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modify crispr qc view sub template to be more flexible in what it sho…
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…ws, also if its used to update crispr es qc information or not
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@sajp
sajp committed Dec 11, 2014
1 parent 9888c68 commit 9d528e5
Showing 1 changed file with 106 additions and 81 deletions.
187 changes: 106 additions & 81 deletions root/lib/crispr_qc_view.tt
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@@ -1,7 +1,11 @@
<td>[% row.well_name %]</td>
[% UNLESS hide_well_name %]
<td>[% row.well_name %]</td>
[% END %]

[% UNLESS hide_crispr_well_id %]
<td>[% row.es_qc_well_id %]</td>
[% END %]

[% IF row.gene %]
<td>[% row.gene %]</td>
[% END %]
Expand Down Expand Up @@ -33,92 +37,113 @@
[% END %]
</td>

[% IF accept %]
<td>
<div class="control-group">
<div class="controls">
[% IF row.show_checkbox %]
<input type="checkbox" name="accepted_[% row.well_id %]" class="update_crispr_es_qc_well" data-crispr_well_id="[% row.es_qc_well_id %]" data-crispr_data_type="accepted" [% row.well_accepted ? "checked='checked'" : "" %] />
[% ELSE %]
Accepted in another run
[% END %]
</div>
</div>
</td>
[% END %]
<!-- If edit flag is true allow setting on crispr damage type and variant size info, otherwise just display info -->
[% IF edit %]

<td>
<div class="control-group">
<div class="controls">
<select name="crispr_damage_[% row.well_id %]" class="update_crispr_es_qc_well input-medium" data-crispr_well_id="[% row.es_qc_well_id %]" data-crispr_data_type="damage_type">
<option value="" [% UNLESS row.damage_type %]selected[% END %]>-</option>
[%- FOR type IN damage_types %]
<option value="[% type %]" [% row.damage_type == type ? 'selected="selected"' : '' %]>[% type %]</option>
[% END %]
</select>
</div>
</div>
</td>
<!--Add accepted checkbox, only want to show this on teh main crispr es qc page -->
[% IF accept %]
<td>
<div class="control-group">
<div class="controls">
[% IF row.show_checkbox %]
<input type="checkbox" name="accepted_[% row.well_id %]" class="update_crispr_es_qc_well" data-crispr_well_id="[% row.es_qc_well_id %]" data-crispr_data_type="accepted" [% row.well_accepted ? "checked='checked'" : "" %] />
[% ELSE %]
Accepted in another run
[% END %]
</div>
</div>
</td>
[% END %]

<td>
<div class="control-group">
<div class="controls">
<input type="text" name="variant_size_[% row.well_id %]" class="update_crispr_es_qc_well input-mini" data-crispr_well_id="[% row.es_qc_well_id %]" data-crispr_data_type="variant_size" value="[% row.variant_size %]" />
</div>
</div>
</td>
<td>
<div class="control-group">
<div class="controls">
<select name="crispr_damage_[% row.well_id %]" class="update_crispr_es_qc_well input-medium" data-crispr_well_id="[% row.es_qc_well_id %]" data-crispr_data_type="damage_type">
<option value="" [% UNLESS row.damage_type %]selected[% END %]>-</option>
[%- FOR type IN damage_types %]
<option value="[% type %]" [% row.damage_type == type ? 'selected="selected"' : '' %]>[% type %]</option>
[% END %]
</select>
</div>
</div>
</td>

<td>
[% IF row.has_vcf_file %]
<a href="[% c.uri_for( '/user/crispr_qc_well', row.es_qc_well_id, 'vcf_file' ) %]" target="_blank" >vcf_file</a>
[% END %]
<br>
[% IF row.has_vep_file %]
<a href="[% c.uri_for( '/user/crispr_qc_well', row.es_qc_well_id, 'vep_file' ) %]" target="_blank" >vep_file</a>
[% END %]
[% IF row.has_non_merged_vcf_file %]
<a href="[% c.uri_for( '/user/crispr_qc_well', row.es_qc_well_id, 'non_merged_vcf_file' ) %]" target="_blank" >non_merged_vcf_file</a>
[% END %]
</td>
<td>
<div class="control-group">
<div class="controls">
<input type="text" name="variant_size_[% row.well_id %]" class="update_crispr_es_qc_well input-mini" data-crispr_well_id="[% row.es_qc_well_id %]" data-crispr_data_type="variant_size" value="[% row.variant_size %]" />
</div>
</div>
</td>
[% ELSE %]

<td>
[% IF row.has_ref_aa_file %]
<a href="[% c.uri_for( '/user/crispr_qc_well', row.es_qc_well_id, 'aa_file', 'ref' ) %]" target="_blank" >reference</a>
[% END %]
<br>
[% IF row.has_mut_aa_file %]
<a href="[% c.uri_for( '/user/crispr_qc_well', row.es_qc_well_id, 'aa_file', 'mut' ) %]" target="_blank" >mutated</a>
[% END %]
<td>
[% IF row.well_accepted %]<span class="label label-success">Accepted</span>[% END %]
</td>

</td>
<td>
[% row.damage_type %]
</td>

<td>
[% IF row.fwd_read %]
<a href="[% c.uri_for( '/user/crispr_qc_well', row.es_qc_well_id, 'read', 'fwd' ) %]" target="_blank" >fwd_read</a>
[% END %]
<br>
[% IF row.rev_read %]
<a href="[% c.uri_for( '/user/crispr_qc_well', row.es_qc_well_id, 'read', 'rev' ) %]" target="_blank" >rev_read</a>
[% END %]
</td>
<td>
[% row.variant_size %]
</td>

<td>
[% FOR dir IN row.deletions.keys %]
[% NEXT UNLESS row.deletions.$dir.keys.size > 0 %]
[% dir %] deletion:<br/>
[% FOR loc IN row.deletions.$dir.keys.sort %]
[% loc %]: <span class="indel_sequence"> [% row.deletions.$dir.$loc.seq %]([% row.deletions.$dir.$loc.length %])</span> <br/>
[% END %]
[% END %]
</td>
[% END %]

<td>
[% FOR dir IN row.insertions.keys %]
[% NEXT UNLESS row.insertions.$dir.keys.size > 0 %]
[% dir %] insertion:<br/>
[% FOR loc IN row.insertions.$dir.keys.sort %]
[% loc %]: <span class="indel_sequence"> [% row.insertions.$dir.$loc.seq %]([% row.insertions.$dir.$loc.length %])</span> <br/>
[% END %]
[% END %]
</td>
[% IF complete_info %]
<td>
[% IF row.has_vcf_file %]
<a href="[% c.uri_for( '/user/crispr_qc_well', row.es_qc_well_id, 'vcf_file' ) %]" target="_blank" >vcf_file</a>
[% END %]
<br>
[% IF row.has_vep_file %]
<a href="[% c.uri_for( '/user/crispr_qc_well', row.es_qc_well_id, 'vep_file' ) %]" target="_blank" >vep_file</a>
[% END %]
[% IF row.has_non_merged_vcf_file %]
<a href="[% c.uri_for( '/user/crispr_qc_well', row.es_qc_well_id, 'non_merged_vcf_file' ) %]" target="_blank" >non_merged_vcf_file</a>
[% END %]
</td>

<td>
[% IF row.has_ref_aa_file %]
<a href="[% c.uri_for( '/user/crispr_qc_well', row.es_qc_well_id, 'aa_file', 'ref' ) %]" target="_blank" >reference</a>
[% END %]
<br>
[% IF row.has_mut_aa_file %]
<a href="[% c.uri_for( '/user/crispr_qc_well', row.es_qc_well_id, 'aa_file', 'mut' ) %]" target="_blank" >mutated</a>
[% END %]

</td>

<td>
[% IF row.fwd_read %]
<a href="[% c.uri_for( '/user/crispr_qc_well', row.es_qc_well_id, 'read', 'fwd' ) %]" target="_blank" >fwd_read</a>
[% END %]
<br>
[% IF row.rev_read %]
<a href="[% c.uri_for( '/user/crispr_qc_well', row.es_qc_well_id, 'read', 'rev' ) %]" target="_blank" >rev_read</a>
[% END %]
</td>

<td>
[% FOR dir IN row.deletions.keys %]
[% NEXT UNLESS row.deletions.$dir.keys.size > 0 %]
[% dir %] deletion:<br/>
[% FOR loc IN row.deletions.$dir.keys.sort %]
[% loc %]: <span class="indel_sequence"> [% row.deletions.$dir.$loc.seq %]([% row.deletions.$dir.$loc.length %])</span> <br/>
[% END %]
[% END %]
</td>

<td>
[% FOR dir IN row.insertions.keys %]
[% NEXT UNLESS row.insertions.$dir.keys.size > 0 %]
[% dir %] insertion:<br/>
[% FOR loc IN row.insertions.$dir.keys.sort %]
[% loc %]: <span class="indel_sequence"> [% row.insertions.$dir.$loc.seq %]([% row.insertions.$dir.$loc.length %])</span> <br/>
[% END %]
[% END %]
</td>
[% END %]

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