yarrrml_template_builder 0.1.54

data/examples/example_timeinstant_process.rb

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+require "yarrrml-template-builder"
+
+#"pid,uniqid,start,data
+
+
+b = YARRRML_Template_Builder.new({
+  source_tag: "cde_timed_process",
+  sio_verbose: 1,
+  }
+  )
+
+
+b.person_identifier_role_mappings({
+                                    personid_column: "pid",
+                                    uniqueid_column: "uniqid",
+                                    person_role_tag: "patientRole_status",
+                                    role_type: 'http://purl.obolibrary.org/obo/OBI_0000093',
+                                    role_label: "Patient for status recording"
+                                    })
+# ===============================================
+# @param params [Hash]  a hash of options
+# @option params :person_role_tag  [String] the tag of the role that is fulfilled in this process (default 'thisRole') - see person_role_tag above, synchronize these tags!
+# @option params :process_type  [String] the URL for the ontological type of the process (defaults to http://semanticscience.org/resource/process)
+# @option params :process_type_column  [String] the column header that contains the URL for the ontological type of the process - overrides process_type
+# @option params :process_tag  [String] some single-word tag for that process; defaults to "thisprocess"
+# @option params :process_label  [String] the label associated with the process type in that row (defaults to "thisprocess")
+# @option params :process_label_column  [String] the column header for the label associated with the process type in that row
+# @option params :process_start_column  [ISO 8601 date (only date)] (optional) the column header for the datestamp when that process started. NOTE:  For instantaneous processes, create ONLY the start date column, and an identical end date will be automatically generated
+# @option params :process_end_column  [ISO 8601 date (only date)]  (optional) the column header for the datestamp when that process ended
+# @option params :make_unique_process [boolean] (true)  (optional) if you want the core URI to be globally unique, or based only on the patient ID.  this can be used to merge nodes over multiple runs of different yarrrml transforms.
+
+b.role_in_process({
+    person_role_tag: "patientRole_status",
+    process_tag:  "patient_status",
+    process_label: "status recording process", 
+    process_type: "http://semanticscience.org/resource/SIO_001052", # data collection
+    process_start_column: "start",
+#    process_end_column: "end"  # without an end, it shiould become an identical start/end
+    })
+
+
+
+# ===================================================================================
+# ========================================Status===========================================
+# pid,uniqid,date,status_uri,status_label,death_date
+
+
+b.process_hasoutput_output({
+    process_with_output_tag: "patient_status",  # connect to the correct process
+    output_type_label_column: "data",
+    output_value_column: "data",
+    })
+
+
+
+puts b.generate

data/examples/example_two_linked_processes.rb

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+require "yarrrml-template-builder"
+
+#"pid,uniqid,  date, status_label, status_uri, death_date
+
+
+b = YARRRML_Template_Builder.new({
+  source_tag: "cde_patient_status",
+  sio_verbose: 1,
+  }
+  )
+
+
+b.person_identifier_role_mappings({
+                                    personid_column: "pid",
+                                    uniqueid_column: "uniqid",
+                                    person_role_tag: "patientRole_status",
+                                    role_type: 'http://purl.obolibrary.org/obo/OBI_0000093',
+                                    role_label: "Patient for status recording"
+                                    })
+# ===============================================
+
+b.role_in_process({
+    person_role_tag: "patientRole_status",
+    process_tag:  "patient_status",
+    process_label: "status recording process", 
+    process_type: "http://semanticscience.org/resource/SIO_001052", # data collection
+    })
+
+
+b.role_in_process({
+    person_role_tag: "patientRole_status",
+    process_tag:  "patient_death_information",
+    process_label: "death information recording process", 
+    process_type: "http://semanticscience.org/resource/SIO_001052", # data collection
+    })
+
+# ===================================================================================
+# ===================================================================================
+# ===================================================================================
+
+b.process_has_part({
+  parent_process_tag: "longitudinal_information_gathering_process_diseaseX",
+  part_process_tag: "patient_status",
+  parent_unique_process: false,
+})
+
+# ===================================================================================
+# ========================================Status===========================================
+# pid,uniqid,date,status_uri,status_label,death_date
+
+
+b.process_hasoutput_output({
+    process_with_output_tag: "patient_status",  # connect to the correct process
+    output_type_label_column: "status_label",
+    output_value_column: "status_label",
+    })
+
+#sio:SIO_010059 (dead)
+#sio:SIO_010058 (alive)
+#obo:NCIT_C70740 (lost to follow-up)
+#obo:NCIT_C124784 (refused to participate)
+b.input_output_refers_to({
+  refers_to_tag: "status_attribute",
+  inout_process_tag:   "patient_status",  # connect to the correct process
+  inout_refers_to_column: "status_uri",
+  inout_refers_to_label: "Patient status",
+  is_attribute: true
+})
+
+b.process_hasoutput_output({
+    process_with_output_tag: "patient_death_information",  # connect to the correct process
+    output_type_label: "patient death information",
+    output_value_column: "death_date",
+    output_value_datatype: "xsd:date",
+    output_timeinstant_column: "death_date"
+    })
+
+b.input_output_refers_to({
+  refers_to_tag: "death_information",
+  inout_process_tag:   "patient_death_information",  # connect to the correct process
+  inout_refers_to: "http://purl.obolibrary.org/obo/NCIT_C70810",
+  inout_refers_to_label: "Date of death",
+  is_attribute: true
+})
+
+
+
+puts b.generate

data/exemplar_docker_compose.yml

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+version: "2.0"
+services:
+
+  graphdb:
+    image: graph-db:9.7.0
+    restart: always
+    hostname: graphdb
+    ports:
+      - 7200:7200
+    volumes:
+      - graphdb-data:/opt/graphdb/home
+
+
+    yarrrml_transform:
+        image: markw/yarrrml-parser-ejp:latest
+        container_name: yarrrml_transform
+        ports:
+            - "3000:3000"
+        volumes:
+            - ./data:/data
+
+
+    rdfizer:
+        image: markw/sdmrdfizer_ejp:0.1.0
+        container_name: rdfizer
+        ports:
+            - "4000:4000"
+        volumes:
+            - ./data:/data
+            - ./config:/config
+
+
+    
+volumes:
+  graphdb-data:
+    external: true

data/lib/yarrrml-template-builder.rb

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+# More logical way to require '
+require File.dirname(__FILE__) + '/yarrrmltemplatebuilder'

data/lib/yarrrml_template_builder/version.rb

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+# frozen_string_literal: true
+
+module YARRRMLTemplateBuilder
+  VERSION = "0.1.54"
+end