caruby-tissue 2.1.2 → 2.1.3

data/History.md

@@ -1,6 +1,10 @@
 This history lists major release themes. See the GitHub commits (https://github.com/caruby/tissue)
 for change details.
 
+2.1.3 / 2012-04-13
+------------------
+* Fix example.
+
 2.1.2 / 2012-04-13
 ------------------
 * Add caruby-core dependency.

data/examples/galena/README.md

@@ -49,17 +49,19 @@ Migrate the Galena `simple` example as follows:
    
    This command initializes the administrative objects in the Galena test database,
    including the Galena collection protocol, site, cancer center, tissue bank and coordinator.
+   
+3. Run `crtmigrate --help` to see the migration options.
 
-3. Run the following:
+4. Run the following:
 
-   `crtmigrate --target TissueSpecimen --mapping conf/simple/fields.yaml data/simple.csv`
+   `crtmigrate --target TissueSpecimen --mapping conf/simple/fields.yaml --defaults conf/defaults.yaml data/simple.csv`
 
    This command migrates the CSV record in the `simple.csv` input file into a caTissue
    `TissueSpecimen` based on the `simple/fields.yaml` mapping file.
    Peruse the configuration and data files to see which data are migrated and
    where this data ends up in caTissue.
    
-4. Open the caTissue application on the test server and verify the content of the
+5. Open the caTissue application on the test server and verify the content of the
    Galena CP collection protocol.
    
 The other examples are run in a similar manner. Each example demonstrates different
@@ -69,10 +71,6 @@ features of the caRuby Migration utility as follows:
 
   `crtmigrate --target CollectionProtocolRegistration --mapping conf/registration/fields.yaml --defaults conf/defaults.yaml data/registration.csv`
 
-* <tt>simple</tt> - migrates one specimen with limited input fields
-
-  `crtmigrate --target TissueSpecimen --mapping conf/simple/fields.yaml --defaults conf/defaults.yaml data/simple.csv`
-
 * <tt>general</tt> - migrates specimens with lots of input fields and a minimal configuration
 
   `crtmigrate --target TissueSpecimen --mapping conf/general/fields.yaml data/general.csv`
@@ -87,11 +85,15 @@ features of the caRuby Migration utility as follows:
 
 * <tt>annotation</tt> - annotates the specimens with Dynamic Extensions
 
-  `crtmigrate --target SpecimenCollectionGroup::Pathology::RadicalProstatectomyPathologyAnnotation --mapping conf/annotation/fields.yaml --defaults conf/defaults.yaml,conf/annotation/defaults.yaml data/annotation.csv`
+  `crtmigrate --debug --log log/galena.log --target SpecimenCollectionGroup::Pathology::RadicalProstatectomyPathologyAnnotation --mapping conf/annotation/fields.yaml --defaults conf/defaults.yaml,conf/annotation/defaults.yaml data/annotation.csv`
 
-Try running an example with the `--debug` flag and look at the `log/migration.log` file to see
+The annotation migration prints debug log messages. Take a look at the `log/migration.log` file to see
 what caRuby is up to behind the scenes (hint: a lot!).
 
+The `--unique` flag is useful for testing. This flag places the migrated objects in a unique name space with their own collection protocol.
+
+If you have a lot of records to migrate, the `--verbose` flag prints the migration progress.
+
 Input data
 ----------
 The sample Galena Tissue Bank CSV input files hold one row for each specimen.

data/examples/galena/lib/galena/seed.rb

@@ -99,8 +99,7 @@ module Galena
       # CPE has default 1.0 event point and label
       cpe = CaTissue::CollectionProtocolEvent.new(
         :collection_protocol => @protocol,
-        :event_point => 1.0,
-        :label => 'Galena Migration_1'
+        :event_point => 1.0
       )
       
       # The sole specimen requirement. Setting the requirement collection_event attribute to a CPE automatically

data/lib/catissue/domain/specimen_collection_group.rb

@@ -319,7 +319,14 @@ module CaTissue
       end
       rcvr = cp.coordinators.first
       if rcvr.nil? then
-        raise Jinx::ValidationError.new("SCG with status Complete default CollectionEventParameters could not be created since there is no collection protocol coordinator: #{self}")
+        # Try to fetch the CP 
+        if cp.identifier.nil? then
+          cp.find
+          rcvr = cp.coordinators.first 
+          if rcvr.nil? then
+            raise Jinx::ValidationError.new("SCG with status Complete default CollectionEventParameters could not be created since there is no collection protocol coordinator: #{self}")
+          end
+        end
       end
       # make the REP
       ev = CaTissue::SpecimenEventParameters.create_parameters(:received, self, :user => rcvr)

data/lib/catissue/version.rb

@@ -1,6 +1,6 @@
 module CaTissue
   # The version of this caRuby Tissue release.
-  VERSION = "2.1.2"
+  VERSION = "2.1.3"
   
   # The supported caTissue release versions.
   CATISSUE_VERSIONS = "1.1.2-1.2"

metadata

@@ -2,7 +2,7 @@
 name: caruby-tissue
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 2.1.2
+  version: 2.1.3
 platform: ruby
 authors: 
   - OHSU