caruby-tissue 1.5.5 → 1.5.6
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- data/History.md +4 -0
- data/lib/catissue/cli/migrate.rb +11 -0
- data/lib/catissue/version.rb +1 -1
- metadata +246 -262
data/History.md
CHANGED
@@ -1,6 +1,10 @@
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1
1
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This history lists major release themes. See the GitHub Commits (https://github.com/caruby/tissue)
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2
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for change details.
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3
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+
1.5.6 / 2011-09-30
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+
------------------
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+
* Added validate function back into migrate.
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+
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4
8
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1.5.5 / 2011-09-22
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9
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------------------
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6
10
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* Use migration value filter option.
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data/lib/catissue/cli/migrate.rb
CHANGED
@@ -46,6 +46,17 @@ module CaTissue
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46
46
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migrator = block_given? ? yield(opts) : CaTissue::Migrator.new(opts)
|
47
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migrator.migrate_to_database
|
48
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end
|
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+
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+
def validate(opts)
|
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+
tgt = opts[:target]
|
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+
if tgt.nil? then raise ArgumentError.new("Missing required migration target class option") end
|
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+
begin
|
54
|
+
opts[:target] = CaTissue.const_get(tgt)
|
55
|
+
rescue Exception
|
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+
logger.fatal("Could not load CaTissue class #{tgt} - #{$!}.\n#{$@.qp}")
|
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+
raise MigrationError.new("Could not load migration target class #{tgt}")
|
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+
end
|
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+
end
|
49
60
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end
|
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end
|
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end
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data/lib/catissue/version.rb
CHANGED
metadata
CHANGED
@@ -1,299 +1,283 @@
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1
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--- !ruby/object:Gem::Specification
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name: caruby-tissue
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version: !ruby/object:Gem::Version
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-
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-
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segments:
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- 1
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-
- 5
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- 5
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10
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-
version: 1.5.5
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+
prerelease:
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version: 1.5.6
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platform: ruby
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authors:
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-
- OHSU
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+
- OHSU
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autorequire:
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bindir: bin
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11
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cert_chain: []
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12
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-
date: 2011-09-
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+
date: 2011-09-30 00:00:00 -07:00
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default_executable:
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dependencies:
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-
- !ruby/object:Gem::Dependency
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-
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-
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- 5
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- 5
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version: 1.5.5
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type: :runtime
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version_requirements: *id001
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+
- !ruby/object:Gem::Dependency
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name: caruby-core
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prerelease: false
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requirement: &id001 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ">="
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+
- !ruby/object:Gem::Version
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version: 1.5.5
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type: :runtime
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version_requirements: *id001
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description: " The caruby-tissue gem applies the caRuby facade to the caTissue application.\n"
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email: caruby.org@gmail.com
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executables:
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- crtdump
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- crtexample
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- crtextract
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- crtmigrate
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- crtsmoke
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+
- crtdump
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- crtexample
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- crtextract
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- crtmigrate
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- crtsmoke
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extensions: []
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extra_rdoc_files: []
|
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files:
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- bin/crtdump
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- bin/crtexample
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- bin/crtextract
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- bin/crtmigrate
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- bin/crtsmoke
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- conf/wustl/log4j.properties
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-
- examples/galena/
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- examples/galena/
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- examples/galena/conf/
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- examples/galena/conf/migration/
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- examples/galena/conf/migration/
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- examples/galena/conf/migration/
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- examples/galena/conf/migration/
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- examples/galena/conf/migration/
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- examples/galena/conf/migration/
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- examples/galena/conf/migration/
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- examples/galena/conf/migration/
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- examples/galena/conf/migration/
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- examples/galena/conf/migration/
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- examples/galena/
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- examples/galena/data/
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- examples/galena/data/
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- examples/galena/data/
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- examples/galena/data/
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- examples/galena/data/
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- examples/galena/
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- examples/galena/lib/galena
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- examples/galena/lib/galena/tissue/
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- examples/galena/lib/galena.rb
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- examples/galena/
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- examples/psbin/
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- examples/psbin/conf/
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- examples/psbin/conf/
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- examples/psbin/conf/
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- examples/psbin/conf/
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- examples/psbin/conf/
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- examples/psbin/conf/
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- examples/psbin/conf/
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- examples/psbin/conf/
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- examples/psbin/conf/
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- examples/psbin/conf/
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- examples/psbin/
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- examples/psbin/data/
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- examples/psbin/data/
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- examples/psbin/data/
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- examples/psbin/data/
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- examples/psbin/data/
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- examples/psbin/data/
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- examples/psbin/data/
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- examples/psbin/
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- examples/psbin/lib/psbin/
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- examples/psbin/
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- lib/catissue
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- lib/catissue/
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- lib/catissue/
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- lib/catissue/
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- lib/catissue/
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- lib/catissue/annotation/
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- lib/catissue/annotation/
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- lib/catissue/annotation/
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- lib/catissue/annotation/
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- lib/catissue/annotation/
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- lib/catissue/
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- lib/catissue/
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- lib/catissue/
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- lib/catissue/
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- lib/catissue/
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- lib/catissue/
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- lib/catissue/
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- lib/catissue/
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- lib/catissue/
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- lib/catissue/database/
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- lib/catissue/database/
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- lib/catissue/database/annotation/
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- lib/catissue/database/
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- lib/catissue/database/
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- lib/catissue/database.rb
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- lib/catissue/
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- lib/catissue/
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- lib/catissue/
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- lib/catissue/
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- lib/catissue/domain/
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- lib/catissue/domain.rb
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- lib/catissue/migration/
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- lib/catissue/
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- lib/catissue/
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- lib/catissue/
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- lib/catissue/
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- lib/catissue.rb
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- test/fixtures/catissue/domain/conf/catissue_override.yaml
|
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- test/fixtures/catissue/extract/conf/scg_extract.yaml
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- test/fixtures/catissue/extract/conf/scg_fields.yaml
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- test/fixtures/catissue/extract/conf/spc_extract.yaml
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- test/fixtures/catissue/extract/conf/spc_fields.yaml
|
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- test/fixtures/lib/catissue/defaults_test_fixture.rb
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- test/fixtures/lib/examples/galena/migration/alt_key_shims.rb
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- test/lib/catissue/
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- test/lib/catissue/
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- test/lib/catissue/domain/
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- test/lib/catissue/domain/
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- test/lib/catissue/domain/
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- test/lib/catissue/domain/
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- test/lib/catissue/domain/
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- test/lib/catissue/domain/
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- test/lib/catissue/domain/
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- test/lib/catissue/
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- test/lib/catissue/extract/
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- test/lib/catissue/
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- test/lib/catissue/
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- test/lib/catissue/test_case.rb
|
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- test/lib/examples/galena/tissue/domain/examples_test.rb
|
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- test/lib/examples/galena/tissue/migration/annotation_test.rb
|
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- test/lib/examples/galena/tissue/migration/filter_test.rb
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- test/lib/examples/galena/tissue/migration/frozen_test.rb
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- test/lib/examples/galena/tissue/migration/general_test.rb
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- test/lib/examples/galena/tissue/migration/participant_test.rb
|
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- test/lib/examples/galena/tissue/migration/registration_test.rb
|
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- test/lib/examples/galena/tissue/migration/seedify.rb
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- test/lib/examples/galena/tissue/migration/simple_test.rb
|
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- test/lib/examples/galena/tissue/migration/test_case.rb
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- test/lib/examples/psbin/migration_test.rb
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-
- History.md
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-
- LEGAL
|
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-
- LICENSE
|
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-
- README.md
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-
has_rdoc:
|
40
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+
- bin/crtdump
|
41
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+
- bin/crtexample
|
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+
- bin/crtextract
|
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- bin/crtmigrate
|
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- bin/crtsmoke
|
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+
- conf/wustl/log4j.properties
|
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+
- examples/galena/README.md
|
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- examples/galena/bin/seed
|
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+
- examples/galena/conf/extract/simple_fields.yaml
|
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+
- examples/galena/conf/migration/annotation_defaults.yaml
|
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- examples/galena/conf/migration/annotation_fields.yaml
|
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+
- examples/galena/conf/migration/filter_defaults.yaml
|
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+
- examples/galena/conf/migration/filter_fields.yaml
|
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+
- examples/galena/conf/migration/filter_values.yaml
|
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+
- examples/galena/conf/migration/frozen_defaults.yaml
|
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+
- examples/galena/conf/migration/frozen_fields.yaml
|
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+
- examples/galena/conf/migration/general_fields.yaml
|
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- examples/galena/conf/migration/participant_fields.yaml
|
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+
- examples/galena/conf/migration/registration_fields.yaml
|
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- examples/galena/conf/migration/simple_fields.yaml
|
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- examples/galena/data/annotation.csv
|
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- examples/galena/data/filter.csv
|
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- examples/galena/data/frozen.csv
|
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- examples/galena/data/general.csv
|
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- examples/galena/data/participant.csv
|
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- examples/galena/data/registration.csv
|
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- examples/galena/data/simple.csv
|
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- examples/galena/lib/galena.rb
|
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+
- examples/galena/lib/galena/tissue/migration/filter_shims.rb
|
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+
- examples/galena/lib/galena/tissue/migration/frozen_shims.rb
|
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+
- examples/galena/lib/galena/tissue/seed/defaults.rb
|
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+
- examples/psbin/README.md
|
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+
- examples/psbin/conf/adjuvant_hormone_defaults.yaml
|
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- examples/psbin/conf/adjuvant_radiation_defaults.yaml
|
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+
- examples/psbin/conf/biopsy_defaults.yaml
|
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- examples/psbin/conf/biopsy_fields.yaml
|
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- examples/psbin/conf/neoadjuvant_hormone_defaults.yaml
|
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- examples/psbin/conf/neoadjuvant_radiation_defaults.yaml
|
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+
- examples/psbin/conf/patient_defaults.yaml
|
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+
- examples/psbin/conf/patient_fields.yaml
|
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+
- examples/psbin/conf/surgery_defaults.yaml
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- examples/psbin/conf/surgery_fields.yaml
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- examples/psbin/conf/t_stage_defaults.yaml
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- examples/psbin/conf/t_stage_fields.yaml
|
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- examples/psbin/conf/therapy_fields.yaml
|
85
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- examples/psbin/data/adjuvant_hormone.csv
|
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- examples/psbin/data/adjuvant_radiation.csv
|
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- examples/psbin/data/biopsy.csv
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- examples/psbin/data/neoadjuvant_hormone.csv
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- examples/psbin/data/neoadjuvant_radiation.csv
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- examples/psbin/data/patient.csv
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- examples/psbin/data/surgery.csv
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- examples/psbin/data/t_stage.csv
|
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- examples/psbin/lib/psbin/biopsy_shims.rb
|
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- examples/psbin/lib/psbin/surgery_shims.rb
|
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- lib/catissue.rb
|
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- lib/catissue/database.rb
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- lib/catissue/domain.rb
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- lib/catissue/resource.rb
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- lib/catissue/version.rb
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- lib/catissue/annotation/annotatable.rb
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- lib/catissue/annotation/annotation_module.rb
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- lib/catissue/annotation/de_integration.rb
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- lib/catissue/annotation/proxy.rb
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- lib/catissue/annotation/proxy_1_1.rb
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- lib/catissue/annotation/proxy_class.rb
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- lib/catissue/annotation/record_entry_proxy.rb
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- lib/catissue/cli/command.rb
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- lib/catissue/cli/example.rb
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- lib/catissue/cli/migrate.rb
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- lib/catissue/cli/smoke.rb
|
114
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- lib/catissue/database/controlled_value_finder.rb
|
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- lib/catissue/database/controlled_values.rb
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- lib/catissue/database/annotation/annotation_service.rb
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- lib/catissue/database/annotation/annotator.rb
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- lib/catissue/database/annotation/entity_facade.rb
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- lib/catissue/database/annotation/id_generator.rb
|
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- lib/catissue/database/annotation/integration_service.rb
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- lib/catissue/database/annotation/integrator.rb
|
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- lib/catissue/database/annotation/record_entry_integrator.rb
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- lib/catissue/database/annotation/reference_writer.rb
|
124
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- lib/catissue/domain/abstract_position.rb
|
125
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+
- lib/catissue/domain/abstract_specimen.rb
|
126
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- lib/catissue/domain/abstract_specimen_collection_group.rb
|
127
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+
- lib/catissue/domain/address.rb
|
128
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+
- lib/catissue/domain/cancer_research_group.rb
|
129
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- lib/catissue/domain/capacity.rb
|
130
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+
- lib/catissue/domain/check_in_check_out_event_parameter.rb
|
131
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- lib/catissue/domain/collection_event_parameters.rb
|
132
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- lib/catissue/domain/collection_protocol.rb
|
133
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+
- lib/catissue/domain/collection_protocol_event.rb
|
134
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- lib/catissue/domain/collection_protocol_registration.rb
|
135
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- lib/catissue/domain/consent_tier_response.rb
|
136
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+
- lib/catissue/domain/consent_tier_status.rb
|
137
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- lib/catissue/domain/container.rb
|
138
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- lib/catissue/domain/container_position.rb
|
139
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+
- lib/catissue/domain/container_type.rb
|
140
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+
- lib/catissue/domain/department.rb
|
141
|
+
- lib/catissue/domain/disposal_event_parameters.rb
|
142
|
+
- lib/catissue/domain/embedded_event_parameters.rb
|
143
|
+
- lib/catissue/domain/external_identifier.rb
|
144
|
+
- lib/catissue/domain/frozen_event_parameters.rb
|
145
|
+
- lib/catissue/domain/hash_code.rb
|
146
|
+
- lib/catissue/domain/institution.rb
|
147
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+
- lib/catissue/domain/new_specimen_array_order_item.rb
|
148
|
+
- lib/catissue/domain/order_details.rb
|
149
|
+
- lib/catissue/domain/participant.rb
|
150
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+
- lib/catissue/domain/participant_medical_identifier.rb
|
151
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- lib/catissue/domain/password.rb
|
152
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- lib/catissue/domain/race.rb
|
153
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+
- lib/catissue/domain/received_event_parameters.rb
|
154
|
+
- lib/catissue/domain/site.rb
|
155
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+
- lib/catissue/domain/specimen.rb
|
156
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+
- lib/catissue/domain/specimen_array.rb
|
157
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+
- lib/catissue/domain/specimen_array_content.rb
|
158
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+
- lib/catissue/domain/specimen_array_type.rb
|
159
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+
- lib/catissue/domain/specimen_characteristics.rb
|
160
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- lib/catissue/domain/specimen_collection_group.rb
|
161
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- lib/catissue/domain/specimen_event_parameters.rb
|
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- lib/catissue/domain/specimen_position.rb
|
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- lib/catissue/domain/specimen_protocol.rb
|
164
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- lib/catissue/domain/specimen_requirement.rb
|
165
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- lib/catissue/domain/storage_container.rb
|
166
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- lib/catissue/domain/storage_type.rb
|
167
|
+
- lib/catissue/domain/transfer_event_parameters.rb
|
168
|
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- lib/catissue/domain/user.rb
|
169
|
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- lib/catissue/domain/participant/clinical/chemotherapy.rb
|
170
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- lib/catissue/domain/participant/clinical/duration.rb
|
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- lib/catissue/domain/participant/clinical/radiation_therapy.rb
|
172
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- lib/catissue/domain/specimen/pathology/prostate_specimen_gleason_score.rb
|
173
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- lib/catissue/domain/specimen/pathology/prostate_specimen_pathology_annotation.rb
|
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- lib/catissue/domain/specimen/pathology/specimen_additional_finding.rb
|
175
|
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- lib/catissue/domain/specimen/pathology/specimen_base_solid_tissue_pathology_annotation.rb
|
176
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- lib/catissue/domain/specimen/pathology/specimen_details.rb
|
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- lib/catissue/domain/specimen/pathology/specimen_histologic_grade.rb
|
178
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- lib/catissue/domain/specimen/pathology/specimen_histologic_type.rb
|
179
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- lib/catissue/domain/specimen/pathology/specimen_histologic_variant_type.rb
|
180
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+
- lib/catissue/domain/specimen/pathology/specimen_invasion.rb
|
181
|
+
- lib/catissue/domain/specimen_collection_group/pathology/base_pathology_annotation.rb
|
182
|
+
- lib/catissue/domain/specimen_collection_group/pathology/base_solid_tissue_pathology_annotation.rb
|
183
|
+
- lib/catissue/extract/command.rb
|
184
|
+
- lib/catissue/extract/delta.rb
|
185
|
+
- lib/catissue/extract/extractor.rb
|
186
|
+
- lib/catissue/migration/migratable.rb
|
187
|
+
- lib/catissue/migration/migrator.rb
|
188
|
+
- lib/catissue/migration/shims.rb
|
189
|
+
- lib/catissue/migration/uniquify.rb
|
190
|
+
- lib/catissue/util/collectible.rb
|
191
|
+
- lib/catissue/util/collectible_event_parameters.rb
|
192
|
+
- lib/catissue/util/controlled_value.rb
|
193
|
+
- lib/catissue/util/location.rb
|
194
|
+
- lib/catissue/util/person.rb
|
195
|
+
- lib/catissue/util/position.rb
|
196
|
+
- lib/catissue/util/storable.rb
|
197
|
+
- lib/catissue/util/storage_type_holder.rb
|
198
|
+
- lib/catissue/util/uniquify.rb
|
199
|
+
- lib/catissue/wustl/logger.rb
|
200
|
+
- test/fixtures/catissue/domain/conf/catissue_override.yaml
|
201
|
+
- test/fixtures/catissue/extract/conf/scg_extract.yaml
|
202
|
+
- test/fixtures/catissue/extract/conf/scg_fields.yaml
|
203
|
+
- test/fixtures/catissue/extract/conf/spc_extract.yaml
|
204
|
+
- test/fixtures/catissue/extract/conf/spc_fields.yaml
|
205
|
+
- test/fixtures/lib/catissue/defaults_test_fixture.rb
|
206
|
+
- test/fixtures/lib/examples/galena/migration/alt_key_shims.rb
|
207
|
+
- test/lib/catissue/test_case.rb
|
208
|
+
- test/lib/catissue/database/controlled_values_test.rb
|
209
|
+
- test/lib/catissue/domain/address_test.rb
|
210
|
+
- test/lib/catissue/domain/base_haemotology_pathology_test.rb
|
211
|
+
- test/lib/catissue/domain/ca_tissue_test_defaults_test.rb
|
212
|
+
- test/lib/catissue/domain/capacity_test.rb
|
213
|
+
- test/lib/catissue/domain/collection_event_parameters_test.rb
|
214
|
+
- test/lib/catissue/domain/collection_protocol_event_test.rb
|
215
|
+
- test/lib/catissue/domain/collection_protocol_registration_test.rb
|
216
|
+
- test/lib/catissue/domain/collection_protocol_test.rb
|
217
|
+
- test/lib/catissue/domain/container_position_test.rb
|
218
|
+
- test/lib/catissue/domain/department_test.rb
|
219
|
+
- test/lib/catissue/domain/disposal_event_parameters_test.rb
|
220
|
+
- test/lib/catissue/domain/external_identifier_test.rb
|
221
|
+
- test/lib/catissue/domain/location_test.rb
|
222
|
+
- test/lib/catissue/domain/participant_medical_identifier_test.rb
|
223
|
+
- test/lib/catissue/domain/participant_test.rb
|
224
|
+
- test/lib/catissue/domain/site_test.rb
|
225
|
+
- test/lib/catissue/domain/specimen_array_test.rb
|
226
|
+
- test/lib/catissue/domain/specimen_array_type_test.rb
|
227
|
+
- test/lib/catissue/domain/specimen_characteristics_test.rb
|
228
|
+
- test/lib/catissue/domain/specimen_collection_group_test.rb
|
229
|
+
- test/lib/catissue/domain/specimen_event_parameters_test.rb
|
230
|
+
- test/lib/catissue/domain/specimen_position_test.rb
|
231
|
+
- test/lib/catissue/domain/specimen_requirement_test.rb
|
232
|
+
- test/lib/catissue/domain/specimen_test.rb
|
233
|
+
- test/lib/catissue/domain/storage_container_test.rb
|
234
|
+
- test/lib/catissue/domain/storage_type_test.rb
|
235
|
+
- test/lib/catissue/domain/transfer_event_parameters_test.rb
|
236
|
+
- test/lib/catissue/domain/user_test.rb
|
237
|
+
- test/lib/catissue/extract/delta_test.rb
|
238
|
+
- test/lib/catissue/extract/extractor_test.rb
|
239
|
+
- test/lib/catissue/import/importable_module_test.rb
|
240
|
+
- test/lib/catissue/migration/test_case.rb
|
241
|
+
- test/lib/examples/galena/tissue/domain/examples_test.rb
|
242
|
+
- test/lib/examples/galena/tissue/migration/annotation_test.rb
|
243
|
+
- test/lib/examples/galena/tissue/migration/filter_test.rb
|
244
|
+
- test/lib/examples/galena/tissue/migration/frozen_test.rb
|
245
|
+
- test/lib/examples/galena/tissue/migration/general_test.rb
|
246
|
+
- test/lib/examples/galena/tissue/migration/participant_test.rb
|
247
|
+
- test/lib/examples/galena/tissue/migration/registration_test.rb
|
248
|
+
- test/lib/examples/galena/tissue/migration/seedify.rb
|
249
|
+
- test/lib/examples/galena/tissue/migration/simple_test.rb
|
250
|
+
- test/lib/examples/galena/tissue/migration/test_case.rb
|
251
|
+
- test/lib/examples/psbin/migration_test.rb
|
252
|
+
- History.md
|
253
|
+
- LEGAL
|
254
|
+
- LICENSE
|
255
|
+
- README.md
|
256
|
+
has_rdoc: true
|
267
257
|
homepage: http://caruby.rubyforge.org/tissue.html
|
268
258
|
licenses:
|
269
|
-
- MIT
|
259
|
+
- MIT
|
270
260
|
post_install_message:
|
271
261
|
rdoc_options: []
|
272
262
|
|
273
263
|
require_paths:
|
274
|
-
- lib
|
264
|
+
- lib
|
275
265
|
required_ruby_version: !ruby/object:Gem::Requirement
|
276
266
|
none: false
|
277
267
|
requirements:
|
278
|
-
|
279
|
-
|
280
|
-
|
281
|
-
segments:
|
282
|
-
- 0
|
283
|
-
version: "0"
|
268
|
+
- - ">="
|
269
|
+
- !ruby/object:Gem::Version
|
270
|
+
version: "0"
|
284
271
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
285
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|
none: false
|
286
273
|
requirements:
|
287
|
-
|
288
|
-
|
289
|
-
|
290
|
-
segments:
|
291
|
-
- 0
|
292
|
-
version: "0"
|
274
|
+
- - ">="
|
275
|
+
- !ruby/object:Gem::Version
|
276
|
+
version: "0"
|
293
277
|
requirements: []
|
294
278
|
|
295
279
|
rubyforge_project: caruby
|
296
|
-
rubygems_version: 1.
|
280
|
+
rubygems_version: 1.5.1
|
297
281
|
signing_key:
|
298
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|
specification_version: 3
|
299
283
|
summary: Ruby facade for caTissue.
|