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Reorganize start page #94

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17 changes: 13 additions & 4 deletions lib/Viroverse/Controller/Homepage.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,18 @@ sub index : Chained('base') PathPart('') Args(0) {
return RedirectToUrl($c, Viroverse::Config->conf->{redirect_root_to});
}

my $nag = !Viroverse::Config->conf->{registered};

$c->stash(
template => 'homepage/index.tt',
nag => $nag
);
$c->detach( $c->view("NG") );
}

sub projects : Chained('base') PathPart('my_projects') Args(0) {
my ($self, $c) = @_;

# The extensive prefetching below bundles a bunch of relationships into a
# single fairly efficient query without resorting to a database view to
# power the homepage.
Expand All @@ -48,13 +60,10 @@ sub index : Chained('base') PathPart('') Args(0) {
reduce { push @{ $a->{ $b->project->name } ||= [] }, $b; $a }
+{}, @assignments;

my $nag = !Viroverse::Config->conf->{registered};

$c->stash(
template => 'homepage/index.tt',
template => 'homepage/assigned-projects.tt',
my_projects => $my_projects,
cohorts => [ $c->model("ViroDB::Cohort")->order_by('name')->all ],
nag => $nag,
);
$c->detach( $c->view("NG") );
}
Expand Down
62 changes: 62 additions & 0 deletions root/ngtemplate/homepage/assigned-projects.tt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,62 @@
[%- page = {
title = "Viroverse: Projects and Cohorts",
}
-%]

[% BLOCK 'input-progress-button' %]
<a href='[% c.uri_for_action(dest, [project_sample.sample.sample_id]) %]'
class="btn btn-[% completed ? 'success' : 'default' %] btn-xs">
[% label %]
</a>
[% END %]

<div class="row">
<div class="col-md-12" ng-controller="LocationHash as locationHash">
[% IF my_projects.size > 0 %]
<h2>My assigned samples</h2>
<uib-tabset active="locationHash.value" ng-cloak>
[% FOR project IN my_projects.keys.sort %]
<uib-tab index="'[% project %]'" heading="[% project %]">
<table class="table">
<thead>
<tr>
<th>Sample Name</th>
<th>Subject</th>
<th>Sample Type</th>
<th>Date Collected</th>
<th></th>
</tr>
</thead>
<tbody>
[% FOR project_sample IN my_projects.$project %]
<tr>
<td><a href="[% c.uri_for_action('/sample/show', [ project_sample.sample.id ]) %]">
[% project_sample.sample.name || '#' _ project_sample.sample.id %]
</a>
</td>
<td><a href="[% c.uri_for_action('/patient/show_by_id', [ project_sample.sample.patient.patient_id ]) %]">
[% project_sample.sample.patient.name || "unnamed subject" %]
</a>
</td>
<td>[% project_sample.sample.tissue_type.name || "unknown tissue" %]</td>
<td>[% project_sample.sample.date.strftime('%Y-%m-%d') || "unknown date" %]</td>
<td>
<div class="input-progress">
[% INCLUDE 'input-progress-button', dest='/sample/new_extraction', label='Extraction', completed=$(project_sample.progress).has_extractions %]
[% INCLUDE 'input-progress-button', dest='/sample/new_rt_product', label='RT', completed=$(project_sample.progress).has_rt_products %]
[% INCLUDE 'input-progress-button', dest='/sample/new_pcr_product', label='PCR', completed=$(project_sample.progress).has_pcr_products %]
[% INCLUDE 'input-progress-button', dest='/sample/new_sequence', label='Sequence', completed=$(project_sample.progress).has_sequences %]
</div>
</td>
</tr>
[% END %]
</tbody>
</table>
</uib-tab>
[% END %]
</uib-tabset>
[% ELSE %]
<h2>No assigned projects found</h2>
[% END %]
</div>
</div>
118 changes: 55 additions & 63 deletions root/ngtemplate/homepage/index.tt
View file
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Original file line number Diff line number Diff line change
@@ -1,73 +1,65 @@
[%- page = {
title = "Viroverse",
}
title = "Viroverse: Start Page",
}
-%]
<div class="row">
<div class="col-md-12" ng-controller="LocationHash as locationHash">
[% IF nag %]
<div class="alert alert-info" role="alert">
<p>Please help us maintain funding for Viroverse development by
<div class="alert alert-info" role="alert">
<p>Please help us maintain funding for Viroverse development by
<a href="mailto:mullspt+cfar@uw.edu?subject=Viroverse">emailing
us</a> and letting us know who you are and what you're using
us</a> and letting us know who you are and what you're using
Viroverse for!</p>
</div>
</div>
[% END %]
[% IF my_projects.size > 0 %]
<h2>My assigned samples</h2>
<uib-tabset active="locationHash.value" ng-cloak>
[% FOR project IN my_projects.keys.sort %]
<uib-tab index="'[% project %]'" heading="[% project %]">
<table class="table">
<thead>
<tr>
<th>Sample Name</th>
<th>Subject</th>
<th>Sample Type</th>
<th>Date Collected</th>
<th></th>
</tr>
</thead>
<tbody>
[% FOR project_sample IN my_projects.$project %]
<tr>
<td><a href="[% c.uri_for_action('/sample/show', [ project_sample.sample.id ]) %]">
[% project_sample.sample.name || '#' _ project_sample.sample.id %]
</a>
</td>
<td><a href="[% c.uri_for_action('/patient/show_by_id', [ project_sample.sample.patient.patient_id ]) %]">
[% project_sample.sample.patient.name || "unnamed subject" %]
</a>
</td>
<td>[% project_sample.sample.tissue_type.name || "unknown tissue" %]</td>
<td>[% project_sample.sample.date.strftime('%Y-%m-%d') || "unknown date" %]</td>
<td>
<div class="input-progress">
[% INCLUDE 'input-progress-button', dest='/sample/new_extraction', label='Extraction', completed=$(project_sample.progress).has_extractions %]
[% INCLUDE 'input-progress-button', dest='/sample/new_rt_product', label='RT', completed=$(project_sample.progress).has_rt_products %]
[% INCLUDE 'input-progress-button', dest='/sample/new_pcr_product', label='PCR', completed=$(project_sample.progress).has_pcr_products %]
[% INCLUDE 'input-progress-button', dest='/sample/new_sequence', label='Sequence', completed=$(project_sample.progress).has_sequences %]
</div>
</td>
</tr>
[% END %]
</tbody>
</table>
</uib-tab>
[% END %]
</uib-tabset>
[% END %]
<h2>Cohorts</h2>
<ul class="cohort-list">
[% FOREACH cohort IN cohorts %]
<li><a href="[% c.uri_for_action("/cohort/show", [cohort.id] ) %]">[% cohort.name %]</a> ([% $(cohort.patient_cohorts).count + 0 %])</li>
[% END %]
</ul>
</div>
</div>
<div class="col-md-12">
<h1>Welcome to Viroverse</h1>

<h2>Projects and Cohorts</h2>
<ul class="list-unstyled">
<li><a href="[% c.uri_for_action('/homepage/projects') %]">Assigned Projects</a></li>
<li><a href="[% c.uri_for_action('/project/index') %]">Browse projects</a></li>
<li><a href="[% c.uri_for_action('/cohort/index') %]">Browse cohorts</a></li>
</ul>

<h2>Subjects</h2>
<ul class="list-unstyled">
<li><a href="[% c.uri_for_action('/cohort/index') %]">Browse subjects</a></li>
<li><a href="[% c.uri_for_action('/patient/select') %]">Look up subject</a></li>
<li><a href="[% c.uri_for_action('/sample/index') %]">Search samples</a></li>
</ul>

<h2>PCR &amp; Sequencing</h2>
<ul class="list-unstyled">
<li><a href="[% c.uri_for_action('/sequence/index') %]">Search sequences</a></li>
<li><a href="[% c.uri_for_action('/primer/index') %]">Search primers</a></li>
<li><a href="[% c.uri_for_action('/gel/index') %]">Search gels</a></li>
[% IF features.pacbio_sequencing %]
<li><a href="[% c.uri_for_action('/pacbiosequencing/index') %]">Browse[% IF scientist.can_edit %]/edit[% END %] PacBio sequencing pools</a></li>
[% END %]
[% IF scientist.is_admin OR scientist.is_supervisor %]
<li><a href="[% c.uri_for_action('/import/index') %]">Import data files</a></li>
[% END %]
[% IF scientist.can_edit %]
<li><a href="[% c.uri_for_action('/input/extraction') %]">Add extraction</a></li>
<li><a href="[% c.uri_for_action('/input/PCR') %]">Add PCR</a></li>
<li><a href="[% c.uri_for_action('/input/PCR_gel') %]">Add gel visualization</a></li>
<li><a href="[% c.uri_for_action('/input/sequence/index') %]">Add sequencing product</a></li>
[% END %]
</ul>

[% BLOCK 'input-progress-button' %]
<a href='[% c.uri_for_action(dest, [project_sample.sample.sample_id]) %]'
class="btn btn-[% completed ? 'success' : 'default' %] btn-xs">
[% label %]
</a>
[% END %]
[% IF scientist.is_admin OR scientist.is_supervisor %]
<h2>Administration</h2>
<ul class="list-unstyled">
[% IF scientist.is_admin %]
<li><a href="[% c.uri_for_action('/admin/scientist/index') %]">Administer Scientists</a></li>
<li><a href="[% c.uri_for_action('/admin/cohort/index') %]">Manage cohorts</a></li>
<li><a href="[% c.uri_for_action('/tissuetype/index') %]">Manage tissue types</a></li>
<li><a href="[% c.uri_for_action('/admin/protocol/index') %]">Manage generic protocols</a></li>
<li><a href="[% c.uri_for_action('/derivationprotocol/index') %]">Manage derivation protocols</a></li>
[% END %]
</ul>
[% END %]
</div>
</div>