yarrrml_template_builder 0.1.54
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- checksums.yaml +7 -0
- data/.gitignore +8 -0
- data/Changelog.md +1 -0
- data/Gemfile +8 -0
- data/Gemfile.lock +39 -0
- data/LICENSE.txt +21 -0
- data/README.md +139 -0
- data/bin/console +15 -0
- data/bin/setup +8 -0
- data/config/height_yarrrml_template.yaml +190 -0
- data/data/height.csv +2 -0
- data/doc/YARRRMLTemplateBuilder.html +121 -0
- data/doc/YARRRML_Template_Builder.html +6392 -0
- data/doc/YARRRML_Transform.html +1940 -0
- data/doc/_index.html +117 -0
- data/doc/class_list.html +51 -0
- data/doc/css/common.css +1 -0
- data/doc/css/full_list.css +58 -0
- data/doc/css/style.css +497 -0
- data/doc/file.README.html +214 -0
- data/doc/file_list.html +56 -0
- data/doc/frames.html +17 -0
- data/doc/index.html +214 -0
- data/doc/js/app.js +314 -0
- data/doc/js/full_list.js +216 -0
- data/doc/js/jquery.js +4 -0
- data/doc/method_list.html +459 -0
- data/doc/top-level-namespace.html +112 -0
- data/examples/example_output_timerange.rb +56 -0
- data/examples/example_timed_process.rb +56 -0
- data/examples/example_timeinstant_process.rb +56 -0
- data/examples/example_two_linked_processes.rb +88 -0
- data/exemplar_docker_compose.yml +36 -0
- data/lib/yarrrml-template-builder.rb +2 -0
- data/lib/yarrrml_template_builder/version.rb +5 -0
- data/lib/yarrrml_template_builder/yarrrml_template_builder.rb +1485 -0
- data/lib/yarrrml_template_builder/yarrrml_transform.rb +181 -0
- data/lib/yarrrmltemplatebuilder.rb +5 -0
- data/run_me_to_test.rb +26 -0
- data/yarrrml_template_builder.gemspec +39 -0
- metadata +115 -0
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require "yarrrml-template-builder"
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#"pid,uniqid,start,end,data
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b = YARRRML_Template_Builder.new({
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b.person_identifier_role_mappings({
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|
+
# @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!
|
|
23
|
+
# @option params :process_type [String] the URL for the ontological type of the process (defaults to http://semanticscience.org/resource/process)
|
|
24
|
+
# @option params :process_type_column [String] the column header that contains the URL for the ontological type of the process - overrides process_type
|
|
25
|
+
# @option params :process_tag [String] some single-word tag for that process; defaults to "thisprocess"
|
|
26
|
+
# @option params :process_label [String] the label associated with the process type in that row (defaults to "thisprocess")
|
|
27
|
+
# @option params :process_label_column [String] the column header for the label associated with the process type in that row
|
|
28
|
+
# @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
|
|
29
|
+
# @option params :process_end_column [ISO 8601 date (only date)] (optional) the column header for the datestamp when that process ended
|
|
30
|
+
# @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.
|
|
31
|
+
|
|
32
|
+
b.role_in_process({
|
|
33
|
+
person_role_tag: "patientRole_status",
|
|
34
|
+
process_tag: "patient_status",
|
|
35
|
+
process_label: "status recording process",
|
|
36
|
+
process_type: "http://semanticscience.org/resource/SIO_001052", # data collection
|
|
37
|
+
})
|
|
38
|
+
|
|
39
|
+
|
|
40
|
+
|
|
41
|
+
# ===================================================================================
|
|
42
|
+
# ========================================Status===========================================
|
|
43
|
+
# pid,uniqid,date,status_uri,status_label,death_date
|
|
44
|
+
|
|
45
|
+
|
|
46
|
+
b.process_hasoutput_output({
|
|
47
|
+
process_with_output_tag: "patient_status", # connect to the correct process
|
|
48
|
+
output_type_label_column: "data",
|
|
49
|
+
output_value_column: "data",
|
|
50
|
+
output_start_column: "start",
|
|
51
|
+
output_end_column: "end"
|
|
52
|
+
})
|
|
53
|
+
|
|
54
|
+
|
|
55
|
+
|
|
56
|
+
puts b.generate
|
|
@@ -0,0 +1,56 @@
|
|
|
1
|
+
require "yarrrml-template-builder"
|
|
2
|
+
|
|
3
|
+
#"pid,uniqid,start,end,data
|
|
4
|
+
|
|
5
|
+
|
|
6
|
+
b = YARRRML_Template_Builder.new({
|
|
7
|
+
source_tag: "cde_timed_process",
|
|
8
|
+
sio_verbose: 1,
|
|
9
|
+
}
|
|
10
|
+
)
|
|
11
|
+
|
|
12
|
+
|
|
13
|
+
b.person_identifier_role_mappings({
|
|
14
|
+
personid_column: "pid",
|
|
15
|
+
uniqueid_column: "uniqid",
|
|
16
|
+
person_role_tag: "patientRole_status",
|
|
17
|
+
role_type: 'http://purl.obolibrary.org/obo/OBI_0000093',
|
|
18
|
+
role_label: "Patient for status recording"
|
|
19
|
+
})
|
|
20
|
+
# ===============================================
|
|
21
|
+
# @param params [Hash] a hash of options
|
|
22
|
+
# @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!
|
|
23
|
+
# @option params :process_type [String] the URL for the ontological type of the process (defaults to http://semanticscience.org/resource/process)
|
|
24
|
+
# @option params :process_type_column [String] the column header that contains the URL for the ontological type of the process - overrides process_type
|
|
25
|
+
# @option params :process_tag [String] some single-word tag for that process; defaults to "thisprocess"
|
|
26
|
+
# @option params :process_label [String] the label associated with the process type in that row (defaults to "thisprocess")
|
|
27
|
+
# @option params :process_label_column [String] the column header for the label associated with the process type in that row
|
|
28
|
+
# @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
|
|
29
|
+
# @option params :process_end_column [ISO 8601 date (only date)] (optional) the column header for the datestamp when that process ended
|
|
30
|
+
# @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.
|
|
31
|
+
|
|
32
|
+
b.role_in_process({
|
|
33
|
+
person_role_tag: "patientRole_status",
|
|
34
|
+
process_tag: "patient_status",
|
|
35
|
+
process_label: "status recording process",
|
|
36
|
+
process_type: "http://semanticscience.org/resource/SIO_001052", # data collection
|
|
37
|
+
process_start_column: "start",
|
|
38
|
+
process_end_column: "end"
|
|
39
|
+
})
|
|
40
|
+
|
|
41
|
+
|
|
42
|
+
|
|
43
|
+
# ===================================================================================
|
|
44
|
+
# ========================================Status===========================================
|
|
45
|
+
# pid,uniqid,date,status_uri,status_label,death_date
|
|
46
|
+
|
|
47
|
+
|
|
48
|
+
b.process_hasoutput_output({
|
|
49
|
+
process_with_output_tag: "patient_status", # connect to the correct process
|
|
50
|
+
output_type_label_column: "data",
|
|
51
|
+
output_value_column: "data",
|
|
52
|
+
})
|
|
53
|
+
|
|
54
|
+
|
|
55
|
+
|
|
56
|
+
puts b.generate
|