caruby-tissue 1.2.2 → 1.2.3
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- data/History.txt +4 -0
- data/bin/crtdump +11 -3
- data/bin/{seed → crtseed} +0 -0
- data/conf/annotation/pathology_scg/AdditionalFinding.hbm.xml +19 -0
- data/conf/annotation/pathology_scg/BasePathologyAnnotation.hbm.xml +260 -0
- data/conf/annotation/pathology_scg/BreastMargin.hbm.xml +21 -0
- data/conf/annotation/pathology_scg/BreastMarginInvolved.hbm.xml +15 -0
- data/conf/annotation/pathology_scg/BreastMarginUninvolved.hbm.xml +14 -0
- data/conf/annotation/pathology_scg/CNSMargin.hbm.xml +19 -0
- data/conf/annotation/pathology_scg/CNSMarginLocation.hbm.xml +14 -0
- data/conf/annotation/pathology_scg/CarcinomaInSituStatus.hbm.xml +14 -0
- data/conf/annotation/pathology_scg/ColorectalLocalExcisionMarginUninvolved.hbm.xml +15 -0
- data/conf/annotation/pathology_scg/ColorectalResectedMarginUninvolved.hbm.xml +22 -0
- data/conf/annotation/pathology_scg/Cytogenetics.hbm.xml +15 -0
- data/conf/annotation/pathology_scg/DeepMelanomaMargin.hbm.xml +16 -0
- data/conf/annotation/pathology_scg/Details.hbm.xml +14 -0
- data/conf/annotation/pathology_scg/DirectExtensionOfTumor.hbm.xml +14 -0
- data/conf/annotation/pathology_scg/DistalMargin.hbm.xml +15 -0
- data/conf/annotation/pathology_scg/DistanceFromAnalVerge.hbm.xml +23 -0
- data/conf/annotation/pathology_scg/DistantMetastasis.hbm.xml +19 -0
- data/conf/annotation/pathology_scg/ExcionalBiopsyMarginUninvolved.hbm.xml +15 -0
- data/conf/annotation/pathology_scg/ExcisionalBiopsyColorectalDeepMargin.hbm.xml +15 -0
- data/conf/annotation/pathology_scg/ExcisionalBiopsyColorectalLateralOrMucosalMargin.hbm.xml +15 -0
- data/conf/annotation/pathology_scg/ExtraprostaticExtension.hbm.xml +20 -0
- data/conf/annotation/pathology_scg/ExtraprostaticExtensionTissueSites.hbm.xml +14 -0
- data/conf/annotation/pathology_scg/GleasonScore.hbm.xml +16 -0
- data/conf/annotation/pathology_scg/HistologicGrade.hbm.xml +16 -0
- data/conf/annotation/pathology_scg/HistologicType.hbm.xml +19 -0
- data/conf/annotation/pathology_scg/HistologicVariantType.hbm.xml +14 -0
- data/conf/annotation/pathology_scg/ImmunoPhenotyping.hbm.xml +16 -0
- data/conf/annotation/pathology_scg/Invasion.hbm.xml +16 -0
- data/conf/annotation/pathology_scg/KidneyMarginLocation.hbm.xml +15 -0
- data/conf/annotation/pathology_scg/KidneyNephrectomyMargin.hbm.xml +19 -0
- data/conf/annotation/pathology_scg/LateralMelanomaMargin.hbm.xml +16 -0
- data/conf/annotation/pathology_scg/LocalExcisionColorectalDeepMargin.hbm.xml +15 -0
- data/conf/annotation/pathology_scg/LocalExcisionColorectalLateralMargin.hbm.xml +20 -0
- data/conf/annotation/pathology_scg/LungResectionMargin.hbm.xml +17 -0
- data/conf/annotation/pathology_scg/LungResectionMarginsUninvolved.hbm.xml +14 -0
- data/conf/annotation/pathology_scg/MacroscopicExtentOfTumor.hbm.xml +14 -0
- data/conf/annotation/pathology_scg/MesentricMargin.hbm.xml +15 -0
- data/conf/annotation/pathology_scg/MetastasisTissueSite.hbm.xml +15 -0
- data/conf/annotation/pathology_scg/Microcalcification.hbm.xml +14 -0
- data/conf/annotation/pathology_scg/NottinghamHistologicScore.hbm.xml +17 -0
- data/conf/annotation/pathology_scg/OtherResectedOrgans.hbm.xml +15 -0
- data/conf/annotation/pathology_scg/PancreasMargin.hbm.xml +20 -0
- data/conf/annotation/pathology_scg/PancreasMarginInvolvedByInvasiveCarcinoma.hbm.xml +15 -0
- data/conf/annotation/pathology_scg/PancreasMarginUninvolvedByInvasiveCarcinoma.hbm.xml +20 -0
- data/conf/annotation/pathology_scg/PathologicalStaging.hbm.xml +16 -0
- data/conf/annotation/pathology_scg/PolypConfiguration.hbm.xml +15 -0
- data/conf/annotation/pathology_scg/PrimaryTumorStage.hbm.xml +14 -0
- data/conf/annotation/pathology_scg/ProstateMarginLocation.hbm.xml +15 -0
- data/conf/annotation/pathology_scg/ProximalMargin.hbm.xml +15 -0
- data/conf/annotation/pathology_scg/RadialMargin.hbm.xml +15 -0
- data/conf/annotation/pathology_scg/RadicalProstatectomyMargin.hbm.xml +20 -0
- data/conf/annotation/pathology_scg/RegionalLymphNode.hbm.xml +19 -0
- data/conf/annotation/pathology_scg/SatelliteNodule.hbm.xml +14 -0
- data/conf/annotation/pathology_scg/SpecimenCollectionGroup.hbm.xml +87 -0
- data/conf/annotation/pathology_scg/SpecimenIntegrity.hbm.xml +15 -0
- data/conf/annotation/pathology_scg/SpecimenSize.hbm.xml +17 -0
- data/conf/annotation/pathology_scg/TissueSide.hbm.xml +14 -0
- data/conf/annotation/pathology_scg/TumorSize.hbm.xml +29 -0
- data/conf/annotation/pathology_scg/TumorTissueSite.hbm.xml +20 -0
- data/conf/annotation/pathology_scg/UninvolvedMelanomaMargin.hbm.xml +15 -0
- data/conf/annotation/pathology_specimen/AdditionalFinding.hbm.xml +19 -0
- data/conf/annotation/pathology_specimen/AdditionalPathologicFinding.hbm.xml +18 -0
- data/conf/annotation/pathology_specimen/Details.hbm.xml +15 -0
- data/conf/annotation/pathology_specimen/GleasonScore.hbm.xml +16 -0
- data/conf/annotation/pathology_specimen/HistologicGrade.hbm.xml +16 -0
- data/conf/annotation/pathology_specimen/HistologicType.hbm.xml +19 -0
- data/conf/annotation/pathology_specimen/HistologicVariantType.hbm.xml +14 -0
- data/conf/annotation/pathology_specimen/Invasion.hbm.xml +16 -0
- data/conf/annotation/pathology_specimen/NottinghamHistologicScore.hbm.xml +17 -0
- data/conf/annotation/pathology_specimen/Specimen.hbm.xml +52 -0
- data/conf/annotation/pathology_specimen/SpecimenBaseSolidTissuePathologyAnnotation.hbm.xml +73 -0
- data/examples/galena/lib/galena/cli/seed.rb +0 -21
- data/examples/galena/lib/galena/migration/frozen_shims.rb +6 -5
- data/examples/galena/lib/galena/seed/defaults.rb +0 -5
- data/{lib → examples/galena/lib}/galena.rb +0 -0
- data/lib/catissue/annotation/annotatable.rb +37 -0
- data/lib/catissue/annotation/annotatable_class.rb +255 -0
- data/lib/catissue/annotation/annotation.rb +49 -0
- data/lib/catissue/annotation/annotation_class.rb +277 -0
- data/lib/catissue/annotation/annotation_module.rb +77 -0
- data/lib/catissue/annotation/hibernate_mapping.rb +46 -0
- data/lib/catissue/annotation/proxy.rb +28 -0
- data/lib/catissue/annotation/proxy_class.rb +68 -0
- data/lib/catissue/cli/migrate.rb +2 -2
- data/lib/catissue/cli/smoke.rb +6 -4
- data/lib/catissue/database/annotation/annotation_service.rb +75 -61
- data/lib/catissue/database/annotation/annotator.rb +17 -76
- data/lib/catissue/database/annotation/entity_facade.rb +265 -0
- data/lib/catissue/database/annotation/id_generator.rb +62 -0
- data/lib/catissue/database/annotation/integration_service.rb +105 -59
- data/lib/catissue/database/annotation/reference_writer.rb +150 -0
- data/lib/catissue/database/controlled_values.rb +12 -12
- data/lib/catissue/database.rb +148 -58
- data/lib/catissue/domain/abstract_specimen.rb +40 -14
- data/lib/catissue/domain/abstract_specimen_collection_group.rb +1 -3
- data/lib/catissue/domain/collection_protocol.rb +13 -5
- data/lib/catissue/domain/collection_protocol_event.rb +1 -14
- data/lib/catissue/domain/consent_tier_response.rb +2 -0
- data/lib/catissue/domain/consent_tier_status.rb +5 -3
- data/lib/catissue/domain/container.rb +14 -10
- data/lib/catissue/domain/container_position.rb +8 -0
- data/lib/catissue/domain/container_type.rb +13 -6
- data/lib/catissue/domain/participant.rb +15 -10
- data/lib/catissue/domain/site.rb +9 -3
- data/lib/catissue/domain/specimen.rb +79 -40
- data/lib/catissue/domain/specimen_array.rb +11 -1
- data/lib/catissue/domain/specimen_collection_group.rb +79 -41
- data/lib/catissue/domain/specimen_event_parameters.rb +5 -8
- data/lib/catissue/domain/specimen_position.rb +0 -2
- data/lib/catissue/domain/specimen_requirement.rb +1 -1
- data/lib/catissue/domain/storage_container.rb +109 -48
- data/lib/catissue/domain/storage_type.rb +1 -1
- data/lib/catissue/migration/migrator.rb +6 -14
- data/lib/catissue/resource.rb +18 -8
- data/lib/catissue/util/position.rb +11 -1
- data/lib/catissue/util/storable.rb +18 -11
- data/lib/catissue/util/storage_type_holder.rb +44 -6
- data/lib/catissue/version.rb +1 -1
- metadata +86 -35
- data/bin/migrate.rb +0 -42
- data/bin/seed.rb +0 -43
- data/examples/galena/doc/CaTissue/Participant.html +0 -241
- data/examples/galena/doc/CaTissue/SpecimenCollectionGroup.html +0 -190
- data/examples/galena/doc/CaTissue/StorageContainer.html +0 -179
- data/examples/galena/doc/CaTissue/TissueSpecimen.html +0 -320
- data/examples/galena/doc/CaTissue.html +0 -93
- data/examples/galena/doc/Galena/Seed/Defaults.html +0 -650
- data/examples/galena/doc/Galena/Seed.html +0 -203
- data/examples/galena/doc/Galena.html +0 -172
- data/examples/galena/doc/_index.html +0 -181
- data/examples/galena/doc/class_list.html +0 -36
- data/examples/galena/doc/css/common.css +0 -1
- data/examples/galena/doc/css/full_list.css +0 -53
- data/examples/galena/doc/css/style.css +0 -307
- data/examples/galena/doc/file.README.html +0 -153
- data/examples/galena/doc/file_list.html +0 -38
- data/examples/galena/doc/frames.html +0 -13
- data/examples/galena/doc/index.html +0 -153
- data/examples/galena/doc/js/app.js +0 -202
- data/examples/galena/doc/js/full_list.js +0 -149
- data/examples/galena/doc/js/jquery.js +0 -154
- data/examples/galena/doc/method_list.html +0 -163
- data/examples/galena/doc/top-level-namespace.html +0 -112
- data/lib/README.html +0 -33
- data/lib/catissue/database/annotation/annotatable_service.rb +0 -25
- data/lib/catissue/database/annotation/entity_manager.rb +0 -10
- data/lib/galena/cli/seed.rb +0 -43
- data/lib/galena/migration/filter_shims.rb +0 -43
- data/lib/galena/migration/frozen_shims.rb +0 -53
- data/lib/galena/seed/defaults.rb +0 -109
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192
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$(framesInit);
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193
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$(createSourceLinks);
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194
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$(createDefineLinks);
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195
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$(createFullTreeLinks);
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196
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$(fixBoxInfoHeights);
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197
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$(searchFrameLinks);
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198
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$(linkSummaries);
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199
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$(keyboardShortcuts);
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$(summaryToggle);
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$(fixOutsideWorldLinks);
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$(generateTOC);
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@@ -1,149 +0,0 @@
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1
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-
var inSearch = null;
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2
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-
var searchIndex = 0;
|
3
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-
var searchCache = [];
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4
|
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var searchString = '';
|
5
|
-
|
6
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function fullListSearch() {
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7
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// generate cache
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8
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searchCache = [];
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9
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$('#full_list li').each(function() {
|
10
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var link = $(this).find('.object_link a');
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11
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searchCache.push({name:link.text(), node:$(this), link:link});
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12
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});
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13
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-
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14
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$('#search input').keyup(function() {
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15
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searchString = this.value.toLowerCase();
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16
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if (searchString == "") {
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17
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clearTimeout(inSearch);
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18
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inSearch = null;
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19
|
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$('#full_list, #content').removeClass('insearch');
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20
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$('#full_list li').removeClass('found').each(function() {
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21
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22
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var link = $(this).find('.object_link a');
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23
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link.text(link.text());
|
24
|
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});
|
25
|
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if (clicked) {
|
26
|
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clicked.parents('ul').each(function() {
|
27
|
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$(this).removeClass('collapsed').prev().removeClass('collapsed');
|
28
|
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});
|
29
|
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}
|
30
|
-
highlight();
|
31
|
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}
|
32
|
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else {
|
33
|
-
if (inSearch) clearTimeout(inSearch);
|
34
|
-
searchIndex = 0;
|
35
|
-
lastRowClass = '';
|
36
|
-
$('#full_list, #content').addClass('insearch');
|
37
|
-
$('#noresults').text('');
|
38
|
-
searchItem();
|
39
|
-
}
|
40
|
-
});
|
41
|
-
|
42
|
-
$('#search input').focus();
|
43
|
-
$('#full_list').after("<div id='noresults'></div>")
|
44
|
-
}
|
45
|
-
|
46
|
-
var lastRowClass = '';
|
47
|
-
function searchItem() {
|
48
|
-
for (var i = 0; i < searchCache.length / 50; i++) {
|
49
|
-
var item = searchCache[searchIndex];
|
50
|
-
if (item.name.toLowerCase().indexOf(searchString) == -1) {
|
51
|
-
item.node.removeClass('found');
|
52
|
-
}
|
53
|
-
else {
|
54
|
-
item.node.css('padding-left', '10px').addClass('found');
|
55
|
-
item.node.removeClass(lastRowClass).addClass(lastRowClass == 'r1' ? 'r2' : 'r1');
|
56
|
-
lastRowClass = item.node.hasClass('r1') ? 'r1' : 'r2';
|
57
|
-
item.link.html(item.name.replace(new RegExp("(" +
|
58
|
-
searchString.replace(/([\/.*+?|()\[\]{}\\])/g, "\\$1") + ")", "ig"),
|
59
|
-
'<strong>$1</strong>'));
|
60
|
-
}
|
61
|
-
|
62
|
-
if (searchCache.length == searchIndex + 1) {
|
63
|
-
return searchDone();
|
64
|
-
}
|
65
|
-
else {
|
66
|
-
searchIndex++;
|
67
|
-
}
|
68
|
-
}
|
69
|
-
inSearch = setTimeout('searchItem()', 0);
|
70
|
-
}
|
71
|
-
|
72
|
-
function searchDone() {
|
73
|
-
highlight(true);
|
74
|
-
if ($('#full_list li:visible').size() == 0) {
|
75
|
-
$('#noresults').text('No results were found.').hide().fadeIn();
|
76
|
-
}
|
77
|
-
else {
|
78
|
-
$('#noresults').text('');
|
79
|
-
}
|
80
|
-
$('#content').removeClass('insearch');
|
81
|
-
clearTimeout(inSearch);
|
82
|
-
inSearch = null;
|
83
|
-
}
|
84
|
-
|
85
|
-
clicked = null;
|
86
|
-
function linkList() {
|
87
|
-
$('#full_list li, #full_list li a:last').click(function(evt) {
|
88
|
-
if ($(this).hasClass('toggle')) return true;
|
89
|
-
if (this.tagName.toLowerCase() == "li") {
|
90
|
-
var toggle = $(this).children('a.toggle');
|
91
|
-
if (toggle.size() > 0 && evt.pageX < toggle.offset().left) {
|
92
|
-
toggle.click();
|
93
|
-
return false;
|
94
|
-
}
|
95
|
-
}
|
96
|
-
if (clicked) clicked.removeClass('clicked');
|
97
|
-
var win = window.top.frames.main ? window.top.frames.main : window.parent;
|
98
|
-
if (this.tagName.toLowerCase() == "a") {
|
99
|
-
clicked = $(this).parent('li').addClass('clicked');
|
100
|
-
win.location = this.href;
|
101
|
-
}
|
102
|
-
else {
|
103
|
-
clicked = $(this).addClass('clicked');
|
104
|
-
win.location = $(this).find('a:last').attr('href');
|
105
|
-
}
|
106
|
-
return false;
|
107
|
-
});
|
108
|
-
}
|
109
|
-
|
110
|
-
function collapse() {
|
111
|
-
if (!$('#full_list').hasClass('class')) return;
|
112
|
-
$('#full_list.class a.toggle').click(function() {
|
113
|
-
$(this).parent().toggleClass('collapsed').next().toggleClass('collapsed');
|
114
|
-
highlight();
|
115
|
-
return false;
|
116
|
-
});
|
117
|
-
$('#full_list.class ul').each(function() {
|
118
|
-
$(this).addClass('collapsed').prev().addClass('collapsed');
|
119
|
-
});
|
120
|
-
$('#full_list.class').children().removeClass('collapsed');
|
121
|
-
highlight();
|
122
|
-
}
|
123
|
-
|
124
|
-
function highlight(no_padding) {
|
125
|
-
var n = 1;
|
126
|
-
$('#full_list li:visible').each(function() {
|
127
|
-
var next = n == 1 ? 2 : 1;
|
128
|
-
$(this).removeClass("r" + next).addClass("r" + n);
|
129
|
-
if (!no_padding && $('#full_list').hasClass('class')) {
|
130
|
-
$(this).css('padding-left', (10 + $(this).parents('ul').size() * 15) + 'px');
|
131
|
-
}
|
132
|
-
n = next;
|
133
|
-
});
|
134
|
-
}
|
135
|
-
|
136
|
-
function escapeShortcut() {
|
137
|
-
$(document).keydown(function(evt) {
|
138
|
-
if (evt.which == 27) {
|
139
|
-
$('#search_frame', window.top.document).slideUp(100);
|
140
|
-
$('#search a', window.top.document).removeClass('active inactive')
|
141
|
-
$(window.top).focus();
|
142
|
-
}
|
143
|
-
});
|
144
|
-
}
|
145
|
-
|
146
|
-
$(escapeShortcut);
|
147
|
-
$(fullListSearch);
|
148
|
-
$(linkList);
|
149
|
-
$(collapse);
|