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Path-first URLs #136

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Feb 20, 2024
Merged

Path-first URLs #136

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2 changes: 1 addition & 1 deletion OConnor/resources/views/experiments.html
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Expand Up @@ -23,7 +23,7 @@
//the function for adding an experiment is defined in addExperiment.js

var buttonBarItems = [
{text: 'Add New Experiment', handler: function() {window.location = '/oconnor' + containerPath + '/experimentInsert.view?'}}
{text: 'Add New Experiment', handler: function() {window.location = containerPath + '/oconnor-experimentInsert.view'}}
];

//list all experiments. sort descending by experiment number so newest experiments are at top of grid
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50 changes: 25 additions & 25 deletions OConnor/resources/views/inventory.html
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<ul>
<li><span style="font-size: small;"><span style="font-size: small;"><strong>Search available</strong>:</span></span>
<ul>
<li><span class="Apple-style-span" style="font-size: small;"><a id="all_samples" href="<%=contextPath%>/query<%=containerPath%>/executeQuery.view?schemaName=oconnor&amp;query.queryName=inventory&amp;query.viewName=all_samples"><strong>all available samples</strong></a></span></li>
<li><span class="Apple-style-span" style="font-size: small;"><strong><a title="available specimens" href="<%=contextPath%>/query<%=containerPath%>/executeQuery.view?schemaName=oconnor&amp;query.queryName=inventory&amp;query.viewName=specimen_available">specimens</a></strong></span></li>
<li><span class="Apple-style-span" style="font-size: small;"><strong><a title="available nucleic acid samples" href="<%=contextPath%>/query<%=containerPath%>/executeQuery.view?schemaName=oconnor&amp;query.queryName=inventory&amp;query.viewName=clinical_nucacid_available">DNA/RNA isolated from clinical samples</a></strong></span></li>
<li><span class="Apple-style-span" style="font-size: small;"><a title="plasmid vectors" href="<%=contextPath%>/query<%=containerPath%>/executeQuery.view?schemaName=oconnor&amp;query.queryName=inventory&amp;query.viewName=dna_available"><strong>plasmid vectors</strong></a></span></li>
<li><span class="Apple-style-span" style="font-size: small;"><strong><a title="cell lines" href="<%=contextPath%>/query<%=containerPath%>/executeQuery.view?schemaName=oconnor&amp;query.queryName=inventory&amp;query.viewName=cells_available">cell lines</a></strong></span></li>
<li><span class="Apple-style-span" style="font-size: small;"><a title="available oligonucleotides" href="<%=contextPath%>/query<%=containerPath%>/executeQuery.view?schemaName=oconnor&amp;query.queryName=inventory&amp;query.viewName=oligo_available"><strong>oligonucleotides</strong></a></span></li>
<li><span class="Apple-style-span" style="font-size: small;"><strong><a title="available virus stocks" href="<%=contextPath%>/query<%=containerPath%>/executeQuery.view?schemaName=oconnor&amp;query.queryName=inventory&amp;query.viewName=virus_available">virus stocks</a></strong></span></li>
<li><span class="Apple-style-span" style="font-size: small;"><a id="all_samples" href="<%=contextPath%><%=containerPath%>/query-executeQuery.view?schemaName=oconnor&amp;query.queryName=inventory&amp;query.viewName=all_samples"><strong>all available samples</strong></a></span></li>
<li><span class="Apple-style-span" style="font-size: small;"><strong><a title="available specimens" href="<%=contextPath%><%=containerPath%>/query-executeQuery.view?schemaName=oconnor&amp;query.queryName=inventory&amp;query.viewName=specimen_available">specimens</a></strong></span></li>
<li><span class="Apple-style-span" style="font-size: small;"><strong><a title="available nucleic acid samples" href="<%=contextPath%><%=containerPath%>/query-executeQuery.view?schemaName=oconnor&amp;query.queryName=inventory&amp;query.viewName=clinical_nucacid_available">DNA/RNA isolated from clinical samples</a></strong></span></li>
<li><span class="Apple-style-span" style="font-size: small;"><a title="plasmid vectors" href="<%=contextPath%><%=containerPath%>/query-executeQuery.view?schemaName=oconnor&amp;query.queryName=inventory&amp;query.viewName=dna_available"><strong>plasmid vectors</strong></a></span></li>
<li><span class="Apple-style-span" style="font-size: small;"><strong><a title="cell lines" href="<%=contextPath%><%=containerPath%>/query-executeQuery.view?schemaName=oconnor&amp;query.queryName=inventory&amp;query.viewName=cells_available">cell lines</a></strong></span></li>
<li><span class="Apple-style-span" style="font-size: small;"><a title="available oligonucleotides" href="<%=contextPath%><%=containerPath%>/query-executeQuery.view?schemaName=oconnor&amp;query.queryName=inventory&amp;query.viewName=oligo_available"><strong>oligonucleotides</strong></a></span></li>
<li><span class="Apple-style-span" style="font-size: small;"><strong><a title="available virus stocks" href="<%=contextPath%><%=containerPath%>/query-executeQuery.view?schemaName=oconnor&amp;query.queryName=inventory&amp;query.viewName=virus_available">virus stocks</a></strong></span></li>
</ul>
</li>
</ul>
<ul>
<li><span style="font-size: small;"><strong>Search removed</strong>: click to see&nbsp;<strong><a title="removed samples" href="<%=contextPath%>/query<%=containerPath%>/executeQuery.view?schemaName=oconnor&amp;query.queryName=inventory_removed">samples that have been removed</a>&nbsp;</strong>from the inventory</span></li>
<li><span style="font-size: small;"><strong>Search removed</strong>: click to see&nbsp;<strong><a title="removed samples" href="<%=contextPath%><%=containerPath%>/query-executeQuery.view?schemaName=oconnor&amp;query.queryName=inventory_removed">samples that have been removed</a>&nbsp;</strong>from the inventory</span></li>
</ul>
<ul>
<li><span class="Apple-style-span" style="font-size: small;"><strong>Data integrity</strong>: add and edit allowable values in validated fields</span></li>
</ul>
<ul>
<ul>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%>/query<%=containerPath%>/executeQuery.view?schemaName=oconnor&amp;query.queryName=all_species">all species</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%>/query<%=containerPath%>/executeQuery.view?schemaName=oconnor&amp;query.queryName=all_specimens">all specimens</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%>/query<%=containerPath%>/executeQuery.view?schemaName=oconnor&amp;query.queryName=availability">availability</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%>/query<%=containerPath%>/executeQuery.view?schemaName=oconnor&amp;query.queryName=cell_type">cell type</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%>/query<%=containerPath%>/executeQuery.view?schemaName=oconnor&amp;query.queryName=dna_type">dna type</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%>/query<%=containerPath%>/executeQuery.view?schemaName=oconnor&amp;query.queryName=freezer_id">freezer</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%>/query<%=containerPath%>/executeQuery.view?schemaName=oconnor&amp;query.queryName=laboratory">laboratory</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%>/query<%=containerPath%>/executeQuery.view?schemaName=oconnor&amp;query.queryName=oligo_purification">oligo purification</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%>/query<%=containerPath%>/executeQuery.view?schemaName=oconnor&amp;query.queryName=oligo_type">oligo type</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%>/query<%=containerPath%>/executeQuery.view?schemaName=oconnor&amp;query.queryName=sample_type">sample type</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%>/query<%=containerPath%>/executeQuery.view?schemaName=oconnor&amp;query.queryName=specimen_additive">specimen additive</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%>/query<%=containerPath%>/executeQuery.view?schemaName=oconnor&amp;query.queryName=specimen_collaborator">specimen collaborator</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%>/query<%=containerPath%>/executeQuery.view?schemaName=oconnor&amp;query.queryName=specimen_geographic_origin">specimen geographic origin</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%>/query<%=containerPath%>/executeQuery.view?schemaName=oconnor&amp;query.queryName=specimen_institution">specimen institution</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%>/query<%=containerPath%>/executeQuery.view?schemaName=oconnor&amp;query.queryName=specimen_species">specimen species</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%>/query<%=containerPath%>/executeQuery.view?schemaName=oconnor&amp;query.queryName=specimen_type">specimen type</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%>/query<%=containerPath%>/executeQuery.view?schemaName=oconnor&amp;query.queryName=virus_strain">virus strain</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%><%=containerPath%>/query-executeQuery.view?schemaName=oconnor&amp;query.queryName=all_species">all species</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%><%=containerPath%>/query-executeQuery.view?schemaName=oconnor&amp;query.queryName=all_specimens">all specimens</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%><%=containerPath%>/query-executeQuery.view?schemaName=oconnor&amp;query.queryName=availability">availability</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%><%=containerPath%>/query-executeQuery.view?schemaName=oconnor&amp;query.queryName=cell_type">cell type</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%><%=containerPath%>/query-executeQuery.view?schemaName=oconnor&amp;query.queryName=dna_type">dna type</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%><%=containerPath%>/query-executeQuery.view?schemaName=oconnor&amp;query.queryName=freezer_id">freezer</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%><%=containerPath%>/query-executeQuery.view?schemaName=oconnor&amp;query.queryName=laboratory">laboratory</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%><%=containerPath%>/query-executeQuery.view?schemaName=oconnor&amp;query.queryName=oligo_purification">oligo purification</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%><%=containerPath%>/query-executeQuery.view?schemaName=oconnor&amp;query.queryName=oligo_type">oligo type</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%><%=containerPath%>/query-executeQuery.view?schemaName=oconnor&amp;query.queryName=sample_type">sample type</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%><%=containerPath%>/query-executeQuery.view?schemaName=oconnor&amp;query.queryName=specimen_additive">specimen additive</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%><%=containerPath%>/query-executeQuery.view?schemaName=oconnor&amp;query.queryName=specimen_collaborator">specimen collaborator</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%><%=containerPath%>/query-executeQuery.view?schemaName=oconnor&amp;query.queryName=specimen_geographic_origin">specimen geographic origin</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%><%=containerPath%>/query-executeQuery.view?schemaName=oconnor&amp;query.queryName=specimen_institution">specimen institution</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%><%=containerPath%>/query-executeQuery.view?schemaName=oconnor&amp;query.queryName=specimen_species">specimen species</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%><%=containerPath%>/query-executeQuery.view?schemaName=oconnor&amp;query.queryName=specimen_type">specimen type</a></strong></span></li>
<li><span style="font-size: small;"><strong><a href="<%=contextPath%><%=containerPath%>/query-executeQuery.view?schemaName=oconnor&amp;query.queryName=virus_strain">virus strain</a></strong></span></li>
</ul>
</ul>
<span style="font-size: x-small;" data-mce-style="font-size: x-small;"><span style="font-size: x-small;" data-mce-style="font-size: x-small;"></span></span><hr /><span style="font-size: x-small;"><em>Labkey inventory module v.2.0 by David O'Connor. Last updated 2011-07-22</em></span></div>
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4 changes: 2 additions & 2 deletions OConnor/resources/views/mhc_haplotypes_search_by_haplotype.html
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Expand Up @@ -10,7 +10,7 @@ <h2>WNPRC MHC Haplotypes</h2>
<p>With so many MHC class I genes per chromosome, it is perhaps not surprising that more than 1,000 MHC class I gene variants, or alleles, have been defined in Indian rhesus macaques. Comparable numbers of alleles have been identified in cynomolgus macaques and in rhesus macaques of other origins. For a long time, this led us to believe that sorting out MHC class I genetics would be unfathomably complex.</p>
<p>Conventional genotyping tests, or assays that determine which MHC class I alleles an animal possesses, have not even tried to understand this complexity. In the most common tests, termed PCR-SSP assays, animals are tested for the presence or absence of 8 MHC class I alleles important to SIV immunity. More recently, our group has performed deep sequencing on MHC class I alleles from a large number of macaques. To our surprise, we discovered that the majority of MHC class I chromosomes follow simple and predictable arrangements. The MHC class I region is subdivided further into MHC class I A and class I B genes; there are simple groups of MHC class I A and B alleles that are consistently inherited together as haplotypes.</p>
<p>We have derived descriptive names for these haplotypes that are based on the most 'major' MHC class I transcript it encodes. For example, the A001 haplotype encodes a set of alleles including Mamu-A1*001, an allele that is transcriptionally abundant and known to be involved in SIV immunity. Looking at an animal's haplotypes allows you to discover, at a glance, up to four MHC class I alleles that are potentially restricting CD8+ T cell responses (two MHC class I A and two MHC class I B haplotypes). We also have generated a dictionary that comprehensively lists all of the major and minor MHC class I transcripts associated with each haplotype.</p>
<p><a href="<%=contextPath%>/query<%=containerPath%>/executeQuery.view?schemaName=oconnor&amp;query.queryName=mhc_haplotypes&amp;query.viewName=enabled_haplotypes_simple">Click here to search MHC haplotypes of WNPRC Indian rhesus macaques</a></p>
<p><a href="<%=contextPath%>/query<%=containerPath%>/executeQuery.view?schemaName=oconnor&amp;query.queryName=mhc_haplotypes_distinct">Click here to view the MHC class I alleles encoded on Indian rhesus macaque MHC haplotypes</a>&nbsp;</p>
<p><a href="<%=contextPath%><%=containerPath%>/query-executeQuery.view?schemaName=oconnor&amp;query.queryName=mhc_haplotypes&amp;query.viewName=enabled_haplotypes_simple">Click here to search MHC haplotypes of WNPRC Indian rhesus macaques</a></p>
<p><a href="<%=contextPath%><%=containerPath%>/query-executeQuery.view?schemaName=oconnor&amp;query.queryName=mhc_haplotypes_distinct">Click here to view the MHC class I alleles encoded on Indian rhesus macaque MHC haplotypes</a>&nbsp;</p>
</body>
</html>
2 changes: 1 addition & 1 deletion OConnor/resources/views/oc_purchase_start.html
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</head>
<body>

<p>Click here to <a href="<%=contextPath%>/oconnor<%=containerPath%>/my_purchases.view">view your orders</a> and begin using the system.</p>
<p>Click here to <a href="<%=contextPath%><%=containerPath%>/oconnor-my_purchases.view">view your orders</a> and begin using the system.</p>
<p>As this system incorporates features from the previous DHO lab system and the Lab Hound system DHO developed with Scott Svendsen, there are likely going to be some bugs in this early version. Please report any problems to Dave.&nbsp;</p>
</body>
</html>
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