From ce549dcec8356c0d243e82afda178e5f887f0538 Mon Sep 17 00:00:00 2001 From: adhemar Date: Fri, 10 Jan 2025 14:16:20 -0300 Subject: [PATCH 1/2] update docs --- docs/html/.buildinfo | 4 +- docs/html/.doctrees/cache.doctree | Bin 6568 -> 6600 bytes docs/html/.doctrees/dataload.doctree | Bin 4170 -> 4202 bytes docs/html/.doctrees/diagrams.doctree | Bin 5948 -> 5981 bytes docs/html/.doctrees/environment.pickle | Bin 354450 -> 56359 bytes docs/html/.doctrees/index.doctree | Bin 5639 -> 5672 bytes docs/html/.doctrees/index_search.doctree | Bin 13263 -> 13297 bytes docs/html/.doctrees/insert_organism.doctree | Bin 6172 -> 6206 bytes docs/html/.doctrees/installation.doctree | Bin 14688 -> 14321 bytes docs/html/.doctrees/jbrowse.doctree | Bin 20063 -> 20100 bytes docs/html/.doctrees/load_blast.doctree | Bin 14034 -> 14069 bytes docs/html/.doctrees/load_coexpression.doctree | Bin 20450 -> 20484 bytes docs/html/.doctrees/load_fasta.doctree | Bin 10665 -> 10699 bytes .../.doctrees/load_feature_annotation.doctree | Bin 21081 -> 21117 bytes docs/html/.doctrees/load_gff.doctree | Bin 11249 -> 11285 bytes docs/html/.doctrees/load_interproscan.doctree | Bin 13293 -> 13328 bytes docs/html/.doctrees/load_ontologies.doctree | Bin 10709 -> 10751 bytes docs/html/.doctrees/load_orthomcl.doctree | Bin 7389 -> 7422 bytes docs/html/.doctrees/load_publication.doctree | Bin 5028 -> 5061 bytes docs/html/.doctrees/load_rnaseq.doctree | Bin 24733 -> 24803 bytes docs/html/.doctrees/load_taxonomy.doctree | Bin 8846 -> 8883 bytes docs/html/.doctrees/load_vcf.doctree | Bin 9056 -> 9090 bytes docs/html/.doctrees/models.doctree | Bin 13080 -> 13113 bytes docs/html/.doctrees/visualization.doctree | Bin 3188 -> 3220 bytes docs/html/.doctrees/webserver.doctree | Bin 11507 -> 11543 bytes docs/html/_sources/installation.rst.txt | 8 +- docs/html/_static/basic.css | 15 +- docs/html/_static/css/badge_only.css | 2 +- docs/html/_static/css/theme.css | 2 +- docs/html/_static/doctools.js | 7 - docs/html/_static/language_data.js | 9 +- docs/html/_static/pygments.css | 66 +++--- docs/html/_static/searchtools.js | 200 +++++++++++------- docs/html/cache.html | 24 +-- docs/html/dataload.html | 24 +-- docs/html/diagrams.html | 24 +-- docs/html/genindex.html | 22 +- docs/html/index.html | 24 +-- docs/html/index_search.html | 24 +-- docs/html/insert_organism.html | 24 +-- docs/html/installation.html | 32 ++- docs/html/jbrowse.html | 24 +-- docs/html/load_blast.html | 24 +-- docs/html/load_coexpression.html | 24 +-- docs/html/load_fasta.html | 24 +-- docs/html/load_feature_annotation.html | 24 +-- docs/html/load_gff.html | 24 +-- docs/html/load_interproscan.html | 24 +-- docs/html/load_ontologies.html | 24 +-- docs/html/load_orthomcl.html | 24 +-- docs/html/load_publication.html | 24 +-- docs/html/load_rnaseq.html | 24 +-- docs/html/load_taxonomy.html | 24 +-- docs/html/load_vcf.html | 24 +-- docs/html/models.html | 24 +-- docs/html/search.html | 24 +-- docs/html/searchindex.js | 2 +- docs/html/visualization.html | 24 +-- docs/html/webserver.html | 24 +-- docs/source/installation.rst | 8 +- setup.py | 2 +- 61 files changed, 479 insertions(+), 452 deletions(-) diff --git a/docs/html/.buildinfo b/docs/html/.buildinfo index 97ccb854..dc839549 100644 --- a/docs/html/.buildinfo +++ b/docs/html/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 -# This file hashes the configuration used when building these files. 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:copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * */ var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; -/* Non-minified version is copied as a separate JS file, is available */ +/* Non-minified version is copied as a separate JS file, if available */ /** * Porter Stemmer diff --git a/docs/html/_static/pygments.css b/docs/html/_static/pygments.css index 0d49244e..5f2b0a25 100644 --- a/docs/html/_static/pygments.css +++ b/docs/html/_static/pygments.css @@ -6,26 +6,26 @@ span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: .highlight .hll { background-color: #ffffcc } .highlight { background: #eeffcc; } .highlight .c { color: #408090; font-style: italic } /* Comment */ -.highlight .err { border: 1px solid #FF0000 } /* Error */ +.highlight .err { border: 1px solid #F00 } /* Error */ .highlight .k { color: #007020; font-weight: bold } /* Keyword */ -.highlight .o { color: #666666 } /* Operator */ +.highlight .o { color: #666 } /* Operator */ .highlight .ch { color: #408090; font-style: italic } /* Comment.Hashbang */ .highlight .cm { color: #408090; font-style: italic } /* Comment.Multiline */ .highlight .cp { color: #007020 } /* Comment.Preproc */ .highlight .cpf { color: #408090; font-style: italic } /* Comment.PreprocFile */ .highlight .c1 { color: #408090; font-style: italic } /* Comment.Single */ -.highlight .cs { color: #408090; background-color: #fff0f0 } /* Comment.Special */ +.highlight .cs { color: #408090; background-color: #FFF0F0 } /* Comment.Special */ .highlight .gd { color: #A00000 } /* Generic.Deleted */ .highlight .ge { font-style: italic } /* Generic.Emph */ .highlight .ges { font-weight: bold; font-style: italic } /* Generic.EmphStrong */ -.highlight .gr { color: #FF0000 } /* Generic.Error */ +.highlight .gr { color: #F00 } /* Generic.Error */ .highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */ .highlight .gi { color: #00A000 } /* Generic.Inserted */ -.highlight .go { color: #333333 } /* Generic.Output */ -.highlight .gp { color: #c65d09; font-weight: bold } /* Generic.Prompt */ +.highlight .go { color: #333 } /* Generic.Output */ +.highlight .gp { color: #C65D09; font-weight: bold } /* Generic.Prompt */ .highlight .gs { font-weight: bold } /* Generic.Strong */ .highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */ -.highlight .gt { color: #0044DD } /* Generic.Traceback */ +.highlight .gt { color: #04D } /* Generic.Traceback */ .highlight .kc { color: #007020; font-weight: bold } /* Keyword.Constant */ .highlight .kd { color: #007020; font-weight: bold } /* Keyword.Declaration */ .highlight .kn { color: #007020; font-weight: bold } /* Keyword.Namespace */ @@ -33,43 +33,43 @@ span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: .highlight .kr { color: #007020; font-weight: bold } /* Keyword.Reserved */ .highlight .kt { color: #902000 } /* Keyword.Type */ .highlight .m { color: #208050 } /* Literal.Number */ -.highlight .s { color: #4070a0 } /* Literal.String */ -.highlight .na { color: #4070a0 } /* Name.Attribute */ +.highlight .s { color: #4070A0 } /* Literal.String */ +.highlight .na { color: #4070A0 } /* Name.Attribute */ .highlight .nb { color: #007020 } /* Name.Builtin */ -.highlight .nc { color: #0e84b5; font-weight: bold } /* Name.Class */ -.highlight .no { color: #60add5 } /* Name.Constant */ -.highlight .nd { color: #555555; font-weight: bold } /* Name.Decorator */ -.highlight .ni { color: #d55537; font-weight: bold } /* Name.Entity */ +.highlight .nc { color: #0E84B5; font-weight: bold } /* Name.Class */ +.highlight .no { color: #60ADD5 } /* Name.Constant */ +.highlight .nd { color: #555; font-weight: bold } /* Name.Decorator */ +.highlight 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color: #bb60d5 } /* Name.Variable.Instance */ -.highlight .vm { color: #bb60d5 } /* Name.Variable.Magic */ +.highlight .fm { color: #06287E } /* Name.Function.Magic */ +.highlight .vc { color: #BB60D5 } /* Name.Variable.Class */ +.highlight .vg { color: #BB60D5 } /* Name.Variable.Global */ +.highlight .vi { color: #BB60D5 } /* Name.Variable.Instance */ +.highlight .vm { color: #BB60D5 } /* Name.Variable.Magic */ .highlight .il { color: #208050 } /* Literal.Number.Integer.Long */ \ No newline at end of file diff --git a/docs/html/_static/searchtools.js b/docs/html/_static/searchtools.js index 7918c3fa..2c774d17 100644 --- a/docs/html/_static/searchtools.js +++ b/docs/html/_static/searchtools.js @@ -1,12 +1,5 @@ /* - * searchtools.js - * ~~~~~~~~~~~~~~~~ - * * Sphinx JavaScript utilities for the full-text search. - * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * */ "use strict"; @@ -20,7 +13,7 @@ if (typeof Scorer === "undefined") { // and returns the new score. /* score: result => { - const [docname, title, anchor, descr, score, filename] = result + const [docname, title, anchor, descr, score, filename, kind] = result return score }, */ @@ -47,6 +40,14 @@ if (typeof Scorer === "undefined") { }; } +// Global search result kind enum, used by themes to style search results. +class SearchResultKind { + static get index() { return "index"; } + static get object() { return "object"; } + static get text() { return "text"; } + static get title() { return "title"; } +} + const _removeChildren = (element) => { while (element && element.lastChild) element.removeChild(element.lastChild); }; @@ -64,9 +65,13 @@ const _displayItem = (item, searchTerms, highlightTerms) => { const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; const contentRoot = document.documentElement.dataset.content_root; - const [docName, title, anchor, descr, score, _filename] = item; + const [docName, title, anchor, descr, score, _filename, kind] = item; let listItem = document.createElement("li"); + // Add a class representing the item's type: + // can be used by a theme's CSS selector for styling + // See SearchResultKind for the class names. + listItem.classList.add(`kind-${kind}`); let requestUrl; let linkUrl; if (docBuilder === "dirhtml") { @@ -99,7 +104,7 @@ const _displayItem = (item, searchTerms, highlightTerms) => { .then((data) => { if (data) listItem.appendChild( - Search.makeSearchSummary(data, searchTerms) + Search.makeSearchSummary(data, searchTerms, anchor) ); // highlight search terms in the summary if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js @@ -115,9 +120,11 @@ const _finishSearch = (resultCount) => { "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." ); else - Search.status.innerText = _( - `Search finished, found ${resultCount} page(s) matching the search query.` - ); + Search.status.innerText = Documentation.ngettext( + "Search finished, found one page matching the search query.", + "Search finished, found ${resultCount} pages matching the search query.", + resultCount, + ).replace('${resultCount}', resultCount); }; const _displayNextItem = ( results, @@ -137,6 +144,22 @@ const _displayNextItem = ( // search finished, update title and status message else _finishSearch(resultCount); }; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; /** * Default splitQuery function. Can be overridden in ``sphinx.search`` with a @@ -160,13 +183,26 @@ const Search = { _queued_query: null, _pulse_status: -1, - htmlToText: (htmlString) => { + htmlToText: (htmlString, anchor) => { const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + for (const removalQuery of [".headerlink", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent !== undefined) return docContent.textContent; + if (docContent) return docContent.textContent; + console.warn( - "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." ); return ""; }, @@ -219,6 +255,7 @@ const Search = { searchSummary.classList.add("search-summary"); searchSummary.innerText = ""; const searchList = document.createElement("ul"); + searchList.setAttribute("role", "list"); searchList.classList.add("search"); const out = document.getElementById("search-results"); @@ -239,16 +276,7 @@ const Search = { else Search.deferQuery(query); }, - /** - * execute search (requires search index to be loaded) - */ - query: (query) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - + _parseQuery: (query) => { // stem the search terms and add them to the correct list const stemmer = new Stemmer(); const searchTerms = new Set(); @@ -284,22 +312,40 @@ const Search = { // console.info("required: ", [...searchTerms]); // console.info("excluded: ", [...excludedTerms]); - // array of [docname, title, anchor, descr, score, filename] - let results = []; + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename, kind]. + const normalResults = []; + const nonMainIndexResults = []; + _removeChildren(document.getElementById("search-progress")); - const queryLower = query.toLowerCase(); + const queryLower = query.toLowerCase().trim(); for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { for (const [file, id] of foundTitles) { - let score = Math.round(100 * queryLower.length / title.length) - results.push([ + const score = Math.round(Scorer.title * queryLower.length / title.length); + const boost = titles[file] === title ? 1 : 0; // add a boost for document titles + normalResults.push([ docNames[file], titles[file] !== title ? `${titles[file]} > ${title}` : title, id !== null ? "#" + id : "", null, - score, + score + boost, filenames[file], + SearchResultKind.title, ]); } } @@ -308,46 +354,48 @@ const Search = { // search for explicit entries in index directives for (const [entry, foundEntries] of Object.entries(indexEntries)) { if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id] of foundEntries) { - let score = Math.round(100 * queryLower.length / entry.length) - results.push([ + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ docNames[file], titles[file], id ? "#" + id : "", null, score, filenames[file], - ]); + SearchResultKind.index, + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } } } } // lookup as object objectTerms.forEach((term) => - results.push(...Search.performObjectSearch(term, objectTerms)) + normalResults.push(...Search.performObjectSearch(term, objectTerms)) ); // lookup as search terms in fulltext - results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); // let the scorer override scores with a custom scoring function - if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); - - // now sort the results by score (in opposite order of appearance, since the - // display function below uses pop() to retrieve items) and then - // alphabetically - results.sort((a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; - }); + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; // remove duplicate search results // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept @@ -361,7 +409,12 @@ const Search = { return acc; }, []); - results = results.reverse(); + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); // for debugging //Search.lastresults = results.slice(); // a copy @@ -432,6 +485,7 @@ const Search = { descr, score, filenames[match[0]], + SearchResultKind.object, ]); }; Object.keys(objects).forEach((prefix) => @@ -466,14 +520,18 @@ const Search = { // add support for partial matches if (word.length > 2) { const escapedWord = _escapeRegExp(word); - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord) && !terms[word]) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord) && !titleTerms[word]) - arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); - }); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } } // no match but word was a required one @@ -496,9 +554,8 @@ const Search = { // create the mapping files.forEach((file) => { - if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) - fileMap.get(file).push(word); - else fileMap.set(file, [word]); + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); }); }); @@ -539,6 +596,7 @@ const Search = { null, score, filenames[file], + SearchResultKind.text, ]); } return results; @@ -549,8 +607,8 @@ const Search = { * search summary for a given text. keywords is a list * of stemmed words. */ - makeSearchSummary: (htmlText, keywords) => { - const text = Search.htmlToText(htmlText); + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); if (text === "") return null; const textLower = text.toLowerCase(); diff --git a/docs/html/cache.html b/docs/html/cache.html index a430a9ff..9ca7b9e2 100644 --- a/docs/html/cache.html +++ b/docs/html/cache.html @@ -1,21 +1,21 @@ + + - + - + 3.4. Cache (optional) — machado 0.1.0 documentation - - - + + + - - - - - + + + + + diff --git a/docs/html/dataload.html b/docs/html/dataload.html index 0b93db82..3f90af21 100644 --- a/docs/html/dataload.html +++ b/docs/html/dataload.html @@ -1,21 +1,21 @@ + + - + - + 2. Data loading — machado 0.1.0 documentation - - - + + + - - - - - + + + + + diff --git a/docs/html/diagrams.html b/docs/html/diagrams.html index f7f91746..c1cac1c7 100644 --- a/docs/html/diagrams.html +++ b/docs/html/diagrams.html @@ -1,21 +1,21 @@ + + - + - + 4. Diagrams — machado 0.1.0 documentation - - - + + + - - - - - + + + + + diff --git a/docs/html/genindex.html b/docs/html/genindex.html index 9d6eb897..0f13efe6 100644 --- a/docs/html/genindex.html +++ b/docs/html/genindex.html @@ -1,20 +1,20 @@ + + - + Index — machado 0.1.0 documentation - - - + + + - - - - - + + + + + diff --git a/docs/html/index.html b/docs/html/index.html index 6621ec27..be9ab0da 100644 --- a/docs/html/index.html +++ b/docs/html/index.html @@ -1,21 +1,21 @@ + + - + - + machado’s documentation — machado 0.1.0 documentation - - - + + + - - - - - + + + + + diff --git a/docs/html/index_search.html b/docs/html/index_search.html index 34997f94..d3f7ad9c 100644 --- a/docs/html/index_search.html +++ b/docs/html/index_search.html @@ -1,21 +1,21 @@ + + - + - + 3.1. Index and search — machado 0.1.0 documentation - - - + + + - - - - - + + + + + diff --git a/docs/html/insert_organism.html b/docs/html/insert_organism.html index 8d6111d4..3cf9d428 100644 --- a/docs/html/insert_organism.html +++ b/docs/html/insert_organism.html @@ -1,21 +1,21 @@ + + - + - + 2.3. Inserting a new organism — machado 0.1.0 documentation - - - + + + - - - - - + + + + + diff --git a/docs/html/installation.html b/docs/html/installation.html index a54d2c9e..7847c9b5 100644 --- a/docs/html/installation.html +++ b/docs/html/installation.html @@ -1,21 +1,21 @@ + + - + - + 1. Installation — machado 0.1.0 documentation - - - + + + - - - - - + + + + + @@ -95,9 +95,9 @@

1.1. Prerequisite
sudo apt install zlib1g-dev libbz2-dev liblzma-dev python3-dev
-

Python 3.8

+

Python 3.12

We strongly recommend creating a new virtualenv for your project

-
virtualenv -p /usr/bin/python3.8 YOURPROJECT
+
virtualenv -p /usr/bin/python3.12 YOURPROJECT
 cd YOURPROJECT
 source bin/activate
 

@@ -114,8 +114,7 @@ 
1.2. PreparationFrom this point on it is assumed you have read the Django introduction and tutorial on the Django project website.

 
Create a Django project

 
Inside YOURPROJECT directory create a Django project with the following command:

-
django-admin startproject WEBPROJECT
-cd WEBPROJECT
+
django-admin startproject WEBPROJECT .
 

 

 
Then, configure the WEBPROJECT/settings.py file to connect to your Chado database.

@@ -162,7 +161,6 @@ 
1.3. Start you app and open the admin in
 
python manage.py runserver
 

 

-
The API interface will be available at http://localhost:8000/machado/api

 
 

 
1.4. References

diff --git a/docs/html/jbrowse.html b/docs/html/jbrowse.html
index 8daf2f13..66f185f8 100644
--- a/docs/html/jbrowse.html
+++ b/docs/html/jbrowse.html
@@ -1,21 +1,21 @@
+
+
 
-
+
 
-  
+  
 
   
   3.3. JBrowse (optional) — machado 0.1.0 documentation
-      
-      
-  
+      
+      
+
   
-        
-        
-        
-        
-        
+      
+      
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+      
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diff --git a/docs/html/load_blast.html b/docs/html/load_blast.html
index 7be18abe..ae1661fa 100644
--- a/docs/html/load_blast.html
+++ b/docs/html/load_blast.html
@@ -1,21 +1,21 @@
+
+
 
-
+
 
-  
+  
 
   
   2.8. Loading Blast results — machado 0.1.0 documentation
-      
-      
-  
+      
+      
+
   
-        
-        
-        
-        
-        
+      
+      
+      
+      
+      
     
     
     
diff --git a/docs/html/load_coexpression.html b/docs/html/load_coexpression.html
index 801214f8..a9ee9e73 100644
--- a/docs/html/load_coexpression.html
+++ b/docs/html/load_coexpression.html
@@ -1,21 +1,21 @@
+
+
 
-
+
 
-  
+  
 
   
   2.12. Loading Coexpression analyzes — machado 0.1.0 documentation
-      
-      
-  
+      
+      
+
   
-        
-        
-        
-        
-        
+      
+      
+      
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diff --git a/docs/html/load_fasta.html b/docs/html/load_fasta.html
index 68ffa8d0..45ba2e99 100644
--- a/docs/html/load_fasta.html
+++ b/docs/html/load_fasta.html
@@ -1,21 +1,21 @@
+
+
 
-
+
 
-  
+  
 
   
   2.5. Loading FASTA files — machado 0.1.0 documentation
-      
-      
-  
+      
+      
+
   
-        
-        
-        
-        
-        
+      
+      
+      
+      
+      
     
     
     
diff --git a/docs/html/load_feature_annotation.html b/docs/html/load_feature_annotation.html
index 56782035..eccdb4e3 100644
--- a/docs/html/load_feature_annotation.html
+++ b/docs/html/load_feature_annotation.html
@@ -1,21 +1,21 @@
+
+
 
-
+
 
-  
+  
 
   
   2.7. Loading Feature Additional Info — machado 0.1.0 documentation
-      
-      
-  
+      
+      
+
   
-        
-        
-        
-        
-        
+      
+      
+      
+      
+      
     
     
     
diff --git a/docs/html/load_gff.html b/docs/html/load_gff.html
index 50bd95b6..b85b9c8b 100644
--- a/docs/html/load_gff.html
+++ b/docs/html/load_gff.html
@@ -1,21 +1,21 @@
+
+
 
-
+
 
-  
+  
 
   
   2.6. Loading GFF files — machado 0.1.0 documentation
-      
-      
-  
+      
+      
+
   
-        
-        
-        
-        
-        
+      
+      
+      
+      
+      
     
     
     
diff --git a/docs/html/load_interproscan.html b/docs/html/load_interproscan.html
index 21ab0778..f195a5c1 100644
--- a/docs/html/load_interproscan.html
+++ b/docs/html/load_interproscan.html
@@ -1,21 +1,21 @@
+
+
 
-
+
 
-  
+  
 
   
   2.9. Loading InterproScan results — machado 0.1.0 documentation
-      
-      
-  
+      
+      
+
   
-        
-        
-        
-        
-        
+      
+      
+      
+      
+      
     
     
     
diff --git a/docs/html/load_ontologies.html b/docs/html/load_ontologies.html
index 1db28886..593d9b5a 100644
--- a/docs/html/load_ontologies.html
+++ b/docs/html/load_ontologies.html
@@ -1,21 +1,21 @@
+
+
 
-
+
 
-  
+  
 
   
   2.1. Loading ontologies — machado 0.1.0 documentation
-      
-      
-  
+      
+      
+
   
-        
-        
-        
-        
-        
+      
+      
+      
+      
+      
     
     
     
diff --git a/docs/html/load_orthomcl.html b/docs/html/load_orthomcl.html
index 875c6b49..a963eb7b 100644
--- a/docs/html/load_orthomcl.html
+++ b/docs/html/load_orthomcl.html
@@ -1,21 +1,21 @@
+
+
 
-
+
 
-  
+  
 
   
   2.10. Loading OrthoMCL results — machado 0.1.0 documentation
-      
-      
-  
+      
+      
+
   
-        
-        
-        
-        
-        
+      
+      
+      
+      
+      
     
     
     
diff --git a/docs/html/load_publication.html b/docs/html/load_publication.html
index 8f6e75f2..c4a4d2b1 100644
--- a/docs/html/load_publication.html
+++ b/docs/html/load_publication.html
@@ -1,21 +1,21 @@
+
+
 
-
+
 
-  
+  
 
   
   2.4. Loading publication files — machado 0.1.0 documentation
-      
-      
-  
+      
+      
+
   
-        
-        
-        
-        
-        
+      
+      
+      
+      
+      
     
     
     
diff --git a/docs/html/load_rnaseq.html b/docs/html/load_rnaseq.html
index 518da92b..6be44553 100644
--- a/docs/html/load_rnaseq.html
+++ b/docs/html/load_rnaseq.html
@@ -1,21 +1,21 @@
+
+
 
-
+
 
-  
+  
 
   
   2.11. Loading RNA-seq data — machado 0.1.0 documentation
-      
-      
-  
+      
+      
+
   
-        
-        
-        
-        
-        
+      
+      
+      
+      
+      
     
     
     
diff --git a/docs/html/load_taxonomy.html b/docs/html/load_taxonomy.html
index d1462f3b..03f1fe94 100644
--- a/docs/html/load_taxonomy.html
+++ b/docs/html/load_taxonomy.html
@@ -1,21 +1,21 @@
+
+
 
-
+
 
-  
+  
 
   
   2.2. Loading taxonomy — machado 0.1.0 documentation
-      
-      
-  
+      
+      
+
   
-        
-        
-        
-        
-        
+      
+      
+      
+      
+      
     
     
     
diff --git a/docs/html/load_vcf.html b/docs/html/load_vcf.html
index 6b756f38..affa1e58 100644
--- a/docs/html/load_vcf.html
+++ b/docs/html/load_vcf.html
@@ -1,21 +1,21 @@
+
+
 
-
+
 
-  
+  
 
   
   2.13. Loading VCF files — machado 0.1.0 documentation
-      
-      
-  
+      
+      
+
   
-        
-        
-        
-        
-        
+      
+      
+      
+      
+      
     
     
     
diff --git a/docs/html/models.html b/docs/html/models.html
index 449a61b2..08d1e4d3 100644
--- a/docs/html/models.html
+++ b/docs/html/models.html
@@ -1,21 +1,21 @@
+
+
 
-
+
 
-  
+  
 
   
   5. Models — machado 0.1.0 documentation
-      
-      
-  
+      
+      
+
   
-        
-        
-        
-        
-        
+      
+      
+      
+      
+      
     
     
     
diff --git a/docs/html/search.html b/docs/html/search.html
index 1c437767..107d145b 100644
--- a/docs/html/search.html
+++ b/docs/html/search.html
@@ -1,21 +1,21 @@
+
+
 
-
+
 
   
   
   Search — machado 0.1.0 documentation
-      
-      
-    
-  
+      
+      
+
   
-        
-        
-        
-        
-        
+    
+      
+      
+      
+      
+      
     
     
     
diff --git a/docs/html/searchindex.js b/docs/html/searchindex.js
index a4e4e9b4..c1df4f6f 100644
--- a/docs/html/searchindex.js
+++ b/docs/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["cache", "dataload", "diagrams", "index", "index_search", "insert_organism", "installation", "jbrowse", "load_blast", "load_coexpression", "load_fasta", "load_feature_annotation", "load_gff", "load_interproscan", "load_ontologies", "load_orthomcl", "load_publication", "load_rnaseq", "load_taxonomy", "load_vcf", "models", "visualization", "webserver"], "filenames": ["cache.rst", "dataload.rst", "diagrams.rst", "index.rst", "index_search.rst", "insert_organism.rst", "installation.rst", "jbrowse.rst", "load_blast.rst", "load_coexpression.rst", "load_fasta.rst", "load_feature_annotation.rst", "load_gff.rst", "load_interproscan.rst", "load_ontologies.rst", "load_orthomcl.rst", "load_publication.rst", "load_rnaseq.rst", "load_taxonomy.rst", "load_vcf.rst", "models.rst", "visualization.rst", "webserver.rst"], "titles": ["3.4. Cache (optional)", "2. Data loading", "4. Diagrams", "machado\u2019s documentation", "3.1. Index and search", "2.3. Inserting a new organism", "1. Installation", "3.3. JBrowse (optional)", "2.8. Loading Blast results", "2.12. Loading Coexpression analyzes", "2.5. Loading FASTA files", "2.7. Loading Feature Additional Info", "2.6. Loading GFF files", "2.9. Loading InterproScan results", "2.1. Loading ontologies", "2.10. Loading OrthoMCL results", "2.4. Loading publication files", "2.11. Loading RNA-seq data", "2.2. Loading taxonomy", "2.13. Loading VCF files", "5. Models", "3. Visualization", "3.2. 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"htslib": [12, 19], "http": [0, 2, 4, 6, 7, 12, 14, 18, 19, 20, 22], "i": [0, 2, 3, 4, 5, 6, 7, 9, 10, 12, 14, 17, 18, 19, 22], "id": [9, 12, 19], "idea": 0, "identifi": 17, "ignor": 12, "includ": [0, 5], "increas": [4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19], "index": [3, 7, 12, 19, 21], "index_nam": 4, "indexedfasta": 7, "individu": [9, 18], "ineditu": 5, "info": [1, 3, 5, 10, 17], "inform": 6, "input": [9, 17, 20], "insert": [17, 18], "insert_organ": [5, 18], "insid": [1, 6, 7, 20], "inspectdb": 20, "instal": [0, 3, 4, 7, 20, 21, 22], "installed_app": [0, 4, 6], "instanc": 7, "instruct": [0, 2, 4, 5, 7, 18], "integ": 17, "integr": 1, "intent": 0, "interact": 3, "interest": 17, "interfac": 21, "interproscan": [1, 3], "interproscan_result": 13, "intro": 6, "introduct": 6, "involv": 9, "io": 2, "issu": [7, 10], "its": [7, 9], "itself": [8, 11], "j": 7, "java": 4, "jbrows": [3, 10, 21], "jdk": 4, "json": [4, 7], "just": [0, 6, 7, 20], "k": 4, "kei": [7, 20], "kinas": 22, "know": 6, "label": 7, "later": 4, "latest": [2, 4], "leaf": 17, "leav": 17, "let": 6, "libapache2": 22, "libbz2": 6, "liblzma": 6, "librari": 22, "like": 8, "limit": 4, "line": [1, 4, 7, 9, 17], "lineag": 18, "lingo": 17, "link": [4, 17], "linux": 6, "list": [6, 12, 20], "ll": [0, 5, 10, 14, 18], "lmb": [6, 20], "ln": 22, "load": [3, 4, 5, 6, 7, 20], "load_coexpression_clust": 9, "load_coexpression_pair": 9, "load_fasta": 10, "load_feature_annot": 11, "load_feature_dbxref": 11, "load_feature_publ": 11, "load_feature_sequ": 11, "load_gene_ontologi": 14, "load_gff": 12, "load_organ": 18, "load_orthomcl": 15, "load_phylotre": 18, "load_publ": [10, 11, 12, 16, 19], "load_relations_ontologi": 14, "load_rnaseq_data": 17, "load_rnaseq_info": 17, "load_sequence_ontologi": 14, "load_similar": [8, 13], "load_similarity_match": [8, 13], "load_vcf": 19, "local": 0, "localhost": [4, 6, 7, 20, 22], "locat": 0, "long": [7, 10, 18], "look": 5, "lstrap": [9, 17], "machado": [0, 4, 6, 7, 9, 17, 20, 21, 22], "machado_cache_t": 0, "machado_example_aa": 22, "machado_example_aa_acc": 22, "machado_example_na": 22, "machado_example_txt": 22, "machado_jbrowse_offset": 7, "machado_jbrowse_track": 7, "machado_jbrowse_url": 7, "machado_offset": 7, "machado_url": 22, "machado_valid_typ": [4, 22], "made": [0, 4], "mai": [7, 10, 17], "make": [7, 17, 22], "manag": [0, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20], "mandatori": [9, 17], "mani": 7, "manner": 9, "match": 8, "max": 7, "max_result_window": 4, "mcl": 9, "memori": [0, 7, 10], "might": [1, 4], "migrat": 6, "mkdir": 7, "mod": 22, "model": 3, "modif": [7, 22], "modifi": [0, 7], "modul": [7, 22], "molecular": 18, "molecular_funct": 14, "more": 18, "most": [4, 5, 10, 14, 18], "mostli": 10, "move": 0, "mrna": [4, 8, 9, 11, 22], "mu": [9, 10, 11, 12, 15, 19], "multispeci": [8, 13], "musculu": [9, 10, 11, 12, 15, 19], "must": [1, 5, 7, 8, 9, 11, 12, 13, 14, 17, 18, 19, 22], "mv": 7, "n": 17, "name": [1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20], "ncbi": [5, 8, 17], "ncbi_taxonomi": 18, "necessari": [4, 17, 22], "need": [5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20], "never": 14, "new": [6, 20], "nih": 18, "nlm": 18, "node": [7, 18], "nodej": 7, "nodesourc": 7, "norm": 17, "normal": [9, 17], "nosequ": 10, "note": [9, 11, 17], "notic": [4, 11], "now": [4, 6, 7, 22], "nr": 8, "number": [4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19], "o": 2, "ob": 9, "obo": 14, "oborel": 14, "oct": 17, "offici": [0, 4, 7], "onc": 7, "one": [7, 9, 17], "onli": 9, "ontologi": [1, 3, 8, 9, 10, 11, 13], "ontology_term": 11, "open": [4, 7, 22], "openjdk": 4, "option": [5, 12, 17, 18], "oracl": 4, "order": [0, 7, 8, 12, 13, 19, 22], "org": [6, 7, 12, 14, 19, 20], "organ": [1, 3, 7, 8, 9, 10, 11, 12, 13, 15, 17, 18, 19], "organism_chr": 10, "organism_genes_sort": 12, "organism_queri": [8, 13], "organism_snv_sort": 19, "organism_subject": [8, 13], "organismdb": 18, "organismu": 5, "orphan": 9, "ortholog": 15, "orthomcl": [1, 3], "oryza": [8, 9, 13, 17], "other": [7, 9], "otherwis": 4, "output": [9, 15, 17], "owner": [6, 20], "p": [6, 7, 20], "packag": 22, "page": [3, 7], "pagin": 4, "pairwis": 9, "paramet": [10, 12], "parti": [4, 21], "pass": 9, "password": [6, 20], "path": [7, 22], "pcc": 9, "pearson": 9, "per": 17, "permiss": 22, "pg_hba": 6, "phylogenet": 18, "pip": [0, 4, 6], "pleas": [4, 5, 11], "png": 2, "point": [6, 7], "polypeptid": [4, 8, 11, 13, 22], "port": [6, 20], "possibl": 10, "postgr": [6, 20], "postgresql": [6, 20], "postgresql_psycopg2": 20, "power": 3, "pre": 0, "prerequisit": 7, "previous": [8, 9, 11, 13], "probabl": [4, 7], "proce": 7, "proced": 4, "process": [7, 10, 22], "product": 11, "program": [8, 13, 17], "programvers": [8, 13, 17], "project": [6, 17, 22], "proper": 7, "protein": [8, 13], "protein_match": [8, 13], "protocol": 7, "provid": [3, 5, 11], "psql": [6, 20], "pub": 18, "public": [1, 3], "put": [7, 8, 13], "py": [0, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22], "py3": 22, "pygraphviz": 2, "python": [0, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22], "python3": [6, 20], "qtl": 12, "qtldb": 12, "queri": [8, 13], "raw": [17, 20], "rdegg": 0, "re": 5, "read": 6, "readi": 20, "readm": 1, "readthedoc": 2, "realli": [7, 10], "reason": [5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19], "rebuild": 4, "rebuild_index": 4, "recommend": [6, 20], "record": [5, 10, 12, 14, 16, 19], "ref_seq": 7, "refer": [10, 11, 12, 16, 19], "referec": 7, "refseq": 7, "regard": [9, 17], "regular": 6, "relat": [9, 17, 20], "relationship": [15, 17, 20], "releas": 7, "reli": 1, "reload": 4, "rememb": 7, "remove_analysi": [8, 13], "remove_feature_annot": [9, 11, 15], "remove_feature_group": 9, "remove_fil": [12, 17, 19], "remove_ontologi": 14, "remove_organ": [5, 10, 18], "remove_phylotre": 18, "remove_publ": [11, 16], "remove_relationship": 9, "renam": 7, "render": [7, 10], "rep1": 17, "repeat": 7, "replac": [7, 11], "repres": 9, "requir": [4, 5, 6, 8, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22], "rest_framework": 6, "restart": [7, 22], "restrict": 4, "result": [4, 20], "revers": 20, "rewrit": 20, "rna": [1, 3, 9], "ro": 14, "run": [0, 4, 6, 7, 8, 9, 17, 20, 22], "runserv": [6, 7], "s12122": [10, 11, 12, 19], "sake": 9, "sampl": [1, 7, 9, 17], "samtool": 7, "sapien": [9, 10, 11, 12, 15, 19], "sativa": [8, 9, 13, 17], "scaffold": 12, "schema": [1, 6, 20], "scientif": [9, 17], "search": [3, 21], "second": [0, 7, 9], "section": [4, 6], "see": [8, 12, 19], "seen": 17, "separ": [9, 11], "seq": [1, 3, 7, 9], "seqfeatur": 7, "seqtyp": 7, "sequenc": [7, 8, 9, 10, 12, 13, 19], "sequencetrack": 7, "seri": 17, "server": [3, 4, 6, 7, 21], "servic": [4, 22], "set": [0, 4, 6, 7, 8, 9, 12, 13, 20, 22], "setup": [7, 20], "setup_12": 7, "sever": 17, "sh": 7, "should": [4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20], "show": 9, "shown": 9, "sinc": [4, 20], "site": 22, "skip": 18, "sl": 7, "small": 1, "snv": 7, "so": [4, 8, 10, 11, 14], "so_queri": [8, 13], "so_subject": [8, 13], "softwar": [4, 6, 7, 9, 15, 17, 20, 21], "solr": 4, "some": [7, 12], "soterm": [9, 10, 11], "sourc": [4, 6, 7, 14, 17, 20, 22], "sourcenam": [8, 13], "speci": [5, 9, 10, 11, 12, 15, 19], "specif": 17, "specifi": 20, "sql": 20, "sra": 17, "src": [4, 6, 20], "srr2302912": 17, "srr4033018": 17, "srr5167848": 17, "standard": 17, "start": [4, 7, 22], "startproject": [6, 20], "static": 22, "static_root": 22, "static_url": 22, "statist": 9, "step": [7, 18], "stop": 22, "store": [0, 3, 7, 8, 10, 11, 12, 13, 19], "storeclass": 7, "stress": 17, "string": 17, "strongli": [6, 20], "structur": 7, "studi": 17, "sub": 22, "subdirectori": 7, "subtract": 9, "sucha": 17, "sudo": [4, 6, 7, 22], "support": [4, 20], "suppos": 17, "sure": [6, 7, 22], "swissprot": 8, "symlink": 22, "system": [7, 22], "systemctl": [4, 7, 22], "t": [6, 7, 10, 20, 22], "tab": [9, 11, 17], "tabix": [12, 19], "tabl": [0, 6, 9, 14, 17, 20], "tabular": 17, "tair10": [9, 17], "take": [5, 7, 10, 18, 22], "taken": 17, "tar": [1, 18], "taxdump": 18, "taxonomi": [1, 3, 5], "term": [8, 9, 10, 11, 13, 15], "test": [4, 6, 7, 8, 13, 22], "text": [11, 17], "thaliana": [7, 9, 10, 11, 12, 19], "than": 18, "thei": 4, "them": 9, "therefor": [1, 14], "thi": [0, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22], "third": [4, 9, 21], "though": 4, "thread": [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19], "three": 9, "time": 18, "timeexecut": 17, "togeth": 1, "too": [7, 10], "tool": [0, 3], "tpm": 17, "track": [7, 10], "tracklist": 7, "transcript": 7, "treatment": 17, "tree": 18, "trembl": 8, "truncat": 4, "tsv": 4, "tutori": [6, 7], "tutorial02": 6, "two": [7, 9, 11, 12, 17], "txt": [9, 15, 17], "type": [4, 7, 9, 12], "u": 20, "ubuntu": [4, 7, 22], "under": 7, "uniprot": 8, "uniqu": 20, "unpack": [18, 20], "unsortedmodel": 20, "unzip": 7, "up": 7, "updat": 22, "upstream": 7, "url": [4, 7, 10, 14, 18], "urltempl": 7, "us": [4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22], "useasrefseqstor": 7, "user": [3, 6, 20], "usernam": [6, 20], "usr": [6, 20], "usual": [9, 12, 17], "valu": [9, 12, 19], "var": [7, 22], "variabl": [4, 7, 22], "vcf": [1, 3], "version": [4, 6, 8, 13, 17, 20], "view": [0, 20], "virtualenv": [6, 20], "visual": [3, 7], "vocabulari": 9, "w": 20, "wa": [4, 8, 11, 13, 17, 20], "want": 4, "we": [6, 17, 20], "web": [3, 6, 21], "webproject": [4, 6, 20, 22], "webserv": 22, "websit": 6, "wget": [4, 7], "whenev": 0, "which": 17, "whoami": 7, "whole": [7, 17, 22], "wiki": [6, 20], "without": 12, "won": 22, "work": [5, 22], "worker": 4, "wsgi": 7, "wsgidaemonprocess": 22, "wsgipythonhom": 22, "wsgipythonpath": 22, "wsgiscriptalia": 22, "www": [7, 12, 18, 19, 22], "x": [4, 7], "xml": [8, 13], "xput": 4, "y": [7, 17], "ye": 17, "you": [0, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22], "your": [0, 6, 7, 20, 22], "yourdatabas": [6, 20], "yourproject": [4, 6, 7, 20, 22], "zip": 7, "zlib1g": [6, 7]}, "titles": ["3.4. Cache (optional)", "2. Data loading", "4. Diagrams", "machado\u2019s documentation", "3.1. Index and search", "2.3. Inserting a new organism", "1. Installation", "3.3. JBrowse (optional)", "2.8. Loading Blast results", "2.12. Loading Coexpression analyzes", "2.5. Loading FASTA files", "2.7. Loading Feature Additional Info", "2.6. Loading GFF files", "2.9. Loading InterproScan results", "2.1. Loading ontologies", "2.10. Loading OrthoMCL results", "2.4. Loading publication files", "2.11. Loading RNA-seq data", "2.2. Loading taxonomy", "2.13. Loading VCF files", "5. Models", "3. Visualization", "3.2. Web server"], "titleterms": {"": 3, "The": 20, "addit": 11, "admin": 6, "analysisfeatur": 2, "analyz": 9, "annot": 11, "apach": 22, "app": 6, "blast": 8, "cach": 0, "cluster": 9, "coexpress": 9, "content": 3, "correl": 9, "data": [1, 17], "dbxref": 11, "diagram": 2, "django": [20, 22], "document": 3, "fasta": [7, 10], "featur": [2, 9, 11], "file": [7, 8, 10, 12, 13, 16, 19], "from": 7, "gene": 14, "gff": 12, "index": 4, "info": 11, "inform": 17, "insert": 5, "instal": 6, "interfac": 6, "interproscan": 13, "jbrows": 7, "load": [1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19], "machado": 3, "manag": 22, "model": 20, "ncbi": 18, "new": 5, "ontologi": [2, 14], "open": 6, "option": [0, 7], "organ": 5, "orthologi": 15, "orthomcl": 15, "pair": 9, "prepar": 6, "prerequisit": [6, 20], "project": 20, "public": [2, 11, 16], "record": [8, 13], "refer": [6, 7, 20], "relat": 14, "remov": [5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19], "result": [8, 13, 15], "rna": 17, "runserv": 22, "search": 4, "seq": 17, "sequenc": [2, 11, 14], "server": 22, "similar": [2, 13], "start": 6, "subject": [8, 13], "taxonomi": [2, 18], "us": 7, "vcf": 19, "visual": 21, "web": 22, "wsgi": 22, "you": 6}})
\ No newline at end of file
diff --git a/docs/html/visualization.html b/docs/html/visualization.html
index 779e6b86..22754eaa 100644
--- a/docs/html/visualization.html
+++ b/docs/html/visualization.html
@@ -1,21 +1,21 @@
+
+
 
-
+
 
-  
+  
 
   
   3. Visualization — machado 0.1.0 documentation
-      
-      
-  
+      
+      
+
   
-        
-        
-        
-        
-        
+      
+      
+      
+      
+      
     
     
     
diff --git a/docs/html/webserver.html b/docs/html/webserver.html
index 8b651b79..81a6ffd8 100644
--- a/docs/html/webserver.html
+++ b/docs/html/webserver.html
@@ -1,21 +1,21 @@
+
+
 
-
+
 
-  
+  
 
   
   3.2. Web server — machado 0.1.0 documentation
-      
-      
-  
+      
+      
+
   
-        
-        
-        
-        
-        
+      
+      
+      
+      
+      
     
     
     
diff --git a/docs/source/installation.rst b/docs/source/installation.rst
index c248178e..8bf2b958 100644
--- a/docs/source/installation.rst
+++ b/docs/source/installation.rst
@@ -30,13 +30,13 @@ Be sure to have the following dependencies installed
 
     sudo apt install zlib1g-dev libbz2-dev liblzma-dev python3-dev
 
-**Python 3.8**
+**Python 3.12**
 
 We strongly recommend creating a new virtualenv for your project
 
 .. code-block:: bash
 
-    virtualenv -p /usr/bin/python3.8 YOURPROJECT
+    virtualenv -p /usr/bin/python3.12 YOURPROJECT
     cd YOURPROJECT
     source bin/activate
 
@@ -60,8 +60,7 @@ Inside YOURPROJECT directory create a Django project with the following command:
 
 .. code-block:: bash
 
-    django-admin startproject WEBPROJECT
-    cd WEBPROJECT
+    django-admin startproject WEBPROJECT .
 
 Then, configure the WEBPROJECT/settings.py file to connect to your Chado database.
 
@@ -121,7 +120,6 @@ Now, just run the DJango server to access the web interface:
 
     python manage.py runserver
 
-The API interface will be available at http://localhost:8000/machado/api
 
 
 References
diff --git a/setup.py b/setup.py
index 55129a9c..72214010 100644
--- a/setup.py
+++ b/setup.py
@@ -38,7 +38,7 @@
         "typing~=3.7.4.3",
         "bibtexparser~=1.4.1",
         "djangorestframework~=3.15.2",
-        "drf-yasg==1.21.7",
+        "drf-yasg==1.21.8",
         "drf-nested-routers~=0.94.1",
         "pysam~=0.22.1",
         "django-haystack~=3.3.0",

From f83103252cbfbfb2d0f983d1442fe1434e52b664 Mon Sep 17 00:00:00 2001
From: adhemar 
Date: Fri, 10 Jan 2025 14:56:11 -0300
Subject: [PATCH 2/2] docs

---
 docs/html/.doctrees/cache.doctree             | Bin 6600 -> 6585 bytes
 docs/html/.doctrees/dataload.doctree          | Bin 4202 -> 4187 bytes
 docs/html/.doctrees/diagrams.doctree          | Bin 5981 -> 5966 bytes
 docs/html/.doctrees/environment.pickle        | Bin 56359 -> 57070 bytes
 docs/html/.doctrees/index.doctree             | Bin 5672 -> 5657 bytes
 docs/html/.doctrees/index_search.doctree      | Bin 13297 -> 13286 bytes
 docs/html/.doctrees/insert_organism.doctree   | Bin 6206 -> 6191 bytes
 docs/html/.doctrees/installation.doctree      | Bin 14321 -> 14600 bytes
 docs/html/.doctrees/jbrowse.doctree           | Bin 20100 -> 20085 bytes
 docs/html/.doctrees/load_blast.doctree        | Bin 14069 -> 14054 bytes
 docs/html/.doctrees/load_coexpression.doctree | Bin 20484 -> 20469 bytes
 docs/html/.doctrees/load_fasta.doctree        | Bin 10699 -> 10684 bytes
 .../.doctrees/load_feature_annotation.doctree | Bin 21117 -> 21102 bytes
 docs/html/.doctrees/load_gff.doctree          | Bin 11285 -> 11270 bytes
 docs/html/.doctrees/load_interproscan.doctree | Bin 13328 -> 13313 bytes
 docs/html/.doctrees/load_ontologies.doctree   | Bin 10751 -> 10736 bytes
 docs/html/.doctrees/load_orthomcl.doctree     | Bin 7422 -> 7407 bytes
 docs/html/.doctrees/load_publication.doctree  | Bin 5061 -> 5046 bytes
 docs/html/.doctrees/load_rnaseq.doctree       | Bin 24803 -> 24788 bytes
 docs/html/.doctrees/load_taxonomy.doctree     | Bin 8883 -> 8868 bytes
 docs/html/.doctrees/load_vcf.doctree          | Bin 9090 -> 9075 bytes
 docs/html/.doctrees/models.doctree            | Bin 13113 -> 13098 bytes
 docs/html/.doctrees/visualization.doctree     | Bin 3220 -> 3205 bytes
 docs/html/.doctrees/webserver.doctree         | Bin 11543 -> 10553 bytes
 docs/html/_sources/index_search.rst.txt       |   4 ++--
 docs/html/_sources/installation.rst.txt       |   7 +++++--
 docs/html/_sources/webserver.rst.txt          |  14 +++-----------
 docs/html/index_search.html                   |   4 ++--
 docs/html/installation.html                   |   9 ++++++---
 docs/html/searchindex.js                      |   2 +-
 docs/html/webserver.html                      |  13 +++----------
 docs/source/index_search.rst                  |   4 ++--
 docs/source/installation.rst                  |   7 +++++--
 docs/source/webserver.rst                     |  14 +++-----------
 34 files changed, 32 insertions(+), 46 deletions(-)

diff --git a/docs/html/.doctrees/cache.doctree b/docs/html/.doctrees/cache.doctree
index 7c1484cc2097c897722c42fb4ccfd1609d1f69ee..6a8164021f3784fc8e69af1a2ef791847e15cdf4 100644
GIT binary patch
delta 28
jcmX?MywjMafpzM-jVwWooVNO9iADP5<>j067^5Trk_8E(

delta 43
ycmdmKe8QNefpzNMjVwWo5BjLHc1

delta 43
ycmcbu@JfNDfpu#9Miwtd34i^J{M=Oi#FUKG+{7aN^8BLg;)2BF)Xm|HEc^gZoDSar

diff --git a/docs/html/.doctrees/diagrams.doctree b/docs/html/.doctrees/diagrams.doctree
index 945ecf4a47a1924c0efc90f43b07acab8bd07d28..59ee176573d9bc21c24e5befe5df3462a10fc411 100644
GIT binary patch
delta 28
jcmcbscTSI`fpx0$MiwVVP6z$6#3KFj^774bjQ>RejWh||

delta 43
ycmX@7cUO<4fpu!oMiwVV34i^J{M=Oi#FUKG+{7aN^8BLg;)2BF)Xn~k|3v{#=?}#K

diff --git a/docs/html/.doctrees/environment.pickle b/docs/html/.doctrees/environment.pickle
index 5e6fb046c23a2d4426aa53e4aa54b41231099c24..4a52e67ed82b228004617f01f639295746615f3e 100644
GIT binary patch
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eHds@CGp4D^bV*<|w<<&y(G?4`G5cb

diff --git a/docs/html/.doctrees/index.doctree b/docs/html/.doctrees/index.doctree
index a32f9e44030356f1a7182c063352cc5ee1cb2270..3bb884bf24bc07d04ee7370b16a40f39323238d3 100644
GIT binary patch
delta 28
kcmZ3XGgF79fpse1MwabNoVNO9iADP5<>i|%GldER0EMOrb^rhX

delta 43
zcmbQKvqFcZfpx0vMwabN5j067#Hy|s!SFXsA4iQo7^Ly4Wf1kv|$me
K-<&GcqX+<+HWy|9

delta 80
zcmaEs{xO}UfpzM$jVwWo62bZz`MIh3i76SWxrs&k<@rU~#RZAUshi^&7x6JFO=c3P
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zq%h_Kr6nc{YtLdV1S+}BSPJGZ(wV|oKG|G%I?#~wx*d#lniADP5<>i|z7;8-dtV#;@

delta 43
ycmaEs`!$!PfpzMujVv*Y5`p>|`MIh3i76SWxrs&k<@rU~#RZAUshcwyYfS-yy%663

diff --git a/docs/html/.doctrees/load_coexpression.doctree b/docs/html/.doctrees/load_coexpression.doctree
index 417e3dfa4e44c102107828c46b0aedf0d042cb66..65c6f015a887bc2005aa6588357e29e705517998 100644
GIT binary patch
delta 30
mcmZo!!1#4OBTED8)K?o>au_*1^~(~A^vlc3H+L}B_yGX2zY9qK

delta 45
zcmex5pRr{DBTED8)Snw!au_8d^fU5vQ}q*5GE#FBi}cI$i?WLg5|dLmS2EW40RW99
B5i$S(

diff --git a/docs/html/.doctrees/load_fasta.doctree b/docs/html/.doctrees/load_fasta.doctree
index de2674ddcda1ee6a3dd17678ae95d0e7d8b85a57..f4033a35dc028c29250538183d7900a7db7e1fe6 100644
GIT binary patch
delta 28
jcmX>dyeF8YfpzM}jVuw2oKE^>iADP5<>i}87{fIHnlTCq

delta 43
ycmdlJd^(t=fpzMEjVuw25`p>|`MIh3i76SWxrs&k<@rU~#RZAUshd+7!!-b9`VaB|

diff --git a/docs/html/.doctrees/load_feature_annotation.doctree b/docs/html/.doctrees/load_feature_annotation.doctree
index 7fde759a9bf90476c348010c017bf48db46687f5..26a70173aa17672fe4813ea59cf41efd6437152c 100644
GIT binary patch
delta 30
mcmeyngz?=HMwSNFsmU8z3K%*4^~(~A^vlc3H}^1p3;+PQE(^i{

delta 45
zcmaF2gz@hZMwSNFsYM%E3K%8g^fU5vQ}q*5GE#FBi}cI$i?WLg5|dLm*D`(#005Br
B5vu?I

diff --git a/docs/html/.doctrees/load_gff.doctree b/docs/html/.doctrees/load_gff.doctree
index be10ecbaa0ed4f9270c136c282776912d5c78531..230204d71e2d93c8f3dec47cef07efc0edd7b9c9 100644
GIT binary patch
delta 29
kcmbOl(H6nlz&iD}_D0rVMotI)vcw|&^78V{1&m9z0G%QVV*mgE

delta 44
zcmZpRm>R*_z&e#nXCrGcqlCYHMt*Lpequ^SYHnhYetCXTc5y*sa_Z(p#-&;SMeh$y

diff --git a/docs/html/.doctrees/load_interproscan.doctree b/docs/html/.doctrees/load_interproscan.doctree
index e0157c8467c986ffba64210343a1408b4f990c53..5fd7e546033bf42d3952cefc50eea88f9d0c56d5 100644
GIT binary patch
delta 29
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delta 44
zcmZq7n2^ERz&e%HWFu=PqeO&$Mt*Lpequ^SYHnhYetCXTc5y*sa_Z)C#x5fOP1FyF

diff --git a/docs/html/.doctrees/load_ontologies.doctree b/docs/html/.doctrees/load_ontologies.doctree
index a62bf32cc0db2063cfdf67cccfa0bd70a527aa61..334caab4feee04b5494925ca36cca084e5591858 100644
GIT binary patch
delta 28
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delta 43
ycmewm{6CnbfpzMajVxh|5@Gro`MIh3i76SWxrs&k<@rU~#RZAUshg7-do=)l+YrS7

diff --git a/docs/html/.doctrees/load_orthomcl.doctree b/docs/html/.doctrees/load_orthomcl.doctree
index 01980b2b2cc7fdf6dc5a9028c2110759c239eac4..3b589bc3be9ced7af0491f3b9cbe6fd1640584f7 100644
GIT binary patch
delta 28
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delta 43
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diff --git a/docs/html/.doctrees/load_publication.doctree b/docs/html/.doctrees/load_publication.doctree
index f19d4cfad5cf69b5f6f9c1d6de6902a5c8babbb6..9e4d037d0258115d5527a5f27eedc9aab4f2ba54 100644
GIT binary patch
delta 28
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delta 43
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diff --git a/docs/html/.doctrees/load_rnaseq.doctree b/docs/html/.doctrees/load_rnaseq.doctree
index 2f10e27aca0383aa283bd12495af719d1ae0940b..1f65380addba5a6a0244fb94fc2d0d2fbaa4659c 100644
GIT binary patch
delta 30
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delta 45
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diff --git a/docs/html/.doctrees/load_taxonomy.doctree b/docs/html/.doctrees/load_taxonomy.doctree
index ee08c69b4938021540cf7f06c3256a4af2dda393..fb27496c63accee477000b30b1cff2df5ce0dec5 100644
GIT binary patch
delta 28
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diff --git a/docs/html/.doctrees/models.doctree b/docs/html/.doctrees/models.doctree
index 32c656c8b9d00298968fb940bfe4e3e2f9aa96b0..6d23d16805b5b18a3f8f31f6d48268d2a9825309 100644
GIT binary patch
delta 28
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delta 43
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diff --git a/docs/html/_sources/index_search.rst.txt b/docs/html/_sources/index_search.rst.txt
index f9f16a27..0ce131d4 100644
--- a/docs/html/_sources/index_search.rst.txt
+++ b/docs/html/_sources/index_search.rst.txt
@@ -21,8 +21,8 @@ Now, proceding with elasticsearch instalation, run the following commands:
     cd YOURPROJECT
     source bin/activate
     cd src
-    wget https://artifacts.elastic.co/downloads/elasticsearch/elasticsearch-7.17.3-amd64.deb
-    sudo dpkg -i elasticsearch-7.17.3-amd64.deb
+    wget https://artifacts.elastic.co/downloads/elasticsearch/elasticsearch-7.17.26-amd64.deb
+    sudo dpkg -i elasticsearch-7.17.26-amd64.deb
     sudo systemctl daemon-reload
     sudo systemctl enable elasticsearch.service
     sudo systemctl start elasticsearch.service
diff --git a/docs/html/_sources/installation.rst.txt b/docs/html/_sources/installation.rst.txt
index 8bf2b958..ef6f94d9 100644
--- a/docs/html/_sources/installation.rst.txt
+++ b/docs/html/_sources/installation.rst.txt
@@ -36,8 +36,10 @@ We strongly recommend creating a new virtualenv for your project
 
 .. code-block:: bash
 
-    virtualenv -p /usr/bin/python3.12 YOURPROJECT
-    cd YOURPROJECT
+    sudo mkdir /var/www/YOURPROJECT
+    sudo chown $USER:$USER /var/www/YOURPROJECT
+    virtualenv -p /usr/bin/python3.12 /var/www/YOURPROJECT
+    cd /var/www/YOURPROJECT
     source bin/activate
 
 **machado**
@@ -108,6 +110,7 @@ You have to run the following command to create django admin tables:
 
     python manage.py migrate
 
+Just ignore the warnings about unapplied migrations.
 Run tests to check the instalation:
 
 .. code-block:: bash
diff --git a/docs/html/_sources/webserver.rst.txt b/docs/html/_sources/webserver.rst.txt
index 4e03b027..e96ddd97 100644
--- a/docs/html/_sources/webserver.rst.txt
+++ b/docs/html/_sources/webserver.rst.txt
@@ -33,20 +33,12 @@ take care of this process. It will be necessary to install the following package
 
     sudo apt install libapache2-mod-wsgi-py3
 
-Now symlink the directory of YOURPROJECT to '/var/www/' (tested in Ubuntu 20.04):
-
-.. code-block:: bash
-
-    sudo ln -s /FULL/PATH/TO/YOURPROJECT /var/www/
-
-* Make sure this directory and sub-directories have 755 permissions
-
 Now configure Apache to use the WSGI module.
 Here is the configuration file (/etc/apache2/sites-available/YOURPROJECT.conf)
 
 .. code-block:: bash
 
-    
+    
     
         Require all granted
     
@@ -60,8 +52,8 @@ Here is the configuration file (/etc/apache2/sites-available/YOURPROJECT.conf)
 
     WSGIDaemonProcess WEBPROJECT
     WSGIPythonHome /var/www/YOURPROJECT
-    WSGIPythonPath /var/www/YOURPROJECT/WEBPROJECT
-    WSGIScriptAlias /YOURPROJECT /var/www/YOURPROJECT/WEBPROJECT/WEBPROJECT/wsgi.py
+    WSGIPythonPath /var/www/YOURPROJECT
+    WSGIScriptAlias /YOURPROJECT /var/www/YOURPROJECT/WEBPROJECT/wsgi.py
 
 * In this example the whole project is in /var/www/YOURPROJECT, but it's not required to be there.
 * This directory and sub-directories must have 755 permissions
diff --git a/docs/html/index_search.html b/docs/html/index_search.html
index d3f7ad9c..06fe4243 100644
--- a/docs/html/index_search.html
+++ b/docs/html/index_search.html
@@ -95,8 +95,8 @@ 
3.1. Index and search
cd YOURPROJECT
 source bin/activate
 cd src
-wget https://artifacts.elastic.co/downloads/elasticsearch/elasticsearch-7.17.3-amd64.deb
-sudo dpkg -i elasticsearch-7.17.3-amd64.deb
+wget https://artifacts.elastic.co/downloads/elasticsearch/elasticsearch-7.17.26-amd64.deb
+sudo dpkg -i elasticsearch-7.17.26-amd64.deb
 sudo systemctl daemon-reload
 sudo systemctl enable elasticsearch.service
 sudo systemctl start elasticsearch.service
diff --git a/docs/html/installation.html b/docs/html/installation.html
index 7847c9b5..65744596 100644
--- a/docs/html/installation.html
+++ b/docs/html/installation.html
@@ -97,8 +97,10 @@ 
1.1. Prerequisite
 
Python 3.12

 
We strongly recommend creating a new virtualenv for your project

-
virtualenv -p /usr/bin/python3.12 YOURPROJECT
-cd YOURPROJECT
+
sudo mkdir /var/www/YOURPROJECT
+sudo chown $USER:$USER /var/www/YOURPROJECT
+virtualenv -p /usr/bin/python3.12 /var/www/YOURPROJECT
+cd /var/www/YOURPROJECT
 source bin/activate
 

 

@@ -153,7 +155,8 @@ 
1.3. Start you app and open the admin in
 
python manage.py migrate
 

 

-
Run tests to check the instalation:

+
Just ignore the warnings about unapplied migrations.
+Run tests to check the instalation:

 
python manage.py test machado
 

 

diff --git a/docs/html/searchindex.js b/docs/html/searchindex.js
index c1df4f6f..f037b1c3 100644
--- a/docs/html/searchindex.js
+++ b/docs/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"AnalysisFeature": [[2, "analysisfeature"]], "Cache (optional)": [[0, null]], "Content": [[3, "content"]], "Data loading": [[1, null]], "Diagrams": [[2, null]], "Django Apache WSGI": [[22, "django-apache-wsgi"]], "Django manage runserver": [[22, "django-manage-runserver"]], "Feature": [[2, "feature"]], "Gene ontology": [[14, "gene-ontology"]], "Index and search": [[4, null]], "Insert organism": [[5, "insert-organism"]], "Inserting a new organism": [[5, null]], "Installation": [[6, null]], "JBrowse (optional)": [[7, null]], "Load Annotation": [[11, "load-annotation"]], "Load BLAST": [[8, "load-blast"]], "Load BLAST subject records": [[8, "load-blast-subject-records"]], "Load Coexpression clusters": [[9, "load-coexpression-clusters"]], "Load Coexpression correlated pairs of features": [[9, "load-coexpression-correlated-pairs-of-features"]], "Load DBxRef": [[11, "load-dbxref"]], "Load FASTA": [[10, "load-fasta"]], "Load GFF": [[12, "load-gff"]], "Load InterproScan similarity": [[13, "load-interproscan-similarity"]], "Load InterproScan subject records": [[13, "load-interproscan-subject-records"]], "Load OrthoMCL": [[15, "load-orthomcl"]], "Load Publication": [[11, "load-publication"]], "Load RNA-seq data": [[17, "load-rna-seq-data"]], "Load RNA-seq information": [[17, "load-rna-seq-information"]], "Load Sequence": [[11, "load-sequence"]], "Load VCF": [[19, "load-vcf"]], "Load publication": [[16, "load-publication"]], "Loading Blast results": [[8, null]], "Loading Coexpression analyzes": [[9, null]], "Loading FASTA files": [[10, null]], "Loading Feature Additional Info": [[11, null]], "Loading GFF files": [[12, null]], "Loading InterproScan results": [[13, null]], "Loading OrthoMCL results": [[15, null]], "Loading RNA-seq data": [[17, null]], "Loading VCF files": [[19, null]], "Loading ontologies": [[14, null]], "Loading publication files": [[16, null]], "Loading taxonomy": [[18, null]], "Models": [[20, null]], "NCBI Taxonomy": [[18, "ncbi-taxonomy"]], "Ontology": [[2, "ontology"]], "Preparation": [[6, "preparation"]], "Prerequisite": [[6, "prerequisite"], [20, "prerequisite"]], "Publication": [[2, "publication"]], "References": [[6, "references"], [20, "references"]], "Relations ontology": [[14, "relations-ontology"]], "Remove Annotation": [[11, "remove-annotation"]], "Remove Publication": [[11, "remove-publication"]], "Remove RNA-seq data": [[17, "remove-rna-seq-data"]], "Remove RNA-seq information": [[17, "remove-rna-seq-information"]], "Remove Sequence": [[11, "remove-sequence"]], "Remove coexpression clusters": [[9, "remove-coexpression-clusters"]], "Remove coexpression pairs": [[9, "remove-coexpression-pairs"]], "Remove file": [[8, "remove-file"], [10, "remove-file"], [12, "remove-file"], [13, "remove-file"], [19, "remove-file"]], "Remove ontology": [[14, "remove-ontology"]], "Remove organism": [[5, "remove-organism"]], "Remove orthology": [[15, "remove-orthology"]], "Remove publication": [[16, "remove-publication"]], "Remove taxonomy": [[18, "remove-taxonomy"]], "Sequence": [[2, "sequence"]], "Sequence ontology": [[14, "sequence-ontology"]], "Similarity": [[2, "similarity"]], "Start you app and open the admin interface": [[6, "start-you-app-and-open-the-admin-interface"]], "Taxonomy": [[2, "taxonomy"]], "The Django project": [[20, "the-django-project"]], "The model": [[20, "the-model"]], "Use reference from FASTA file (optional)": [[7, "use-reference-from-fasta-file-optional"]], "Visualization": [[21, null]], "Web server": [[22, null]], "machado\u2019s documentation": [[3, null]]}, "docnames": ["cache", "dataload", "diagrams", "index", "index_search", "insert_organism", "installation", "jbrowse", "load_blast", "load_coexpression", "load_fasta", "load_feature_annotation", "load_gff", "load_interproscan", "load_ontologies", "load_orthomcl", "load_publication", "load_rnaseq", "load_taxonomy", "load_vcf", "models", "visualization", "webserver"], "envversion": {"sphinx": 64, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2}, "filenames": ["cache.rst", "dataload.rst", "diagrams.rst", "index.rst", "index_search.rst", "insert_organism.rst", "installation.rst", "jbrowse.rst", "load_blast.rst", "load_coexpression.rst", "load_fasta.rst", "load_feature_annotation.rst", "load_gff.rst", "load_interproscan.rst", "load_ontologies.rst", "load_orthomcl.rst", "load_publication.rst", "load_rnaseq.rst", "load_taxonomy.rst", "load_vcf.rst", "models.rst", "visualization.rst", "webserver.rst"], "indexentries": {}, "objects": {}, "objnames": {}, "objtypes": {}, "terms": {"": [0, 1, 4, 7, 8, 10, 12, 13, 17, 19, 22], "0": [4, 8, 9, 17, 22], "000": [4, 18], "012": [10, 11, 12, 19], "04": [4, 7, 22], "1": [0, 4, 6, 7, 9, 17, 20, 22], "10": [4, 10, 11, 12, 19], 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9, "ortholog": 15, "orthomcl": [1, 3], "oryza": [8, 9, 13, 17], "other": [7, 9], "otherwis": 4, "output": [9, 15, 17], "owner": [6, 20], "p": [6, 7, 20], "packag": 22, "page": [3, 7], "pagin": 4, "pairwis": 9, "paramet": [10, 12], "parti": [4, 21], "pass": 9, "password": [6, 20], "path": 7, "pcc": 9, "pearson": 9, "per": 17, "permiss": 22, "pg_hba": 6, "phylogenet": 18, "pip": [0, 4, 6], "pleas": [4, 5, 11], "png": 2, "point": [6, 7], "polypeptid": [4, 8, 11, 13, 22], "port": [6, 20], "possibl": 10, "postgr": [6, 20], "postgresql": [6, 20], "postgresql_psycopg2": 20, "power": 3, "pre": 0, "prerequisit": 7, "previous": [8, 9, 11, 13], "probabl": [4, 7], "proce": 7, "proced": 4, "process": [7, 10, 22], "product": 11, "program": [8, 13, 17], "programvers": [8, 13, 17], "project": [6, 17, 22], "proper": 7, "protein": [8, 13], "protein_match": [8, 13], "protocol": 7, "provid": [3, 5, 11], "psql": [6, 20], "pub": 18, "public": [1, 3], "put": [7, 8, 13], "py": [0, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22], "py3": 22, "pygraphviz": 2, "python": [0, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22], "python3": [6, 20], "qtl": 12, "qtldb": 12, "queri": [8, 13], "raw": [17, 20], "rdegg": 0, "re": 5, "read": 6, "readi": 20, "readm": 1, "readthedoc": 2, "realli": [7, 10], "reason": [5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19], "rebuild": 4, "rebuild_index": 4, "recommend": [6, 20], "record": [5, 10, 12, 14, 16, 19], "ref_seq": 7, "refer": [10, 11, 12, 16, 19], "referec": 7, "refseq": 7, "regard": [9, 17], "regular": 6, "relat": [9, 17, 20], "relationship": [15, 17, 20], "releas": 7, "reli": 1, "reload": 4, "rememb": 7, "remove_analysi": [8, 13], "remove_feature_annot": [9, 11, 15], "remove_feature_group": 9, "remove_fil": [12, 17, 19], "remove_ontologi": 14, "remove_organ": [5, 10, 18], "remove_phylotre": 18, "remove_publ": [11, 16], "remove_relationship": 9, "renam": 7, "render": [7, 10], "rep1": 17, "repeat": 7, "replac": [7, 11], "repres": 9, "requir": [4, 5, 6, 8, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22], "rest_framework": 6, "restart": [7, 22], "restrict": 4, "result": [4, 20], "revers": 20, "rewrit": 20, "rna": [1, 3, 9], "ro": 14, "run": [0, 4, 6, 7, 8, 9, 17, 20, 22], "runserv": [6, 7], "s12122": [10, 11, 12, 19], "sake": 9, "sampl": [1, 7, 9, 17], "samtool": 7, "sapien": [9, 10, 11, 12, 15, 19], "sativa": [8, 9, 13, 17], "scaffold": 12, "schema": [1, 6, 20], "scientif": [9, 17], "search": [3, 21], "second": [0, 7, 9], "section": [4, 6], "see": [8, 12, 19], "seen": 17, "separ": [9, 11], "seq": [1, 3, 7, 9], "seqfeatur": 7, "seqtyp": 7, "sequenc": [7, 8, 9, 10, 12, 13, 19], "sequencetrack": 7, "seri": 17, "server": [3, 4, 6, 7, 21], "servic": [4, 22], "set": [0, 4, 6, 7, 8, 9, 12, 13, 20, 22], "setup": [7, 20], "setup_12": 7, "sever": 17, "sh": 7, "should": [4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20], "show": 9, "shown": 9, "sinc": [4, 20], "site": 22, "skip": 18, "sl": 7, "small": 1, "snv": 7, "so": [4, 8, 10, 11, 14], "so_queri": [8, 13], "so_subject": [8, 13], "softwar": [4, 6, 7, 9, 15, 17, 20, 21], "solr": 4, "some": [7, 12], "soterm": [9, 10, 11], "sourc": [4, 6, 7, 14, 17, 20, 22], "sourcenam": [8, 13], "speci": [5, 9, 10, 11, 12, 15, 19], "specif": 17, "specifi": 20, "sql": 20, "sra": 17, "src": [4, 6, 20], "srr2302912": 17, "srr4033018": 17, "srr5167848": 17, "standard": 17, "start": [4, 7, 22], "startproject": [6, 20], "static": 22, "static_root": 22, "static_url": 22, "statist": 9, "step": [7, 18], "stop": 22, "store": [0, 3, 7, 8, 10, 11, 12, 13, 19], "storeclass": 7, "stress": 17, "string": 17, "strongli": [6, 20], "structur": 7, "studi": 17, "sub": 22, "subdirectori": 7, "subtract": 9, "sucha": 17, "sudo": [4, 6, 7, 22], "support": [4, 20], "suppos": 17, "sure": [6, 7, 22], "swissprot": 8, "symlink": 22, "system": [7, 22], "systemctl": [4, 7, 22], "t": [6, 7, 10, 20, 22], "tab": [9, 11, 17], "tabix": [12, 19], "tabl": [0, 6, 9, 14, 17, 20], "tabular": 17, "tair10": [9, 17], "take": [5, 7, 10, 18, 22], "taken": 17, "tar": [1, 18], "taxdump": 18, "taxonomi": [1, 3, 5], "term": [8, 9, 10, 11, 13, 15], "test": [4, 6, 7, 8, 13, 22], "text": [11, 17], "thaliana": [7, 9, 10, 11, 12, 19], "than": 18, "thei": 4, "them": 9, "therefor": [1, 14], "thi": [0, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22], "third": [4, 9, 21], "though": 4, "thread": [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19], "three": 9, "time": 18, "timeexecut": 17, "togeth": 1, "too": [7, 10], "tool": [0, 3], "tpm": 17, "track": [7, 10], "tracklist": 7, "transcript": 7, "treatment": 17, "tree": 18, "trembl": 8, "truncat": 4, "tsv": 4, "tutori": [6, 7], "tutorial02": 6, "two": [7, 9, 11, 12, 17], "txt": [9, 15, 17], "type": [4, 7, 9, 12], "u": 20, "ubuntu": [4, 7, 22], "unappli": 6, "under": 7, "uniprot": 8, "uniqu": 20, "unpack": [18, 20], "unsortedmodel": 20, "unzip": 7, "up": 7, "updat": 22, "upstream": 7, "url": [4, 7, 10, 14, 18], "urltempl": 7, "us": [4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22], "useasrefseqstor": 7, "user": [3, 6, 20], "usernam": [6, 20], "usr": [6, 20], "usual": [9, 12, 17], "valu": [9, 12, 19], "var": [6, 7, 22], "variabl": [4, 7, 22], "vcf": [1, 3], "version": [4, 6, 8, 13, 17, 20], "view": [0, 20], "virtualenv": [6, 20], "visual": [3, 7], "vocabulari": 9, "w": 20, "wa": [4, 8, 11, 13, 17, 20], "want": 4, "warn": 6, "we": [6, 17, 20], "web": [3, 6, 21], "webproject": [4, 6, 20, 22], "webserv": 22, "websit": 6, "wget": [4, 7], "whenev": 0, "which": 17, "whoami": 7, "whole": [7, 17, 22], "wiki": [6, 20], "without": 12, "won": 22, "work": [5, 22], "worker": 4, "wsgi": 7, "wsgidaemonprocess": 22, "wsgipythonhom": 22, "wsgipythonpath": 22, "wsgiscriptalia": 22, "www": [6, 7, 12, 18, 19, 22], "x": [4, 7], "xml": [8, 13], "xput": 4, "y": [7, 17], "ye": 17, "you": [0, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22], "your": [0, 6, 7, 20, 22], "yourdatabas": [6, 20], "yourproject": [4, 6, 7, 20, 22], "zip": 7, "zlib1g": [6, 7]}, "titles": ["3.4. Cache (optional)", "2. Data loading", "4. Diagrams", "machado\u2019s documentation", "3.1. Index and search", "2.3. Inserting a new organism", "1. Installation", "3.3. JBrowse (optional)", "2.8. Loading Blast results", "2.12. Loading Coexpression analyzes", "2.5. Loading FASTA files", "2.7. Loading Feature Additional Info", "2.6. Loading GFF files", "2.9. Loading InterproScan results", "2.1. Loading ontologies", "2.10. Loading OrthoMCL results", "2.4. Loading publication files", "2.11. Loading RNA-seq data", "2.2. Loading taxonomy", "2.13. Loading VCF files", "5. Models", "3. Visualization", "3.2. Web server"], "titleterms": {"": 3, "The": 20, "addit": 11, "admin": 6, "analysisfeatur": 2, "analyz": 9, "annot": 11, "apach": 22, "app": 6, "blast": 8, "cach": 0, "cluster": 9, "coexpress": 9, "content": 3, "correl": 9, "data": [1, 17], "dbxref": 11, "diagram": 2, "django": [20, 22], "document": 3, "fasta": [7, 10], "featur": [2, 9, 11], "file": [7, 8, 10, 12, 13, 16, 19], "from": 7, "gene": 14, "gff": 12, "index": 4, "info": 11, "inform": 17, "insert": 5, "instal": 6, "interfac": 6, "interproscan": 13, "jbrows": 7, "load": [1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19], "machado": 3, "manag": 22, "model": 20, "ncbi": 18, "new": 5, "ontologi": [2, 14], "open": 6, "option": [0, 7], "organ": 5, "orthologi": 15, "orthomcl": 15, "pair": 9, "prepar": 6, "prerequisit": [6, 20], "project": 20, "public": [2, 11, 16], "record": [8, 13], "refer": [6, 7, 20], "relat": 14, "remov": [5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19], "result": [8, 13, 15], "rna": 17, "runserv": 22, "search": 4, "seq": 17, "sequenc": [2, 11, 14], "server": 22, "similar": [2, 13], "start": 6, "subject": [8, 13], "taxonomi": [2, 18], "us": 7, "vcf": 19, "visual": 21, "web": 22, "wsgi": 22, "you": 6}})
\ No newline at end of file
diff --git a/docs/html/webserver.html b/docs/html/webserver.html
index 81a6ffd8..0331cbe4 100644
--- a/docs/html/webserver.html
+++ b/docs/html/webserver.html
@@ -105,16 +105,9 @@ 
3.2.2. Django Apache WSGI
sudo apt install libapache2-mod-wsgi-py3
 

 

-
Now symlink the directory of YOURPROJECT to ‘/var/www/’ (tested in Ubuntu 20.04):

-
sudo ln -s /FULL/PATH/TO/YOURPROJECT /var/www/
-

-

-
    
-
  • Make sure this directory and sub-directories have 755 permissions
    • 
-

 
Now configure Apache to use the WSGI module.
 Here is the configuration file (/etc/apache2/sites-available/YOURPROJECT.conf)

-
<Directory "/var/www/YOURPROJECT/WEBPROJECT/WEBPROJECT">
+
<Directory "/var/www/YOURPROJECT/WEBPROJECT">
 <Files "wsgi.py">
     Require all granted
 </Files>
@@ -128,8 +121,8 @@ 
3.2.2. Django Apache WSGI WEBPROJECT
 WSGIPythonHome /var/www/YOURPROJECT
-WSGIPythonPath /var/www/YOURPROJECT/WEBPROJECT
-WSGIScriptAlias /YOURPROJECT /var/www/YOURPROJECT/WEBPROJECT/WEBPROJECT/wsgi.py
+WSGIPythonPath /var/www/YOURPROJECT
+WSGIScriptAlias /YOURPROJECT /var/www/YOURPROJECT/WEBPROJECT/wsgi.py
 

 

 
    
diff --git a/docs/source/index_search.rst b/docs/source/index_search.rst
index f9f16a27..0ce131d4 100644
--- a/docs/source/index_search.rst
+++ b/docs/source/index_search.rst
@@ -21,8 +21,8 @@ Now, proceding with elasticsearch instalation, run the following commands:
     cd YOURPROJECT
     source bin/activate
     cd src
-    wget https://artifacts.elastic.co/downloads/elasticsearch/elasticsearch-7.17.3-amd64.deb
-    sudo dpkg -i elasticsearch-7.17.3-amd64.deb
+    wget https://artifacts.elastic.co/downloads/elasticsearch/elasticsearch-7.17.26-amd64.deb
+    sudo dpkg -i elasticsearch-7.17.26-amd64.deb
     sudo systemctl daemon-reload
     sudo systemctl enable elasticsearch.service
     sudo systemctl start elasticsearch.service
diff --git a/docs/source/installation.rst b/docs/source/installation.rst
index 8bf2b958..ef6f94d9 100644
--- a/docs/source/installation.rst
+++ b/docs/source/installation.rst
@@ -36,8 +36,10 @@ We strongly recommend creating a new virtualenv for your project
 
 .. code-block:: bash
 
-    virtualenv -p /usr/bin/python3.12 YOURPROJECT
-    cd YOURPROJECT
+    sudo mkdir /var/www/YOURPROJECT
+    sudo chown $USER:$USER /var/www/YOURPROJECT
+    virtualenv -p /usr/bin/python3.12 /var/www/YOURPROJECT
+    cd /var/www/YOURPROJECT
     source bin/activate
 
 **machado**
@@ -108,6 +110,7 @@ You have to run the following command to create django admin tables:
 
     python manage.py migrate
 
+Just ignore the warnings about unapplied migrations.
 Run tests to check the instalation:
 
 .. code-block:: bash
diff --git a/docs/source/webserver.rst b/docs/source/webserver.rst
index 4e03b027..e96ddd97 100644
--- a/docs/source/webserver.rst
+++ b/docs/source/webserver.rst
@@ -33,20 +33,12 @@ take care of this process. It will be necessary to install the following package
 
     sudo apt install libapache2-mod-wsgi-py3
 
-Now symlink the directory of YOURPROJECT to '/var/www/' (tested in Ubuntu 20.04):
-
-.. code-block:: bash
-
-    sudo ln -s /FULL/PATH/TO/YOURPROJECT /var/www/
-
-* Make sure this directory and sub-directories have 755 permissions
-
 Now configure Apache to use the WSGI module.
 Here is the configuration file (/etc/apache2/sites-available/YOURPROJECT.conf)
 
 .. code-block:: bash
 
-    
+    
     
         Require all granted
     
@@ -60,8 +52,8 @@ Here is the configuration file (/etc/apache2/sites-available/YOURPROJECT.conf)
 
     WSGIDaemonProcess WEBPROJECT
     WSGIPythonHome /var/www/YOURPROJECT
-    WSGIPythonPath /var/www/YOURPROJECT/WEBPROJECT
-    WSGIScriptAlias /YOURPROJECT /var/www/YOURPROJECT/WEBPROJECT/WEBPROJECT/wsgi.py
+    WSGIPythonPath /var/www/YOURPROJECT
+    WSGIScriptAlias /YOURPROJECT /var/www/YOURPROJECT/WEBPROJECT/wsgi.py
 
 * In this example the whole project is in /var/www/YOURPROJECT, but it's not required to be there.
 * This directory and sub-directories must have 755 permissions