879450f84abeea7f424bde8ab9ad95669eef3b53 hiram Thu Sep 5 10:12:26 2024 -0700 upper case corrections refs #32596 diff --git src/hg/js/assemblySearch.js src/hg/js/assemblySearch.js index c4127d0..ad092a5 100644 --- src/hg/js/assemblySearch.js +++ src/hg/js/assemblySearch.js @@ -244,53 +244,53 @@ searchInput.value = query; document.getElementById('submitSearch').click(); } } document.getElementById("measureTiming").style.display = "none"; }); // refresh the thead columns in the specified table function headerRefresh(tableHead) { // clear existing content tableHead.innerHTML = ''; // re-populate header row - the sortable system added a class to // the last sorted column, need to rebuild the headerRow to get the // header back to pristine condition for the next sort var headerRow = '<tr>'; - headerRow += '<th><div class=tooltip>view/<br>request ⓘ<span onclick="event.stopPropagation()" class="tooltiptext"><em>"view"</em> opens the genome browser for an existing assembly, <em>"request"</em> opens an assembly request form.</span></div></th>'; + headerRow += '<th><div class=tooltip>View/<br>Request ⓘ<span onclick="event.stopPropagation()" class="tooltiptext"><em>"view"</em> opens the genome browser for an existing assembly, <em>"request"</em> opens an assembly request form.</span></div></th>'; headerRow += '<th><div class="tooltip">English common name ⓘ<span onclick="event.stopPropagation()" class="tooltiptext">English common name</span></div></th>'; - headerRow += '<th><div class="tooltip">scientific name ⓘ<span onclick="event.stopPropagation()" class="tooltiptext">scientific name</span></div></th>'; + headerRow += '<th><div class="tooltip">Scientific name ⓘ<span onclick="event.stopPropagation()" class="tooltiptext">scientific name</span></div></th>'; headerRow += '<th><div class="tooltip">NCBI Assembly ⓘ<span onclick="event.stopPropagation()" class="tooltiptext">Links to NCBI resource record<br>or UCSC downloads for local UCSC assemblies</span></div></th>'; - headerRow += '<th><div class="tooltip">year ⓘ<span onclick="event.stopPropagation()" class="tooltiptextright">Year assembly was released.</span></div></th>'; - headerRow += '<th><div class="tooltip"><em>genark</em> clade ⓘ<span onclick="event.stopPropagation()" class="tooltiptextright">clade specification as found in the GenArk system.</span></div></th>'; - headerRow += '<th><div class="tooltip">description ⓘ<span onclick="event.stopPropagation()" class="tooltiptextright">other meta data for this assembly.</span></div></th>'; - headerRow += '<th><div class="tooltip">status ⓘ<span onclick="event.stopPropagation()" class="tooltiptextright">various other status</span></div></th>'; + headerRow += '<th><div class="tooltip">Year ⓘ<span onclick="event.stopPropagation()" class="tooltiptextright">Year assembly was released.</span></div></th>'; + headerRow += '<th><div class="tooltip"><em>GenArk</em> clade ⓘ<span onclick="event.stopPropagation()" class="tooltiptextright">clade specification as found in the GenArk system.</span></div></th>'; + headerRow += '<th><div class="tooltip">Description ⓘ<span onclick="event.stopPropagation()" class="tooltiptextright">other meta data for this assembly.</span></div></th>'; + headerRow += '<th><div class="tooltip">Status ⓘ<span onclick="event.stopPropagation()" class="tooltiptextright">various other status</span></div></th>'; headerRow += '</tr>'; tableHead.innerHTML = headerRow; } // call with visible true to make visible, false to hide function advancedSearchVisible(visible) { var advancedSearchButton = document.getElementById("advancedSearchButton"); var searchOptions = document.getElementById("advancedSearchOptions"); if (visible) { searchOptions.style.display = "flex"; - advancedSearchButton.textContent = "hide advanced search options"; + advancedSearchButton.textContent = "Hide advanced search options"; stateObject.advancedSearchVisible = true; } else { searchOptions.style.display = "none"; - advancedSearchButton.textContent = "show advanced search options"; + advancedSearchButton.textContent = "Show advanced search options"; stateObject.advancedSearchVisible = false; } } // Function to highlight words in the result that match the words // in the queryString. Work through each item of the rowData object, // for each string, find out if it matches any of the words in the // queryString. This is tricky, there are extra characters besides // just [a-zA-Z] that are getting in the way of these matches, where // the MySQL could match, for example: checking: // 'HG02257' =? '(HG02257.pat' // 'HG02257' =? 'HG02257.alt.pat.f1_v2' // doesn't match here, but MySQL match did function highlightMatch(queryString, rowData) { @@ -377,39 +377,39 @@ } else { extraInfo[key] = jsonData[key]; } } headerRefresh(tableHeader); var count = 0; for (var id in genomicEntries) { highlightMatch(extraInfo.q, genomicEntries[id]); var dataRow = '<tr>'; var browserUrl = id; var asmInfoUrl = id; if (genomicEntries[id].browserExists) { if (id.startsWith("GC")) { - browserUrl = "<a href='/h/" + id + "?position=lastDbPos' target=_blank>view</a>"; + browserUrl = "<a href='/h/" + id + "?position=lastDbPos' target=_blank>View</a>"; asmInfoUrl = "<a href='https://www.ncbi.nlm.nih.gov/assembly/" + id + "' target=_blank>" + id + "</a>"; } else { - browserUrl = "<a href='/cgi-bin/hgTracks?db=" + id + "' target=_blank>view</a>"; + browserUrl = "<a href='/cgi-bin/hgTracks?db=" + id + "' target=_blank>View</a>"; asmInfoUrl = "<a href='https://hgdownload.soe.ucsc.edu/goldenPath/" + id + "/bigZips/' target=_blank>" + id + "</a>"; } dataRow += "<th>" + browserUrl + "</th>"; } else { - dataRow += "<th><button type=button' onclick='asmOpenModal(this)' name=" + id + "'>request</button></th>"; + dataRow += "<th><button type=button' onclick='asmOpenModal(this)' name=" + id + "'>Request</button></th>"; } dataRow += "<td>" + genomicEntries[id].commonName + "</td>"; dataRow += "<td>" + genomicEntries[id].scientificName + "</td>"; dataRow += "<th>" + asmInfoUrl + "</th>"; dataRow += "<td>" + genomicEntries[id].year + "</td>"; dataRow += "<td>" + genomicEntries[id].clade + "</td>"; dataRow += "<td>" + genomicEntries[id].description + "</td>"; var status = "<td>" + genomicEntries[id].priority + " "; var hardSpace = " "; if (genomicEntries[id].refSeqCategory) { status += " " + genomicEntries[id].refSeqCategory; hardSpace = ""; } if (genomicEntries[id].versionStatus) { status += " " + genomicEntries[id].versionStatus; @@ -743,31 +743,31 @@ historyUrl += ";advancedSearch=true"; } else { stateObject.advancedSearchVisible = false; } stateObject.maxItemsOutput = maxItemsOutput; stateObject.browser = browserExist; stateObject.debug = debug; stateObject.measureTiming = measureTiming; stateObject.wordMatch = wordMatch; stateObject.asmStatus = asmStatus; stateObject.refSeqCategory = refSeqCategory; stateObject.asmLevel = asmLevel; let shareThisSearch = document.getElementById('shareThisSearch'); let thisPageHref = "<a href='assemblySearch.html"; thisPageHref += historyUrl; - thisPageHref += "'>share this search</a>"; + thisPageHref += "'>Share this search</a>"; shareThisSearch.innerHTML = thisPageHref; xhr.open('GET', urlPrefix + url, true); xhr.onload = function() { if (xhr.status === 200) { // Hide the wait spinner once the AJAX request is complete document.querySelector(".submitContainer").classList.remove("loading"); document.getElementById("loadingSpinner").style.display = "none"; enableButtons(); stateObject.jsonData = xhr.responseText; history.pushState(stateObject, '', historyUrl); var data = JSON.parse(xhr.responseText);