e){var n=[e];1==o&&(n=this.index[t].expandToken(e));var r={};n.forEach(function(n){var o=this.index[t].getDocs(n),a=this.idf(n,t);if(s&&"AND"==i){var l={};for(var c in s)c in o&&(l[c]=o[c]);o=l}n==e&&this.fieldSearchStats(u,n,o);for(var c in o){var d=this.index[t].getTermFrequency(n,c),f=this.documentStore.getFieldLength(c,t),h=1;0!=f&&(h=1/Math.sqrt(f));var p=1;n!=e&&(p=.15*(1-(n.length-e.length)/n.length));var v=d*a*h*p;c in r?r[c]+=v:r[c]=v}},this),s=this.mergeScores(s,r,i)},this),s=this.coordNorm(s,u,e.length)):void 0},t.Index.prototype.mergeScores=function(e,t,n){if(!e)return t;if("AND"==n){var i={};for(var o in t)o in e&&(i[o]=e[o]+t[o]);return i}for(var o in t)o in e?e[o]+=t[o]:e[o]=t[o];return e},t.Index.prototype.fieldSearchStats=function(e,t,n){for(var i in n)i in e?e[i].push(t):e[i]=[t]},t.Index.prototype.coordNorm=function(e,t,n){for(var i in e)if(i in t){var o=t[i].length;e[i]=e[i]*o/n}return e},t.Index.prototype.toJSON=function(){var e={};return this._fields.forEach(function(t){e[t]=this.index[t].toJSON()},this),{version:t.version,fields:this._fields,ref:this._ref,documentStore:this.documentStore.toJSON(),index:e,pipeline:this.pipeline.toJSON()}},t.Index.prototype.use=function(e){var t=Array.prototype.slice.call(arguments,1);t.unshift(this),e.apply(this,t)},t.DocumentStore=function(e){this._save=null===e||void 0===e?!0:e,this.docs={},this.docInfo={},this.length=0},t.DocumentStore.load=function(e){var t=new this;return t.length=e.length,t.docs=e.docs,t.docInfo=e.docInfo,t._save=e.save,t},t.DocumentStore.prototype.isDocStored=function(){return this._save},t.DocumentStore.prototype.addDoc=function(t,n){this.hasDoc(t)||this.length++,this.docs[t]=this._save===!0?e(n):null},t.DocumentStore.prototype.getDoc=function(e){return this.hasDoc(e)===!1?null:this.docs[e]},t.DocumentStore.prototype.hasDoc=function(e){return e in this.docs},t.DocumentStore.prototype.removeDoc=function(e){this.hasDoc(e)&&(delete this.docs[e],delete this.docInfo[e],this.length--)},t.DocumentStore.prototype.addFieldLength=function(e,t,n){null!==e&&void 0!==e&&0!=this.hasDoc(e)&&(this.docInfo[e]||(this.docInfo[e]={}),this.docInfo[e][t]=n)},t.DocumentStore.prototype.updateFieldLength=function(e,t,n){null!==e&&void 0!==e&&0!=this.hasDoc(e)&&this.addFieldLength(e,t,n)},t.DocumentStore.prototype.getFieldLength=function(e,t){return null===e||void 0===e?0:e in this.docs&&t in this.docInfo[e]?this.docInfo[e][t]:0},t.DocumentStore.prototype.toJSON=function(){return{docs:this.docs,docInfo:this.docInfo,length:this.length,save:this._save}},t.stemmer=function(){var e={ational:"ate",tional:"tion",enci:"ence",anci:"ance",izer:"ize",bli:"ble",alli:"al",entli:"ent",eli:"e",ousli:"ous",ization:"ize",ation:"ate",ator:"ate",alism:"al",iveness:"ive",fulness:"ful",ousness:"ous",aliti:"al",iviti:"ive",biliti:"ble",logi:"log"},t={icate:"ic",ative:"",alize:"al",iciti:"ic",ical:"ic",ful:"",ness:""},n="[^aeiou]",i="[aeiouy]",o=n+"[^aeiouy]*",r=i+"[aeiou]*",s="^("+o+")?"+r+o,u="^("+o+")?"+r+o+"("+r+")?$",a="^("+o+")?"+r+o+r+o,l="^("+o+")?"+i,c=new RegExp(s),d=new RegExp(a),f=new RegExp(u),h=new RegExp(l),p=/^(.+?)(ss|i)es$/,v=/^(.+?)([^s])s$/,g=/^(.+?)eed$/,m=/^(.+?)(ed|ing)$/,y=/.$/,S=/(at|bl|iz)$/,x=new RegExp("([^aeiouylsz])\\1$"),w=new RegExp("^"+o+i+"[^aeiouwxy]$"),I=/^(.+?[^aeiou])y$/,b=/^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/,E=/^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/,D=/^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/,F=/^(.+?)(s|t)(ion)$/,_=/^(.+?)e$/,P=/ll$/,k=new RegExp("^"+o+i+"[^aeiouwxy]$"),z=function(n){var i,o,r,s,u,a,l;if(n.length<3)return n;if(r=n.substr(0,1),"y"==r&&(n=r.toUpperCase()+n.substr(1)),s=p,u=v,s.test(n)?n=n.replace(s,"$1$2"):u.test(n)&&(n=n.replace(u,"$1$2")),s=g,u=m,s.test(n)){var z=s.exec(n);s=c,s.test(z[1])&&(s=y,n=n.replace(s,""))}else if(u.test(n)){var z=u.exec(n);i=z[1],u=h,u.test(i)&&(n=i,u=S,a=x,l=w,u.test(n)?n+="e":a.test(n)?(s=y,n=n.replace(s,"")):l.test(n)&&(n+="e"))}if(s=I,s.test(n)){var z=s.exec(n);i=z[1],n=i+"i"}if(s=b,s.test(n)){var z=s.exec(n);i=z[1],o=z[2],s=c,s.test(i)&&(n=i+e[o])}if(s=E,s.test(n)){var z=s.exec(n);i=z[1],o=z[2],s=c,s.test(i)&&(n=i+t[o])}if(s=D,u=F,s.test(n)){var z=s.exec(n);i=z[1],s=d,s.test(i)&&(n=i)}else if(u.test(n)){var z=u.exec(n);i=z[1]+z[2],u=d,u.test(i)&&(n=i)}if(s=_,s.test(n)){var z=s.exec(n);i=z[1],s=d,u=f,a=k,(s.test(i)||u.test(i)&&!a.test(i))&&(n=i)}return s=P,u=d,s.test(n)&&u.test(n)&&(s=y,n=n.replace(s,"")),"y"==r&&(n=r.toLowerCase()+n.substr(1)),n};return z}(),t.Pipeline.registerFunction(t.stemmer,"stemmer"),t.stopWordFilter=function(e){return e&&t.stopWordFilter.stopWords[e]!==!0?e:void 0},t.clearStopWords=function(){t.stopWordFilter.stopWords={}},t.addStopWords=function(e){null!=e&&Array.isArray(e)!==!1&&e.forEach(function(e){t.stopWordFilter.stopWords[e]=!0},this)},t.resetStopWords=function(){t.stopWordFilter.stopWords=t.defaultStopWords},t.defaultStopWords={"":!0,a:!0,able:!0,about:!0,across:!0,after:!0,all:!0,almost:!0,also:!0,am:!0,among:!0,an:!0,and:!0,any:!0,are:!0,as:!0,at:!0,be:!0,because:!0,been:!0,but:!0,by:!0,can:!0,cannot:!0,could:!0,dear:!0,did:!0,"do":!0,does:!0,either:!0,"else":!0,ever:!0,every:!0,"for":!0,from:!0,get:!0,got:!0,had:!0,has:!0,have:!0,he:!0,her:!0,hers:!0,him:!0,his:!0,how:!0,however:!0,i:!0,"if":!0,"in":!0,into:!0,is:!0,it:!0,its:!0,just:!0,least:!0,let:!0,like:!0,likely:!0,may:!0,me:!0,might:!0,most:!0,must:!0,my:!0,neither:!0,no:!0,nor:!0,not:!0,of:!0,off:!0,often:!0,on:!0,only:!0,or:!0,other:!0,our:!0,own:!0,rather:!0,said:!0,say:!0,says:!0,she:!0,should:!0,since:!0,so:!0,some:!0,than:!0,that:!0,the:!0,their:!0,them:!0,then:!0,there:!0,these:!0,they:!0,"this":!0,tis:!0,to:!0,too:!0,twas:!0,us:!0,wants:!0,was:!0,we:!0,were:!0,what:!0,when:!0,where:!0,which:!0,"while":!0,who:!0,whom:!0,why:!0,will:!0,"with":!0,would:!0,yet:!0,you:!0,your:!0},t.stopWordFilter.stopWords=t.defaultStopWords,t.Pipeline.registerFunction(t.stopWordFilter,"stopWordFilter"),t.trimmer=function(e){if(null===e||void 0===e)throw new Error("token should not be undefined");return e.replace(/^\W+/,"").replace(/\W+$/,"")},t.Pipeline.registerFunction(t.trimmer,"trimmer"),t.InvertedIndex=function(){this.root={docs:{},df:0}},t.InvertedIndex.load=function(e){var t=new this;return t.root=e.root,t},t.InvertedIndex.prototype.addToken=function(e,t,n){for(var n=n||this.root,i=0;i<=e.length-1;){var o=e[i];o in n||(n[o]={docs:{},df:0}),i+=1,n=n[o]}var r=t.ref;n.docs[r]?n.docs[r]={tf:t.tf}:(n.docs[r]={tf:t.tf},n.df+=1)},t.InvertedIndex.prototype.hasToken=function(e){if(!e)return!1;for(var t=this.root,n=0;n<e.length;n++){if(!t[e[n]])return!1;t=t[e[n]]}return!0},t.InvertedIndex.prototype.getNode=function(e){if(!e)return null;for(var t=this.root,n=0;n<e.length;n++){if(!t[e[n]])return null;t=t[e[n]]}return t},t.InvertedIndex.prototype.getDocs=function(e){var t=this.getNode(e);return null==t?{}:t.docs},t.InvertedIndex.prototype.getTermFrequency=function(e,t){var n=this.getNode(e);return null==n?0:t in n.docs?n.docs[t].tf:0},t.InvertedIndex.prototype.getDocFreq=function(e){var t=this.getNode(e);return null==t?0:t.df},t.InvertedIndex.prototype.removeToken=function(e,t){if(e){var n=this.getNode(e);null!=n&&t in n.docs&&(delete n.docs[t],n.df-=1)}},t.InvertedIndex.prototype.expandToken=function(e,t,n){if(null==e||""==e)return[];var t=t||[];if(void 0==n&&(n=this.getNode(e),null==n))return t;n.df>0&&t.push(e);for(var i in n)"docs"!==i&&"df"!==i&&this.expandToken(e+i,t,n[i]);return t},t.InvertedIndex.prototype.toJSON=function(){return{root:this.root}},t.Configuration=function(e,n){var e=e||"";if(void 0==n||null==n)throw new Error("fields should not be null");this.config={};var i;try{i=JSON.parse(e),this.buildUserConfig(i,n)}catch(o){t.utils.warn("user configuration parse failed, will use default configuration"),this.buildDefaultConfig(n)}},t.Configuration.prototype.buildDefaultConfig=function(e){this.reset(),e.forEach(function(e){this.config[e]={boost:1,bool:"OR",expand:!1}},this)},t.Configuration.prototype.buildUserConfig=function(e,n){var i="OR",o=!1;if(this.reset(),"bool"in e&&(i=e.bool||i),"expand"in e&&(o=e.expand||o),"fields"in e)for(var r in e.fields)if(n.indexOf(r)>-1){var s=e.fields[r],u=o;void 0!=s.expand&&(u=s.expand),this.config[r]={boost:s.boost||0===s.boost?s.boost:1,bool:s.bool||i,expand:u}}else t.utils.warn("field name in user configuration not found in index instance fields");else this.addAllFields2UserConfig(i,o,n)},t.Configuration.prototype.addAllFields2UserConfig=function(e,t,n){n.forEach(function(n){this.config[n]={boost:1,bool:e,expand:t}},this)},t.Configuration.prototype.get=function(){return this.config},t.Configuration.prototype.reset=function(){this.config={}},lunr.SortedSet=function(){this.length=0,this.elements=[]},lunr.SortedSet.load=function(e){var t=new this;return t.elements=e,t.length=e.length,t},lunr.SortedSet.prototype.add=function(){var e,t;for(e=0;e<arguments.length;e++)t=arguments[e],~this.indexOf(t)||this.elements.splice(this.locationFor(t),0,t);this.length=this.elements.length},lunr.SortedSet.prototype.toArray=function(){return this.elements.slice()},lunr.SortedSet.prototype.map=function(e,t){return this.elements.map(e,t)},lunr.SortedSet.prototype.forEach=function(e,t){return this.elements.forEach(e,t)},lunr.SortedSet.prototype.indexOf=function(e){for(var t=0,n=this.elements.length,i=n-t,o=t+Math.floor(i/2),r=this.elements[o];i>1;){if(r===e)return o;e>r&&(t=o),r>e&&(n=o),i=n-t,o=t+Math.floor(i/2),r=this.elements[o]}return r===e?o:-1},lunr.SortedSet.prototype.locationFor=function(e){for(var t=0,n=this.elements.length,i=n-t,o=t+Math.floor(i/2),r=this.elements[o];i>1;)e>r&&(t=o),r>e&&(n=o),i=n-t,o=t+Math.floor(i/2),r=this.elements[o];return r>e?o:e>r?o+1:void 0},lunr.SortedSet.prototype.intersect=function(e){for(var t=new lunr.SortedSet,n=0,i=0,o=this.length,r=e.length,s=this.elements,u=e.elements;;){if(n>o-1||i>r-1)break;s[n]!==u[i]?s[n]<u[i]?n++:s[n]>u[i]&&i++:(t.add(s[n]),n++,i++)}return t},lunr.SortedSet.prototype.clone=function(){var e=new lunr.SortedSet;return e.elements=this.toArray(),e.length=e.elements.length,e},lunr.SortedSet.prototype.union=function(e){var t,n,i;this.length>=e.length?(t=this,n=e):(t=e,n=this),i=t.clone();for(var o=0,r=n.toArray();o<r.length;o++)i.add(r[o]);return i},lunr.SortedSet.prototype.toJSON=function(){return this.toArray()},function(e,t){"function"==typeof define&&define.amd?define(t):"object"==typeof exports?module.exports=t():e.elasticlunr=t()}(this,function(){return t})}();
/** pdoc search index */const docs = {"version": "0.9.5", "fields": ["qualname", "fullname", "annotation", "default_value", "signature", "bases", "doc"], "ref": "fullname", "documentStore": {"docs": {"acmc": {"fullname": "acmc", "modulename": "acmc", "kind": "module", "doc": "<p></p>\n"}, "acmc.logging_config": {"fullname": "acmc.logging_config", "modulename": "acmc.logging_config", "kind": "module", "doc": "<p>logging_config.py</p>\n\n<p>This module defines functions to setup logging for acmc across all module.</p>\n"}, "acmc.logging_config.DEFAULT_LOG_FILE": {"fullname": "acmc.logging_config.DEFAULT_LOG_FILE", "modulename": "acmc.logging_config", "qualname": "DEFAULT_LOG_FILE", "kind": "variable", "doc": "<p>The default acmc application log filename.</p>\n", "default_value": "'acmc.log'"}, "acmc.logging_config.setup_logger": {"fullname": "acmc.logging_config.setup_logger", "modulename": "acmc.logging_config", "qualname": "setup_logger", "kind": "function", "doc": "<p>Sets up acmc logger as a singleton outputing to file and sysout syserr.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">log_level</span><span class=\"p\">:</span> <span class=\"nb\">int</span> <span class=\"o\">=</span> <span class=\"mi\">20</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.logging_config.set_log_level": {"fullname": "acmc.logging_config.set_log_level", "modulename": "acmc.logging_config", "qualname": "set_log_level", "kind": "function", "doc": "<p>Sets the log level for the acmc logger.</p>\n\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>log_level (int):</strong> log level from the python logging libraru</li>\n</ul>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">log_level</span><span class=\"p\">:</span> <span class=\"nb\">int</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main": {"fullname": "acmc.main", "modulename": "acmc.main", "kind": "module", "doc": "<p>main.py module</p>\n\n<p>This module provides the functionality for the acmc command line interface</p>\n"}, "acmc.main.DEFAULT_WORKSPACE_PATH": {"fullname": "acmc.main.DEFAULT_WORKSPACE_PATH", "modulename": "acmc.main", "qualname": "DEFAULT_WORKSPACE_PATH", "kind": "variable", "doc": "<p>Default phenotype workspace path</p>\n", "default_value": "PosixPath('workspace')"}, "acmc.main.main": {"fullname": "acmc.main.main", "modulename": "acmc.main", "qualname": "main", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.omop": {"fullname": "acmc.omop", "modulename": "acmc.omop", "kind": "module", "doc": "<p>omop.py module</p>\n\n<p>This module provides functionality to manage OMOP vocabularies.</p>\n"}, "acmc.omop.VOCAB_PATH": {"fullname": "acmc.omop.VOCAB_PATH", "modulename": "acmc.omop", "qualname": "VOCAB_PATH", "kind": "variable", "doc": "<p>Default OMOP vocabulary path</p>\n", "default_value": "PosixPath('vocab/omop')"}, "acmc.omop.OMOP_CDM_Version": {"fullname": "acmc.omop.OMOP_CDM_Version", "modulename": "acmc.omop", "qualname": "OMOP_CDM_Version", "kind": "variable", "doc": "<p>Supported OMOP CDM version number</p>\n", "default_value": "'54'"}, "acmc.omop.OMOP_DB_FILENAME": {"fullname": "acmc.omop.OMOP_DB_FILENAME", "modulename": "acmc.omop", "qualname": "OMOP_DB_FILENAME", "kind": "variable", "doc": "<p>Default OMOP sqllite database filename</p>\n", "default_value": "'omop_54.sqlite'"}, "acmc.omop.DB_PATH": {"fullname": "acmc.omop.DB_PATH", "modulename": "acmc.omop", "qualname": "DB_PATH", "kind": "variable", "doc": "<p>Default OMOP sqllite database path</p>\n", "default_value": "PosixPath('vocab/omop/omop_54.sqlite')"}, "acmc.omop.VERSION_FILE": {"fullname": "acmc.omop.VERSION_FILE", "modulename": "acmc.omop", "qualname": "VERSION_FILE", "kind": "variable", "doc": "<p>Default OMOP version file</p>\n", "default_value": "'omop_version.yml'"}, "acmc.omop.VERSION_PATH": {"fullname": "acmc.omop.VERSION_PATH", "modulename": "acmc.omop", "qualname": "VERSION_PATH", "kind": "variable", "doc": "<p>Default OMOP version path</p>\n", "default_value": "PosixPath('vocab/omop/omop_version.yml')"}, "acmc.omop.EXPORT_FILE": {"fullname": "acmc.omop.EXPORT_FILE", "modulename": "acmc.omop", "qualname": "EXPORT_FILE", "kind": "variable", "doc": "<p>Default OMOP export database filename</p>\n", "default_value": "'omop_54_export.sqlite'"}, "acmc.omop.vocabularies": {"fullname": "acmc.omop.vocabularies", "modulename": "acmc.omop", "qualname": "vocabularies", "kind": "variable", "doc": "<p>Required OMOP vocabularies definition</p>\n", "default_value": "{'source': 'OHDSI Athena', 'url': 'https://athena.ohdsi.org/vocabulary/list', 'cdm_version': '54', 'version': '', 'vocabularies': [{'id': 1, 'name': 'SNOMED'}, {'id': 2, 'name': 'ICD9CM'}, {'id': 17, 'name': 'Readv2'}, {'id': 21, 'name': 'ATC'}, {'id': 55, 'name': 'OPCS4'}, {'id': 57, 'name': 'HES Specialty'}, {'id': 70, 'name': 'ICD10CM'}, {'id': 75, 'name': 'dm+d'}, {'id': 144, 'name': 'UK Biobank'}, {'id': 154, 'name': 'NHS Ethnic Category'}, {'id': 155, 'name': 'NHS Place of Service'}], 'tables': []}"}, "acmc.omop.omop_vocab_types": {"fullname": "acmc.omop.omop_vocab_types", "modulename": "acmc.omop", "qualname": "omop_vocab_types", "kind": "variable", "doc": "<p>Type mappings from acmc medical coding types to OMOP vocabulary types</p>\n", "default_value": "{'read2': 'Read', 'read3': None, 'icd10': 'ICD10CM', 'snomed': 'SNOMED', 'opcs4': 'OPCS4', 'atc': 'ATC', 'med': None, 'cprd': None}"}, "acmc.omop.install": {"fullname": "acmc.omop.install", "modulename": "acmc.omop", "qualname": "install", "kind": "function", "doc": "<p>\"Installs the OMOP release csv files in a file-based sql database</p>\n\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>omop_zip_file (str):</strong> vocabularies zip file distributed by OHDSI Athena</li>\n<li><strong>version (str):</strong> version of the vocabularies distributed by OHDSI Athena</li>\n</ul>\n\n<h6 id=\"raises\">Raises:</h6>\n\n<ul>\n<li><strong>ValueError:</strong> if the zip file does not exist</li>\n<li><strong>ValueError:</strong> if the file is not a zip file</li>\n<li><strong>Exception:</strong> if error reading omop csv files</li>\n</ul>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">omop_zip_file</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.omop.write_version_file": {"fullname": "acmc.omop.write_version_file", "modulename": "acmc.omop", "qualname": "write_version_file", "kind": "function", "doc": "<p>Writes the OMOP vocaburaries and version to a file</p>\n\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>version (str):</strong> version of the vocabularies distributed by OHDSI Athena</li>\n</ul>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.omop.clear": {"fullname": "acmc.omop.clear", "modulename": "acmc.omop", "qualname": "clear", "kind": "function", "doc": "<p>Clears the OMOP sql database</p>\n\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>db_path (Path):</strong> the path to the omop sqllite database</li>\n</ul>\n\n<h6 id=\"raises\">Raises:</h6>\n\n<ul>\n<li><strong>FileNotFoundError:</strong> if the omop sqllite database does not exist</li>\n</ul>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">db_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.omop.delete": {"fullname": "acmc.omop.delete", "modulename": "acmc.omop", "qualname": "delete", "kind": "function", "doc": "<p>Deletes the OMOP sql database</p>\n\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>db_path (Path):</strong> the path to the omop sqllite database</li>\n</ul>\n\n<h6 id=\"raises\">Raises:</h6>\n\n<ul>\n<li><strong>FileNotFoundError:</strong> if the omop sqllite database does not exist</li>\n</ul>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">db_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.omop.table_exists": {"fullname": "acmc.omop.table_exists", "modulename": "acmc.omop", "qualname": "table_exists", "kind": "function", "doc": "<p>Query to check if the table exists</p>\n\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>cursor (sqlite3.Cursor):</strong> a sqllite database cursor</li>\n<li><strong>table_name (str):</strong> the table name to check</li>\n</ul>\n\n<h6 id=\"returns\">Returns:</h6>\n\n<blockquote>\n <p>bool: true if table exists</p>\n</blockquote>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">cursor</span><span class=\"p\">:</span> <span class=\"n\">sqlite3</span><span class=\"o\">.</span><span class=\"n\">Cursor</span>, </span><span class=\"param\"><span class=\"n\">table_name</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">bool</span>:</span></span>", "funcdef": "def"}, "acmc.omop.vocab_exists": {"fullname": "acmc.omop.vocab_exists", "modulename": "acmc.omop", "qualname": "vocab_exists", "kind": "function", "doc": "<p>Query to check if the vocabulary exists</p>\n\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>cursor (sqlite3.Cursor):</strong> a sqllite database cursor</li>\n<li><strong>vocab_id (str):</strong> the vocabulary id to check</li>\n</ul>\n\n<h6 id=\"returns\">Returns:</h6>\n\n<blockquote>\n <p>bool: true if vocabulary id exists</p>\n</blockquote>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">cursor</span><span class=\"p\">:</span> <span class=\"n\">sqlite3</span><span class=\"o\">.</span><span class=\"n\">Cursor</span>, </span><span class=\"param\"><span class=\"n\">vocab_id</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">bool</span>:</span></span>", "funcdef": "def"}, "acmc.omop.concept_set_exist": {"fullname": "acmc.omop.concept_set_exist", "modulename": "acmc.omop", "qualname": "concept_set_exist", "kind": "function", "doc": "<p>Query to check if the concept set exists</p>\n\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>cursor (sqlite3.Cursor):</strong> a sqllite database cursor</li>\n<li><strong>concept_set_name (str):</strong> the concept set name to check</li>\n</ul>\n\n<h6 id=\"returns\">Returns:</h6>\n\n<blockquote>\n <p>bool: true if concept set exists</p>\n</blockquote>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">cursor</span><span class=\"p\">:</span> <span class=\"n\">sqlite3</span><span class=\"o\">.</span><span class=\"n\">Cursor</span>, </span><span class=\"param\"><span class=\"n\">concept_set_name</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">bool</span>:</span></span>", "funcdef": "def"}, "acmc.omop.export": {"fullname": "acmc.omop.export", "modulename": "acmc.omop", "qualname": "export", "kind": "function", "doc": "<p>Export concept sets to omop database in csv format</p>\n\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>map_path (Path):</strong> path to the acmc map directory containing concept sets in csv format</li>\n<li><strong>export_path (Path):</strong> path to the directory where the omop database csv files are to be written</li>\n<li><strong>version (str):</strong> phenotype version for omop vocabulary version</li>\n<li><strong>omop_metadata (dict):</strong> phenotype omop metadata for omop vocabulary metadata</li>\n</ul>\n\n<h6 id=\"returns\">Returns:</h6>\n\n<blockquote>\n <p>Path: path to the exported sqllite database</p>\n</blockquote>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">map_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>,</span><span class=\"param\">\t<span class=\"n\">export_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>,</span><span class=\"param\">\t<span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">omop_metadata</span><span class=\"p\">:</span> <span class=\"nb\">dict</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>:</span></span>", "funcdef": "def"}, "acmc.parse": {"fullname": "acmc.parse", "modulename": "acmc.parse", "kind": "module", "doc": "<p>parse.py module</p>\n\n<p>This module provides functionality to set up medical code translation classes</p>\n"}, "acmc.parse.SUPPORTED_CODE_TYPES": {"fullname": "acmc.parse.SUPPORTED_CODE_TYPES", "modulename": "acmc.parse", "qualname": "SUPPORTED_CODE_TYPES", "kind": "variable", "doc": "<p>List of support medical coding types</p>\n", "default_value": "{'snomed', 'atc', 'read2', 'read3', 'icd10', 'opcs4'}"}, "acmc.parse.CodesError": {"fullname": "acmc.parse.CodesError", "modulename": "acmc.parse", "qualname": "CodesError", "kind": "class", "doc": "<p>A class used in InvalidCodesException to report an error if a code parser check fails</p>\n"}, "acmc.parse.CodesError.__init__": {"fullname": "acmc.parse.CodesError.__init__", "modulename": "acmc.parse", "qualname": "CodesError.__init__", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">message</span>, </span><span class=\"param\"><span class=\"n\">codes</span><span class=\"o\">=</span><span class=\"kc\">None</span>, </span><span class=\"param\"><span class=\"n\">codes_file</span><span class=\"o\">=</span><span class=\"kc\">None</span>, </span><span class=\"param\"><span class=\"n\">mask</span><span class=\"o\">=</span><span class=\"kc\">None</span>, </span><span class=\"param\"><span class=\"n\">code_type</span><span class=\"o\">=</span><span class=\"kc\">None</span></span>)</span>"}, "acmc.parse.InvalidCodesException": {"fullname": "acmc.parse.InvalidCodesException", "modulename": "acmc.parse", "qualname": "InvalidCodesException", "kind": "class", "doc": "<p>Custom exception class raised when invalid codes are found that cannot be resolved by processing</p>\n", "bases": "builtins.Exception"}, "acmc.parse.InvalidCodesException.__init__": {"fullname": "acmc.parse.InvalidCodesException.__init__", "modulename": "acmc.parse", "qualname": "InvalidCodesException.__init__", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">error</span></span>)</span>"}, "acmc.parse.InvalidCodesException.error": {"fullname": "acmc.parse.InvalidCodesException.error", "modulename": "acmc.parse", "qualname": "InvalidCodesException.error", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Proto": {"fullname": "acmc.parse.Proto", "modulename": "acmc.parse", "qualname": "Proto", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n"}, "acmc.parse.Proto.__init__": {"fullname": "acmc.parse.Proto.__init__", "modulename": "acmc.parse", "qualname": "Proto.__init__", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">name</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">trud_codes_path</span><span class=\"p\">:</span> <span class=\"n\">Optional</span><span class=\"p\">[</span><span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span><span class=\"p\">]</span> <span class=\"o\">=</span> <span class=\"kc\">None</span></span>)</span>"}, "acmc.parse.Proto.checks": {"fullname": "acmc.parse.Proto.checks", "modulename": "acmc.parse", "qualname": "Proto.checks", "kind": "variable", "doc": "<p></p>\n", "annotation": ": list[tuple[str, typing.Callable[[pandas.core.frame.DataFrame], pandas.core.series.Series], typing.Callable[[pandas.core.frame.DataFrame, pathlib.Path], pandas.core.frame.DataFrame]]]"}, "acmc.parse.Proto.name": {"fullname": "acmc.parse.Proto.name", "modulename": "acmc.parse", "qualname": "Proto.name", "kind": "variable", "doc": "<p></p>\n", "annotation": ": str"}, "acmc.parse.Proto.raise_exception": {"fullname": "acmc.parse.Proto.raise_exception", "modulename": "acmc.parse", "qualname": "Proto.raise_exception", "kind": "function", "doc": "<p>Raises an exception inside a lambda function. Python does not allow using raise statement inside lambda because lambda can only contain expressions, not statements. Using raise_exception not raise_ as it's more explict</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"bp\">self</span>, </span><span class=\"param\"><span class=\"n\">ex</span><span class=\"p\">:</span> <span class=\"ne\">Exception</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.parse.Proto.in_database": {"fullname": "acmc.parse.Proto.in_database", "modulename": "acmc.parse", "qualname": "Proto.in_database", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"bp\">self</span>,</span><span class=\"param\">\t<span class=\"n\">codes</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">db</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">col</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>:</span></span>", "funcdef": "def"}, "acmc.parse.Proto.process": {"fullname": "acmc.parse.Proto.process", "modulename": "acmc.parse", "qualname": "Proto.process", "kind": "function", "doc": "<p>identify issues that do not pass and fix them with define/d process</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"bp\">self</span>,</span><span class=\"param\">\t<span class=\"n\">codes</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">codes_file</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">) -> <span class=\"n\">Tuple</span><span class=\"p\">[</span><span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span><span class=\"p\">,</span> <span class=\"nb\">list</span><span class=\"p\">]</span>:</span></span>", "funcdef": "def"}, "acmc.parse.Proto.verify": {"fullname": "acmc.parse.Proto.verify", "modulename": "acmc.parse", "qualname": "Proto.verify", "kind": "function", "doc": "<p>verify codes in codes file</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"bp\">self</span>, </span><span class=\"param\"><span class=\"n\">codes</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>, </span><span class=\"param\"><span class=\"n\">codes_file</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.parse.Read2": {"fullname": "acmc.parse.Read2", "modulename": "acmc.parse", "qualname": "Read2", "kind": "class", "doc": "<p>This Read2 class extends Proto, adding custom validation checks for a dataset of \"Read2\" codes. It ensures that the dataset is loaded, validates the codes based on several rules, and applies corrections or logs errors when necessary.</p>\n", "bases": "Proto"}, "acmc.parse.Read2.checks": {"fullname": "acmc.parse.Read2.checks", "modulename": "acmc.parse", "qualname": "Read2.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Read3": {"fullname": "acmc.parse.Read3", "modulename": "acmc.parse", "qualname": "Read3", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Read3.checks": {"fullname": "acmc.parse.Read3.checks", "modulename": "acmc.parse", "qualname": "Read3.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Icd10": {"fullname": "acmc.parse.Icd10", "modulename": "acmc.parse", "qualname": "Icd10", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Icd10.checks": {"fullname": "acmc.parse.Icd10.checks", "modulename": "acmc.parse", "qualname": "Icd10.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Snomed": {"fullname": "acmc.parse.Snomed", "modulename": "acmc.parse", "qualname": "Snomed", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Snomed.checks": {"fullname": "acmc.parse.Snomed.checks", "modulename": "acmc.parse", "qualname": "Snomed.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Opcs4": {"fullname": "acmc.parse.Opcs4", "modulename": "acmc.parse", "qualname": "Opcs4", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Opcs4.checks": {"fullname": "acmc.parse.Opcs4.checks", "modulename": "acmc.parse", "qualname": "Opcs4.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Atc": {"fullname": "acmc.parse.Atc", "modulename": "acmc.parse", "qualname": "Atc", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Atc.checks": {"fullname": "acmc.parse.Atc.checks", "modulename": "acmc.parse", "qualname": "Atc.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Med": {"fullname": "acmc.parse.Med", "modulename": "acmc.parse", "qualname": "Med", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Med.checks": {"fullname": "acmc.parse.Med.checks", "modulename": "acmc.parse", "qualname": "Med.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Cprd": {"fullname": "acmc.parse.Cprd", "modulename": "acmc.parse", "qualname": "Cprd", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Cprd.checks": {"fullname": "acmc.parse.Cprd.checks", "modulename": "acmc.parse", "qualname": "Cprd.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.CodeTypeParser": {"fullname": "acmc.parse.CodeTypeParser", "modulename": "acmc.parse", "qualname": "CodeTypeParser", "kind": "class", "doc": "<p>A class used in InvalidCodesException to report an error if a code parser check fails</p>\n"}, "acmc.parse.CodeTypeParser.__init__": {"fullname": "acmc.parse.CodeTypeParser.__init__", "modulename": "acmc.parse", "qualname": "CodeTypeParser.__init__", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">trud_processed_dir</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span> <span class=\"o\">=</span> <span class=\"n\">PosixPath</span><span class=\"p\">(</span><span class=\"s1\">'vocab/trud/processed'</span><span class=\"p\">)</span></span>)</span>"}, "acmc.parse.CodeTypeParser.code_types": {"fullname": "acmc.parse.CodeTypeParser.code_types", "modulename": "acmc.parse", "qualname": "CodeTypeParser.code_types", "kind": "variable", "doc": "<p></p>\n"}, "acmc.phen": {"fullname": "acmc.phen", "modulename": "acmc.phen", "kind": "module", "doc": "<p>phenotype.py module</p>\n\n<p>This module provides functionality for managing phenotypes.</p>\n"}, "acmc.phen.PHEN_DIR": {"fullname": "acmc.phen.PHEN_DIR", "modulename": "acmc.phen", "qualname": "PHEN_DIR", "kind": "variable", "doc": "<p>Default phenotype directory name</p>\n", "default_value": "'phen'"}, "acmc.phen.DEFAULT_PHEN_PATH": {"fullname": "acmc.phen.DEFAULT_PHEN_PATH", "modulename": "acmc.phen", "qualname": "DEFAULT_PHEN_PATH", "kind": "variable", "doc": "<p>Default phenotype directory path</p>\n", "default_value": "PosixPath('workspace/phen')"}, "acmc.phen.CONCEPTS_DIR": {"fullname": "acmc.phen.CONCEPTS_DIR", "modulename": "acmc.phen", "qualname": "CONCEPTS_DIR", "kind": "variable", "doc": "<p>Default concepts directory name</p>\n", "default_value": "'concepts'"}, "acmc.phen.MAP_DIR": {"fullname": "acmc.phen.MAP_DIR", "modulename": "acmc.phen", "qualname": "MAP_DIR", "kind": "variable", "doc": "<p>Default map directory name</p>\n", "default_value": "'map'"}, "acmc.phen.CONCEPT_SET_DIR": {"fullname": "acmc.phen.CONCEPT_SET_DIR", "modulename": "acmc.phen", "qualname": "CONCEPT_SET_DIR", "kind": "variable", "doc": "<p>Default concept set directory name</p>\n", "default_value": "'concept-sets'"}, "acmc.phen.CSV_PATH": {"fullname": "acmc.phen.CSV_PATH", "modulename": "acmc.phen", "qualname": "CSV_PATH", "kind": "variable", "doc": "<p>Default CSV concept set directory path</p>\n", "default_value": "PosixPath('concept-sets/csv')"}, "acmc.phen.OMOP_PATH": {"fullname": "acmc.phen.OMOP_PATH", "modulename": "acmc.phen", "qualname": "OMOP_PATH", "kind": "variable", "doc": "<p>Default OMOP concept set directory path</p>\n", "default_value": "PosixPath('concept-sets/omop')"}, "acmc.phen.DEFAULT_PHEN_DIR_LIST": {"fullname": "acmc.phen.DEFAULT_PHEN_DIR_LIST", "modulename": "acmc.phen", "qualname": "DEFAULT_PHEN_DIR_LIST", "kind": "variable", "doc": "<p>List of default phenotype directories</p>\n", "default_value": "['concepts', 'map', 'concept-sets']"}, "acmc.phen.CONFIG_FILE": {"fullname": "acmc.phen.CONFIG_FILE", "modulename": "acmc.phen", "qualname": "CONFIG_FILE", "kind": "variable", "doc": "<p>Default configuration filename</p>\n", "default_value": "'config.yml'"}, "acmc.phen.VOCAB_VERSION_FILE": {"fullname": "acmc.phen.VOCAB_VERSION_FILE", "modulename": "acmc.phen", "qualname": "VOCAB_VERSION_FILE", "kind": "variable", "doc": "<p>Default vocabulary version filename</p>\n", "default_value": "'vocab_version.yml'"}, "acmc.phen.SEMANTIC_VERSION_TYPES": {"fullname": "acmc.phen.SEMANTIC_VERSION_TYPES", "modulename": "acmc.phen", "qualname": "SEMANTIC_VERSION_TYPES", "kind": "variable", "doc": "<p>List of semantic version increment types</p>\n", "default_value": "['major', 'minor', 'patch']"}, "acmc.phen.DEFAULT_VERSION_INC": {"fullname": "acmc.phen.DEFAULT_VERSION_INC", "modulename": "acmc.phen", "qualname": "DEFAULT_VERSION_INC", "kind": "variable", "doc": "<p>Default semantic version increment type</p>\n", "default_value": "'patch'"}, "acmc.phen.DEFAULT_GIT_BRANCH": {"fullname": "acmc.phen.DEFAULT_GIT_BRANCH", "modulename": "acmc.phen", "qualname": "DEFAULT_GIT_BRANCH", "kind": "variable", "doc": "<p>Default phenotype repo branch name</p>\n", "default_value": "'main'"}, "acmc.phen.SPLIT_COL_ACTION": {"fullname": "acmc.phen.SPLIT_COL_ACTION", "modulename": "acmc.phen", "qualname": "SPLIT_COL_ACTION", "kind": "variable", "doc": "<p>Split column preprocessing action type</p>\n", "default_value": "'split_col'"}, "acmc.phen.CODES_COL_ACTION": {"fullname": "acmc.phen.CODES_COL_ACTION", "modulename": "acmc.phen", "qualname": "CODES_COL_ACTION", "kind": "variable", "doc": "<p>Codes column preprocessing action type</p>\n", "default_value": "'codes_col'"}, "acmc.phen.DIVIDE_COL_ACTION": {"fullname": "acmc.phen.DIVIDE_COL_ACTION", "modulename": "acmc.phen", "qualname": "DIVIDE_COL_ACTION", "kind": "variable", "doc": "<p>Divide column preprocessing action type</p>\n", "default_value": "'divide_col'"}, "acmc.phen.COL_ACTIONS": {"fullname": "acmc.phen.COL_ACTIONS", "modulename": "acmc.phen", "qualname": "COL_ACTIONS", "kind": "variable", "doc": "<p>List of column preprocessing action types</p>\n", "default_value": "['split_col', 'codes_col', 'divide_col']"}, "acmc.phen.CODE_FILE_TYPES": {"fullname": "acmc.phen.CODE_FILE_TYPES", "modulename": "acmc.phen", "qualname": "CODE_FILE_TYPES", "kind": "variable", "doc": "<p>List of supported source concept coding list file types</p>\n", "default_value": "['.xlsx', '.xls', '.csv']"}, "acmc.phen.CONFIG_SCHEMA": {"fullname": "acmc.phen.CONFIG_SCHEMA", "modulename": "acmc.phen", "qualname": "CONFIG_SCHEMA", "kind": "variable", "doc": "<p>Phenotype config.yml schema definition</p>\n", "default_value": "{'phenotype': {'type': 'dict', 'required': True, 'schema': {'version': {'type': 'string', 'required': True, 'regex': '^\\\\d+\\\\.\\\\d+\\\\.\\\\d+$'}, 'omop': {'type': 'dict', 'required': True, 'schema': {'vocabulary_id': {'type': 'string', 'required': True}, 'vocabulary_name': {'type': 'string', 'required': True}, 'vocabulary_reference': {'type': 'string', 'required': True, 'regex': '^https?://.*'}}}, 'map': {'type': 'list', 'schema': {'type': 'string', 'allowed': ['snomed', 'atc', 'read2', 'read3', 'icd10', 'opcs4']}}, 'concept_sets': {'type': 'list', 'required': True, 'schema': {'type': 'dict', 'schema': {'name': {'type': 'string', 'required': True}, 'file': {'type': 'dict', 'required': False, 'schema': {'path': {'type': 'string', 'required': True}, 'columns': {'type': 'dict', 'required': True}, 'category': {'type': 'string'}, 'actions': {'type': 'dict', 'schema': {'divide_col': {'type': 'string'}}}}}, 'metadata': {'type': 'dict', 'required': True}}}}}}}"}, "acmc.phen.PhenValidationException": {"fullname": "acmc.phen.PhenValidationException", "modulename": "acmc.phen", "qualname": "PhenValidationException", "kind": "class", "doc": "<p>Custom exception class raised when validation errors in phenotype configuration file</p>\n", "bases": "builtins.Exception"}, "acmc.phen.PhenValidationException.__init__": {"fullname": "acmc.phen.PhenValidationException.__init__", "modulename": "acmc.phen", "qualname": "PhenValidationException.__init__", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">message</span>, </span><span class=\"param\"><span class=\"n\">validation_errors</span><span class=\"o\">=</span><span class=\"kc\">None</span></span>)</span>"}, "acmc.phen.PhenValidationException.validation_errors": {"fullname": "acmc.phen.PhenValidationException.validation_errors", "modulename": "acmc.phen", "qualname": "PhenValidationException.validation_errors", "kind": "variable", "doc": "<p></p>\n"}, "acmc.phen.init": {"fullname": "acmc.phen.init", "modulename": "acmc.phen", "qualname": "init", "kind": "function", "doc": "<p>Initial phenotype directory as git repo with standard structure</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">remote_url</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.fork": {"fullname": "acmc.phen.fork", "modulename": "acmc.phen", "qualname": "fork", "kind": "function", "doc": "<p>Forks an upstream phenotype in a remote repo at a specific version to a local director, and optionally sets to a new remote origin\"</p>\n\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>phen_dir (str):</strong> local directory path where the upstream repo is to be cloned</li>\n<li><strong>upstream_url (str):</strong> url to the upstream repo</li>\n<li><strong>upstream_version (str):</strong> version in the upstream repo to clone</li>\n<li><strong>new_origin_url (str, optional):</strong> url of the remote repo to set as the new origin. Defaults to None.</li>\n</ul>\n\n<h6 id=\"raises\">Raises:</h6>\n\n<ul>\n<li><strong>ValueError:</strong> if the specified version is not in the upstream repo</li>\n<li><strong>ValueError:</strong> if the upstream repo is not a valid phenotype repo</li>\n<li><strong>ValueError:</strong> if there's any other problems with Git</li>\n</ul>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">upstream_url</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">upstream_version</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">new_origin_url</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.validate": {"fullname": "acmc.phen.validate", "modulename": "acmc.phen", "qualname": "validate", "kind": "function", "doc": "<p>Validates the phenotype directory is a git repo with standard structure</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.translate_codes": {"fullname": "acmc.phen.translate_codes", "modulename": "acmc.phen", "qualname": "translate_codes", "kind": "function", "doc": "<p>Translates each source code type the source coding list into a target type and returns all conversions as a concept set</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">source_df</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">target_code_type</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">concept_name</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>:</span></span>", "funcdef": "def"}, "acmc.phen.write_vocab_version": {"fullname": "acmc.phen.write_vocab_version", "modulename": "acmc.phen", "qualname": "write_vocab_version", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.map": {"fullname": "acmc.phen.map", "modulename": "acmc.phen", "qualname": "map", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">target_code_type</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.publish": {"fullname": "acmc.phen.publish", "modulename": "acmc.phen", "qualname": "publish", "kind": "function", "doc": "<p>Publishes updates to the phenotype by commiting all changes to the repo directory</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">msg</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">remote_url</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">increment</span><span class=\"p\">:</span> <span class=\"nb\">str</span> <span class=\"o\">=</span> <span class=\"s1\">'patch'</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.export": {"fullname": "acmc.phen.export", "modulename": "acmc.phen", "qualname": "export", "kind": "function", "doc": "<p>Exports a phen repo at a specific tagged version into a target directory</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.copy": {"fullname": "acmc.phen.copy", "modulename": "acmc.phen", "qualname": "copy", "kind": "function", "doc": "<p>Copys a phen repo at a specific tagged version into a target directory</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">target_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.extract_concepts": {"fullname": "acmc.phen.extract_concepts", "modulename": "acmc.phen", "qualname": "extract_concepts", "kind": "function", "doc": "<p>Extracts concepts as {name: file_path} dictionary and a name set.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">config_data</span><span class=\"p\">:</span> <span class=\"nb\">dict</span></span><span class=\"return-annotation\">) -> <span class=\"n\">Tuple</span><span class=\"p\">[</span><span class=\"nb\">dict</span><span class=\"p\">,</span> <span class=\"n\">Set</span><span class=\"p\">[</span><span class=\"nb\">str</span><span class=\"p\">]]</span>:</span></span>", "funcdef": "def"}, "acmc.phen.diff_config": {"fullname": "acmc.phen.diff_config", "modulename": "acmc.phen", "qualname": "diff_config", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">old_config</span><span class=\"p\">:</span> <span class=\"nb\">dict</span>, </span><span class=\"param\"><span class=\"n\">new_config</span><span class=\"p\">:</span> <span class=\"nb\">dict</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">str</span>:</span></span>", "funcdef": "def"}, "acmc.phen.diff_map_files": {"fullname": "acmc.phen.diff_map_files", "modulename": "acmc.phen", "qualname": "diff_map_files", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">old_map_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>, </span><span class=\"param\"><span class=\"n\">new_map_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">str</span>:</span></span>", "funcdef": "def"}, "acmc.phen.diff_phen": {"fullname": "acmc.phen.diff_phen", "modulename": "acmc.phen", "qualname": "diff_phen", "kind": "function", "doc": "<p>Compare the differences between two versions of a phenotype</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">new_phen_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>,</span><span class=\"param\">\t<span class=\"n\">new_version</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">old_phen_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>,</span><span class=\"param\">\t<span class=\"n\">old_version</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">report_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.diff": {"fullname": "acmc.phen.diff", "modulename": "acmc.phen", "qualname": "diff", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">old_phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">old_version</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud": {"fullname": "acmc.trud", "modulename": "acmc.trud", "kind": "module", "doc": "<p>trud.py module</p>\n\n<p>This module provides functionality to manage installation of the NHS TRUD vocabularies.</p>\n"}, "acmc.trud.FQDN": {"fullname": "acmc.trud.FQDN", "modulename": "acmc.trud", "qualname": "FQDN", "kind": "variable", "doc": "<p>Fully Qualified Domain Name of NHS digital TRUD service API</p>\n", "default_value": "'isd.digital.nhs.uk'"}, "acmc.trud.VOCAB_PATH": {"fullname": "acmc.trud.VOCAB_PATH", "modulename": "acmc.trud", "qualname": "VOCAB_PATH", "kind": "variable", "doc": "<p>Default path to the TRUD vocabulary directory relative to the the acmc execution directory</p>\n", "default_value": "PosixPath('vocab/trud')"}, "acmc.trud.VERSION_FILE": {"fullname": "acmc.trud.VERSION_FILE", "modulename": "acmc.trud", "qualname": "VERSION_FILE", "kind": "variable", "doc": "<p>TRUD version file</p>\n", "default_value": "'trud_version.yml'"}, "acmc.trud.VERSION_PATH": {"fullname": "acmc.trud.VERSION_PATH", "modulename": "acmc.trud", "qualname": "VERSION_PATH", "kind": "variable", "doc": "<p>Default path to the TRUD version file</p>\n", "default_value": "PosixPath('vocab/trud/trud_version.yml')"}, "acmc.trud.DOWNLOADS_PATH": {"fullname": "acmc.trud.DOWNLOADS_PATH", "modulename": "acmc.trud", "qualname": "DOWNLOADS_PATH", "kind": "variable", "doc": "<p>Default path to the TRUD vocabulary downloads directory</p>\n", "default_value": "PosixPath('vocab/trud/downloads')"}, "acmc.trud.PROCESSED_PATH": {"fullname": "acmc.trud.PROCESSED_PATH", "modulename": "acmc.trud", "qualname": "PROCESSED_PATH", "kind": "variable", "doc": "<p>Default path to the processed TRUD mappings directory</p>\n", "default_value": "PosixPath('vocab/trud/processed')"}, "acmc.trud.get_releases": {"fullname": "acmc.trud.get_releases", "modulename": "acmc.trud", "qualname": "get_releases", "kind": "function", "doc": "<p>Retrieve release information for an item from the TRUD API.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">item_id</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">API_KEY</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">latest</span><span class=\"o\">=</span><span class=\"kc\">False</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">list</span>:</span></span>", "funcdef": "def"}, "acmc.trud.download_release_file": {"fullname": "acmc.trud.download_release_file", "modulename": "acmc.trud", "qualname": "download_release_file", "kind": "function", "doc": "<p>Download specified file type for a given release of an item.</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">item_id</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">release_ordinal</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">release</span><span class=\"p\">:</span> <span class=\"nb\">dict</span>,</span><span class=\"param\">\t<span class=\"n\">file_json_prefix</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>:</span></span>", "funcdef": "def"}, "acmc.trud.validate_download_hash": {"fullname": "acmc.trud.validate_download_hash", "modulename": "acmc.trud", "qualname": "validate_download_hash", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">file_destination</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">item_hash</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.unzip_download": {"fullname": "acmc.trud.unzip_download", "modulename": "acmc.trud", "qualname": "unzip_download", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">file_destination</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.extract_icd10": {"fullname": "acmc.trud.extract_icd10", "modulename": "acmc.trud", "qualname": "extract_icd10", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.extract_opsc4": {"fullname": "acmc.trud.extract_opsc4", "modulename": "acmc.trud", "qualname": "extract_opsc4", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.extract_nhs_data_migrations": {"fullname": "acmc.trud.extract_nhs_data_migrations", "modulename": "acmc.trud", "qualname": "extract_nhs_data_migrations", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.extract_nhs_read_browser": {"fullname": "acmc.trud.extract_nhs_read_browser", "modulename": "acmc.trud", "qualname": "extract_nhs_read_browser", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.create_map_directories": {"fullname": "acmc.trud.create_map_directories", "modulename": "acmc.trud", "qualname": "create_map_directories", "kind": "function", "doc": "<p>Create map directories.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.install": {"fullname": "acmc.trud.install", "modulename": "acmc.trud", "qualname": "install", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.util": {"fullname": "acmc.util", "modulename": "acmc.util", "kind": "module", "doc": "<p></p>\n"}, "acmc.util.QuotedDumper": {"fullname": "acmc.util.QuotedDumper", "modulename": "acmc.util", "qualname": "QuotedDumper", "kind": "class", "doc": "<p>Custom Dumper to retain quotes on strings in yaml library</p>\n", "bases": "yaml.dumper.Dumper"}, "acmc.util.QuotedDumper.increase_indent": {"fullname": "acmc.util.QuotedDumper.increase_indent", "modulename": "acmc.util", "qualname": "QuotedDumper.increase_indent", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"bp\">self</span>, </span><span class=\"param\"><span class=\"n\">flow</span><span class=\"o\">=</span><span class=\"kc\">False</span>, </span><span class=\"param\"><span class=\"n\">indentless</span><span class=\"o\">=</span><span class=\"kc\">False</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}}, "docInfo": {"acmc": {"qualname": 0, "fullname": 1, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.logging_config": {"qualname": 0, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 20}, "acmc.logging_config.DEFAULT_LOG_FILE": {"qualname": 3, "fullname": 6, "annotation": 0, "default_value": 6, "signature": 0, "bases": 0, "doc": 9}, "acmc.logging_config.setup_logger": {"qualname": 2, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 24, "bases": 0, "doc": 16}, "acmc.logging_config.set_log_level": {"qualname": 3, "fullname": 6, "annotation": 0, "default_value": 0, "signature": 17, "bases": 0, "doc": 33}, "acmc.main": {"qualname": 0, "fullname": 2, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 18}, "acmc.main.DEFAULT_WORKSPACE_PATH": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 6}, "acmc.main.main": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 7, "bases": 0, "doc": 3}, "acmc.omop": {"qualname": 0, "fullname": 2, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 16}, "acmc.omop.VOCAB_PATH": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 6}, "acmc.omop.OMOP_CDM_Version": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 7}, "acmc.omop.OMOP_DB_FILENAME": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 7, "signature": 0, "bases": 0, "doc": 7}, "acmc.omop.DB_PATH": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 7, "signature": 0, "bases": 0, "doc": 7}, "acmc.omop.VERSION_FILE": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 7, "signature": 0, "bases": 0, "doc": 6}, "acmc.omop.VERSION_PATH": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 7, "signature": 0, "bases": 0, "doc": 6}, "acmc.omop.EXPORT_FILE": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 8, "signature": 0, "bases": 0, "doc": 7}, "acmc.omop.vocabularies": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 202, "signature": 0, "bases": 0, "doc": 6}, "acmc.omop.omop_vocab_types": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 51, "signature": 0, "bases": 0, "doc": 13}, "acmc.omop.install": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 28, "bases": 0, "doc": 96}, "acmc.omop.write_version_file": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 16, "bases": 0, "doc": 33}, "acmc.omop.clear": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 22, "bases": 0, "doc": 49}, "acmc.omop.delete": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 22, "bases": 0, "doc": 49}, "acmc.omop.table_exists": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 35, "bases": 0, "doc": 55}, "acmc.omop.vocab_exists": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 35, "bases": 0, "doc": 56}, "acmc.omop.concept_set_exist": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 36, "bases": 0, "doc": 59}, "acmc.omop.export": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 71, "bases": 0, "doc": 104}, "acmc.parse": {"qualname": 0, "fullname": 2, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 18}, "acmc.parse.SUPPORTED_CODE_TYPES": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 20, "signature": 0, "bases": 0, "doc": 8}, "acmc.parse.CodesError": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 17}, "acmc.parse.CodesError.__init__": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 51, "bases": 0, "doc": 3}, "acmc.parse.InvalidCodesException": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 2, "doc": 17}, "acmc.parse.InvalidCodesException.__init__": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 9, "bases": 0, "doc": 3}, "acmc.parse.InvalidCodesException.error": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Proto": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 59}, "acmc.parse.Proto.__init__": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 44, "bases": 0, "doc": 3}, "acmc.parse.Proto.checks": {"qualname": 2, "fullname": 4, "annotation": 22, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Proto.name": {"qualname": 2, "fullname": 4, "annotation": 2, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Proto.raise_exception": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 36}, "acmc.parse.Proto.in_database": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 93, "bases": 0, "doc": 3}, "acmc.parse.Proto.process": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 85, "bases": 0, "doc": 14}, "acmc.parse.Proto.verify": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 52, "bases": 0, "doc": 7}, "acmc.parse.Read2": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 1, "doc": 40}, "acmc.parse.Read2.checks": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Read3": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 1, "doc": 59}, "acmc.parse.Read3.checks": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Icd10": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 1, "doc": 59}, "acmc.parse.Icd10.checks": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Snomed": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 1, "doc": 59}, "acmc.parse.Snomed.checks": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Opcs4": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 1, "doc": 59}, "acmc.parse.Opcs4.checks": {"qualname": 2, "fullname": 4, 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"i": {"docs": {}, "df": 0, "f": {"docs": {}, "df": 0, "i": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "d": {"docs": {"acmc.trud.FQDN": {"tf": 1}}, "df": 1}}}}}}}, "o": {"docs": {}, "df": 0, "t": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "s": {"docs": {"acmc.util.QuotedDumper": {"tf": 1}}, "df": 1}}}}}}, "y": {"docs": {}, "df": 0, "m": {"docs": {}, "df": 0, "l": {"docs": {"acmc.phen.CONFIG_SCHEMA": {"tf": 1}}, "df": 1}}, "a": {"docs": {}, "df": 0, "m": {"docs": {}, "df": 0, "l": {"docs": {"acmc.util.QuotedDumper": {"tf": 1}}, "df": 1}}}}, "g": {"docs": {}, "df": 0, "i": {"docs": {}, "df": 0, "t": {"docs": {"acmc.phen.init": {"tf": 1}, "acmc.phen.fork": {"tf": 1}, "acmc.phen.validate": {"tf": 1}}, "df": 3}, "v": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "n": {"docs": {"acmc.trud.download_release_file": {"tf": 1}}, "df": 1}}}}}}}}, "pipeline": ["trimmer"], "_isPrebuiltIndex": true};
// mirrored in build-search-index.js (part 1)
// Also split on html tags. this is a cheap heuristic, but good enough.
elasticlunr.tokenizer.setSeperator(/[\s\-.;&_'"=,()]+|<[^>]*>/);
let searchIndex;
if (docs._isPrebuiltIndex) {
console.info("using precompiled search index");
searchIndex = elasticlunr.Index.load(docs);
} else {
console.time("building search index");
// mirrored in build-search-index.js (part 2)
searchIndex = elasticlunr(function () {
this.pipeline.remove(elasticlunr.stemmer);
this.pipeline.remove(elasticlunr.stopWordFilter);
this.addField("qualname");
this.addField("fullname");
this.addField("annotation");
this.addField("default_value");
this.addField("signature");
this.addField("bases");
this.addField("doc");
this.setRef("fullname");
});
for (let doc of docs) {
searchIndex.addDoc(doc);
}
console.timeEnd("building search index");
}
return (term) => searchIndex.search(term, {
fields: {
qualname: {boost: 4},
fullname: {boost: 2},
annotation: {boost: 2},
default_value: {boost: 2},
signature: {boost: 2},
bases: {boost: 2},
doc: {boost: 1},
},
expand: true
});
})();