loadmop 0.0.3 → 0.0.4

checksums.yaml

@@ -1,7 +1,7 @@
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data/CHANGELOG.md

@@ -1,6 +1,21 @@
 # Changelog
 All notable changes to this project will be documented in this file.
 
+## 0.0.4 - 2014-08-29
+
+### Added
+- Require database name as argument for each command.
+
+### Deprecated
+- Nothing.
+
+### Removed
+- Nothing.
+
+### Fixed
+- #slow_load option was skipping rows and misreading headers.
+
+
 ## 0.0.3 - 2014-07-16
 
 ### Added
@@ -15,6 +30,7 @@ All notable changes to this project will be documented in this file.
 ### Fixed
 - Nothing.
 
+
 ## 0.0.2 - 2014-07-11
 
 ### Added
@@ -29,6 +45,7 @@ All notable changes to this project will be documented in this file.
 ### Fixed
 - Bug where schemas directory was not found when loadmop was installed as a gem
 
+
 ## 0.0.1 - 2014-07-10
 
 ### Added

data/README.md

@@ -72,7 +72,7 @@ Then:
 
 
 ### Loading CDM Data
-- Run `bundle exec loadmop create_vocab_database /path/to/directory/holding/cdm/data/files`
+- Run `bundle exec loadmop create_cdmv4_data /path/to/directory/holding/cdm/data/files`
     - This runs all the steps for loading CDM data into a database, namely
         - Creating the proper CDM tables
         - Prepping the CSV files to load into the database

data/lib/loadmop/cli.rb

@@ -10,16 +10,16 @@ module Loadmop
       aliases: :s,
       desc: 'schema for database (PostgreSQL only)'
 
-    desc 'create_vocab_database vocab_files_dir', 'Connects to database specified in the .env file and loads the OMOP Vocabulary schema and data into it'
-    def create_vocab_database(vocab_files_dir)
-      loader = VocabLoader.new(vocab_files_dir, options)
+    desc 'create_vocab_database database_name vocab_files_dir', 'Creates the vocabulary tables in database_name and loads the OMOP Vocabulary data into them.'
+    def create_vocab_database(database_name, vocab_files_dir)
+      loader = VocabLoader.new(database_name, vocab_files_dir, options)
       loader.create_database
     end
 
-    desc 'create_cdmv4_data data_dir', 'Creates a schema in a database for OMOP CDMv4 then loads data into it as specified by data_files_dir'
-    def create_cdmv4_database(data_files_dir)
-      cdm_loader = CDMv4Loader.new(data_files_dir, options)
-      cdm_loader.create_database
+    desc 'create_cdmv4_database database_name data_dir', 'Creates a set of tables in database_name for OMOP CDMv4 then loads data into them as specified by data_files_dir.'
+    def create_cdmv4_database(database_name, data_files_dir)
+      loader = CDMv4Loader.new(database_name, data_files_dir, options)
+      loader.create_database
     end
   end
 end

data/lib/loadmop/loader.rb

@@ -8,11 +8,11 @@ module Loadmop
 
     attr :options, :data_files_dir, :headers
 
-    def initialize(data_files_dir, options = {})
+    def initialize(database_name, data_files_dir, options = {})
       @data_files_dir = Pathname.new(data_files_dir)
       @options = options
       @headers = {}
-      db(options)
+      db(options.merge(database: database_name))
     end
 
     def create_database
@@ -100,10 +100,10 @@ module Loadmop
       all_files.each do |table_name, files|
         files.each do |file|
           puts "Loading #{file} into #{table_name}"
-          CSV.open(file, headers: true) do |csv|
+          CSV.open(file) do |csv|
             csv.each_slice(1000) do |rows|
               print '.'
-              db[table_name].import(headers_for(file), rows.map(&:fields))
+              db[table_name].import(headers_for(file), rows)
             end
           end
           puts
@@ -120,6 +120,9 @@ module Loadmop
     end
 
     def headers_for(file)
+      if file.to_s =~ /split/
+        file = Pathname.new(file.dirname.to_s.sub('split', 'cleaned') + '.csv')
+      end
       header_line = File.open(file, &:readline).downcase.gsub(/\|$/, '')
       CSV.parse(header_line).first.map(&:to_sym)
     end

data/lib/loadmop/version.rb

@@ -1,3 +1,3 @@
 module Loadmop
-  VERSION = "0.0.3"
+  VERSION = "0.0.4"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: loadmop
 version: !ruby/object:Gem::Version
-  version: 0.0.3
+  version: 0.0.4
 platform: ruby
 authors:
 - Ryan Duryea
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-07-16 00:00:00.000000000 Z
+date: 2014-08-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler