yarrrml_template_builder 0.1.54

checksums.yaml

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+SHA256:
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+  data.tar.gz: 614587381f1744f21e50cdcee3b9c30be566e092f832238a4d10af050152812a
+SHA512:
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data/.gitignore

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+/.bundle/
+/.yardoc
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/

data/Changelog.md

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+Start

data/Gemfile

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+# frozen_string_literal: true
+
+source "https://rubygems.org"
+
+# Specify your gem's dependencies in yarrrml_template_builder.gemspec
+gemspec
+
+gem "rake", "~> 13.0"

data/Gemfile.lock

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+PATH
+  remote: .
+  specs:
+    yarrrml_template_builder (0.1.54)
+      rest-client (~> 2.1.0)
+      yaml (~> 0.1.0)
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    domain_name (0.5.20190701)
+      unf (>= 0.0.5, < 1.0.0)
+    http-accept (1.7.0)
+    http-cookie (1.0.5)
+      domain_name (~> 0.5)
+    mime-types (3.4.1)
+      mime-types-data (~> 3.2015)
+    mime-types-data (3.2022.0105)
+    netrc (0.11.0)
+    rake (13.0.6)
+    rest-client (2.1.0)
+      http-accept (>= 1.7.0, < 2.0)
+      http-cookie (>= 1.0.2, < 2.0)
+      mime-types (>= 1.16, < 4.0)
+      netrc (~> 0.8)
+    unf (0.1.4)
+      unf_ext
+    unf_ext (0.0.8.2)
+    yaml (0.1.1)
+
+PLATFORMS
+  x86_64-linux
+
+DEPENDENCIES
+  rake (~> 13.0)
+  yarrrml_template_builder!
+
+BUNDLED WITH
+   2.3.12

data/LICENSE.txt

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+The MIT License (MIT)
+
+Copyright (c) 2021 Mark Wilkinson
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

data/README.md

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+# INSTRUCTIONS
+        $  bundle install
+        
+        $  gem build
+        
+        $  gem install yarrrml_template_builder-{VERSION}.gem
+
+VERSION is some version that will appear in the filename of the gem.
+
+## Execute a CDE Transformation from CSV
+
+0) Default folder structure, relative to where you will run the transformation script:
+
+        .
+        ./data/   (this folder is mounted into sdmrdfizer - see step 1 below)
+        ./data/mydataX.csv  (input csv files)
+        ./data/mydataY.csv...
+        ./data/triples/  (output FAIR data ends up here)
+        ./config/
+        ./config/***_yarrrml_template.yaml (*** is a one-word tag of the "type" of data, e.g. "height")
+
+1) Need to have sdmrdfizer and yarrrml-parser services running ./data mounted as /data and ./config as /config. You can use docker-compose to run both services:
+
+    ```yaml
+    version: "2.0"
+    services:
+
+
+        yarrrml_transform:
+            image: markw/yarrrml-parser-ejp:latest
+            container_name: yarrrml_transform
+            ports:
+                - "3000:3000"
+            volumes:
+                - ./data:/data
+
+
+        rdfizer:
+            image: markw/sdmrdfizer_ejp:0.3.0
+            container_name: rdfizer
+            ports:
+                - "4000:4000"
+            volumes:
+                - ./data:/data
+                - ./config:/config
+    ```
+
+2) Create your template by running build_xxx_template or select the appropriate YARRRML template (in the ./config folder, e.g. "height_yarrrml_template.yaml"). See "example of creating a template" below if you need to create one from-scratch.
+
+3) In the ./data folder, create a CSV file with the necessary headings for your desired transform.
+
+4) Identify the "tag" of the YARRML template you want to use (e.g. 'height' for "height_yarrrml_template.yaml"). This tag is used to coordinate between many of the components during the automation steps, so it must match exactly with the "tag" portion of the template name.
+
+5) Execute the transformation: You can use [run_me_to_test.rb](run_me_to_test.rb) by changing the tag described as datatype_tag parameter at YARRRML_Transform:
+
+    ```ruby
+        y = YARRRML_Transform.new(datafile: "./data/myHeightData.csv", datatype_tag: "height")
+        y.yarrrml_transform
+        y.make_fair_data   # output goes to ./data/triples
+    ```
+
+
+
+
+## Example of creating a template:
+
+### General Discussion:  
+The objective of the library is to make it easy to generate a YARRRML template that matches your situation.  There is a fair amount of flexibility in what parameters are used, which are optional, and which have defaults (SIO-compliant).  *NOTE: What comes out of the yarrrml_template_builder is NOT a complete YARRRML file!  It has place-holders for the source filename and reference formulation.  you add those when calling the yarrrml_transform library.*
+
+personid_column and unique_id column are absolutely mandatory, and do not have a default.
+
+There are three ways of representing a data column (or its default, if that column doesn't exist):
+
+  * You can specify the default value (these parameters are designated "xxxx"  for example "process_type".  
+  * You can specify the column header.  These parameters are designated "xxxxxx_column" - for example 'process_type_column'. Specifying "process_type_column" will override any value you provided in "process_type"
+  * You can specify nothing, in which case the internal defaults will be used (based on the "base" type for that node in SIO.  Some data is allowed to be nil, and those nodes will not be created.
+  
+Almost all cases will allow any of those three methods (see detailed documentation for more)
+
+"tags" are used for creating human-readable section names in the output YARRRML.  They may not contain spaces or other odd characters... letters and underscores are fine.  This is not currently sanity-checked, so... 
+
+With that said, here's what a template-building script looks like:
+
+    require "yarrrml-template-builder"
+
+    # this is the header of the CSV we are going to transform
+    # "pid,uniqid,qualityURI,qualityLabel,measurementURI,measurementLabel,processURI,processLabel,height,unitURI,unitLabel,date,comments"
+
+    b = YARRRML_Template_Builder.new({
+      baseURI: "http://marks.test/this/", # this should resolve to wherever you are going to serve the data from.
+                                          # RDF URLs become e.g. http://marks.test/this/individual_X_Y#patientRole
+      source_name: "patient_height"}
+      )
+
+    b.person_identifier_role_mappings({
+                                        personid_column: "pid",
+                                        uniqueid_column: "uniqid",
+                                        identifier_type: "https://ejp-rd.eu/vocab/identifier",
+                                        person_type: "https://ejp-rd.eu/vocab/Person",
+                                        person_role_tag: "patientRole",
+                                        role_type: 'obo:OBI_0000093'
+                                        role_label: "Patient"
+                                        })
+    b.role_in_process({
+        process_type_column: "processURI",  
+        process_tag:  "some_height_measuring_process",
+        process_label_column: "processLabel", 
+        process_start_column: "date", 
+        process_end_column: nil,
+        })
+
+    b.person_has_quality({
+        quality_type_column: "qualityURI",  
+        quality_tag:  "height_quality",
+        quality_label_column: "qualityLabel", 
+        })
+
+    b.process_hasoutput_output({
+        output_nature: "quantitative",
+        output_type_column: "measurementURI",
+        output_type_label_column: "measurementLabel",
+        output_value_column: "height",
+        output_value_datatype: "xsd:float",
+        output_comments_column: "comments",
+        })
+
+    b.output_has_unit({
+        output_unit_column: "unitURI",
+        output_unit_label: "unitLabel"  
+    })
+
+    puts b.generate
+
+
+Note that this will output the template to STDOUT, so capture it to a file.  For everything else to work "correctly" that file should be named
+XXXXXX_yarrrml_template.yaml, and should live in the ./config folder.   XXXXXX is the 'tag' of the data type (e.g. 'height')
+
+
+The "run_me_to_test.rb" script will run as a demo - using the demo height data in the ./data folder, and the template that is created by the code above.  Output will appear in the ./data/triples folder.

data/bin/console

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+#!/usr/bin/env ruby
+# frozen_string_literal: true
+
+require "bundler/setup"
+require "yarrrml_template_builder"
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require "irb"
+IRB.start(__FILE__)

data/bin/setup

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+#!/usr/bin/env bash
+set -euo pipefail
+IFS=$'\n\t'
+set -vx
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/config/height_yarrrml_template.yaml

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+---
+prefixes:
+  rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
+  rdfs: http://www.w3.org/2000/01/rdf-schema#
+  ex: http://ejp-rd.eu/ids/
+  obo: http://purl.obolibrary.org/obo/
+  sio: https://semanticscience.org/resource/
+  vocab: https://ejp-rd.eu/vocab/
+  pico: http://data.cochrane.org/ontologies/pico/
+  ndfrt: http://purl.bioontology.org/ontology/NDFRT/
+  this: http://marks.test/this/
+sources:
+  patient_height_experimental-source:
+    access: "|||DATA|||"
+    referenceFormulation: "|||FORMULATION|||"
+    iterator: "$"
+mappings:
+  identifier_has_value:
+    sources:
+    - patient_height_experimental-source
+    s: this:individual_$(pid)_$(uniqid)#ID
+    po:
+    - predicates: sio:has-value
+      objects:
+        value: "$(pid)"
+        datatype: xsd:string
+  identifier_denotes:
+    sources:
+    - patient_height_experimental-source
+    s: this:individual_$(pid)_$(uniqid)#ID
+    po:
+    - predicates: a
+      objects:
+        value: https://ejp-rd.eu/vocab/identifier
+        type: iri
+    - predicates: sio:denotes
+      objects:
+        value: this:individual_$(pid)_$(uniqid)#thisRole
+        type: iri
+  person_has_role:
+    sources:
+    - patient_height_experimental-source
+    s: this:individual_$(pid)#Person
+    po:
+    - predicates: a
+      objects:
+        value: https://ejp-rd.eu/vocab/Person
+        type: iri
+    - predicates: sio:has-role
+      objects:
+        value: this:individual_$(pid)_$(uniqid)#thisRole
+        type: iri
+  thisRole_annotation:
+    sources:
+    - patient_height_experimental-source
+    s: this:individual_$(pid)_$(uniqid)#thisRole
+    po:
+    - predicates: a
+      objects:
+        value: obo:OBI_0000093
+        type: iri
+    - predicates: rdfs:label
+      objects:
+        value: Patient
+        datatype: xsd:string
+  thisRole_realized_some_height_measuring_process:
+    sources:
+    - patient_height_experimental-source
+    s: this:individual_$(pid)_$(uniqid)#thisRole
+    po:
+    - predicates: sio:is-realized-in
+      objects:
+        value: this:individual_$(pid)_$(uniqid)#some_height_measuring_process
+        type: iri
+  some_height_measuring_process_process_annotation:
+    sources:
+    - patient_height_experimental-source
+    s: this:individual_$(pid)_$(uniqid)#some_height_measuring_process
+    po:
+    - predicates: rdf:type
+      objects:
+        value: "$(processURI)"
+        type: iri
+    - predicates: rdfs:label
+      objects:
+        value: "$(processLabel)"
+        datatype: xsd:string
+  some_height_measuring_process_process_annotation_start:
+    sources:
+    - patient_height_experimental-source
+    s: this:individual_$(pid)_$(uniqid)#some_height_measuring_process
+    po:
+    - predicates: sio:start-time
+      objects:
+        value: "$(date)"
+        datatype: xsd:dateTime
+  person_has_height_quality_quality:
+    sources:
+    - patient_height_experimental-source
+    s: this:individual_$(pid)#Person
+    po:
+    - predicates: sio:has-quality
+      objects:
+        value: this:individual__$(pid)_$(uniqid)#height_quality
+        type: iri
+  height_quality_quality_annotation:
+    sources:
+    - patient_height_experimental-source
+    s: this:individual__$(pid)_$(uniqid)#height_quality
+    po:
+    - predicates: rdf:type
+      objects:
+        value: "$(qualityURI)"
+        type: iri
+    - predicates: rdfs:label
+      objects:
+        value: "$(qualityLabel)"
+        datatype: xsd:string
+  some_height_measuring_process_process_has_output:
+    sources:
+    - patient_height_experimental-source
+    s: this:individual_$(pid)_$(uniqid)#some_height_measuring_process
+    po:
+    - predicates: sio:has-output
+      objects:
+        value: this:individual__$(pid)_$(uniqid)#some_height_measuring_process_Output
+        type: iri
+  some_height_measuring_process_Output_annotation:
+    sources:
+    - patient_height_experimental-source
+    s: this:individual__$(pid)_$(uniqid)#some_height_measuring_process_Output
+    po:
+    - predicates: rdf:type
+      objects:
+        value: sio:measurement-value
+        type: iri
+  some_height_measuring_process_Output_type_annotation:
+    sources:
+    - patient_height_experimental-source
+    s: this:individual__$(pid)_$(uniqid)#some_height_measuring_process_Output
+    po:
+    - predicates: rdf:type
+      objects:
+        value: "$(measurementURI)"
+        type: iri
+  some_height_measuring_process_Output_type_label_annotation:
+    sources:
+    - patient_height_experimental-source
+    s: this:individual__$(pid)_$(uniqid)#some_height_measuring_process_Output
+    po:
+    - predicates: rdfs:label
+      objects:
+        value: "$(measurementLabel)"
+        datatype: xsd:string
+  some_height_measuring_process_Output_value_annotation:
+    sources:
+    - patient_height_experimental-source
+    s: this:individual__$(pid)_$(uniqid)#some_height_measuring_process_Output
+    po:
+    - predicates: sio:has-value
+      objects:
+        value: "$(height)"
+        datatype: xsd:float
+  some_height_measuring_process_Output_value_comments:
+    sources:
+    - patient_height_experimental-source
+    s: this:individual__$(pid)_$(uniqid)#some_height_measuring_process_Output
+    po:
+    - predicates: rdfs:comment
+      objects:
+        value: "$(comments)"
+        datatype: xsd:string
+  some_height_measuring_process_Output_hasunit_unit:
+    sources:
+    - patient_height_experimental-source
+    s: this:individual__$(pid)_$(uniqid)#some_height_measuring_process_Output
+    po:
+    - predicates: sio:has-unit
+      objects:
+        value: this:individual__$(pid)_$(uniqid)#some_height_measuring_process_Output_unit
+        type: iri
+  some_height_measuring_process_Output_unit_annotation:
+    sources:
+    - patient_height_experimental-source
+    s: this:individual__$(pid)_$(uniqid)#some_height_measuring_process_Output_unit
+    po:
+    - predicates: rdfs:label
+      objects:
+        value: "$(unitLabel)"
+        datatype: xsd:string

data/data/height.csv

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+pid,uniqid,qualityURI,qualityLabel,measurementURI,measurementLabel,processURI,processLabel,height,unitLabel,date,comments
+12345,abcde,http://purl.obolibrary.org/obo/PATO_0000119,Height quality (PATO),http://www.ebi.ac.uk/efo/EFO_0004339,body height (EFO),http://purl.obolibrary.org/obo/VT_0004370,ulnar length (VT),23,cm,2019-02-28T00:00:00.000Z,Notes:  Height measurement type (default http://www.ebi.ac.uk/efo/EFO_0004339) may be estimated by ulnar length (recorded as ulnar length trait - http://purl.obolibrary.org/obo/VT_0004370 - and ulnar length measurement type - (http://purl.obolibrary.org/obo/CMO_0000440) 

data/doc/YARRRMLTemplateBuilder.html

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+<!DOCTYPE html>
+<html>
+  <head>
+    <meta charset="utf-8">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+<title>
+  Module: YARRRMLTemplateBuilder
+  
+    &mdash; Documentation by YARD 0.9.26
+  
+</title>
+
+  <link rel="stylesheet" href="css/style.css" type="text/css" />
+
+  <link rel="stylesheet" href="css/common.css" type="text/css" />
+
+<script type="text/javascript">
+  pathId = "YARRRMLTemplateBuilder";
+  relpath = '';
+</script>
+
+
+  <script type="text/javascript" charset="utf-8" src="js/jquery.js"></script>
+
+  <script type="text/javascript" charset="utf-8" src="js/app.js"></script>
+
+
+  </head>
+  <body>
+    <div class="nav_wrap">
+      <iframe id="nav" src="class_list.html?1"></iframe>
+      <div id="resizer"></div>
+    </div>
+
+    <div id="main" tabindex="-1">
+      <div id="header">
+        <div id="menu">
+  
+    <a href="_index.html">Index (Y)</a> &raquo;
+    
+    
+    <span class="title">YARRRMLTemplateBuilder</span>
+  
+</div>
+
+        <div id="search">
+  
+    <a class="full_list_link" id="class_list_link"
+        href="class_list.html">
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+    </a>
+  
+</div>
+        <div class="clear"></div>
+      </div>
+
+      <div id="content"><h1>Module: YARRRMLTemplateBuilder
+  
+  
+  
+</h1>
+<div class="box_info">
+  
+
+  
+  
+  
+  
+  
+
+  
+
+  
+  <dl>
+    <dt>Defined in:</dt>
+    <dd>lib/yarrrml_template_builder/version.rb</dd>
+  </dl>
+  
+</div>
+
+
+  
+    <h2>
+      Constant Summary
+      <small><a href="#" class="constants_summary_toggle">collapse</a></small>
+    </h2>
+
+    <dl class="constants">
+      
+        <dt id="VERSION-constant" class="">VERSION =
+          
+        </dt>
+        <dd><pre class="code"><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>0.1.47</span><span class='tstring_end'>&quot;</span></span></pre></dd>
+      
+    </dl>
+  
+
+
+
+
+
+
+
+
+
+</div>
+
+      <div id="footer">
+  Generated on Sat Dec 18 09:07:59 2021 by
+  <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
+  0.9.26 (ruby-2.7.2).
+</div>
+
+    </div>
+  </body>
+</html>