-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathUpdate_LOINC.properties
197 lines (178 loc) · 9.9 KB
/
Update_LOINC.properties
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
#*********************************************
# Properties for LOINC vocabulary update *
# Version 0.0.7 *
#*********************************************
# Common
vocabulary.display.name=LOINC
basePath=vocabulary_data/dev_loinc
baseLogPath=.logs
manualTableName=mock_manual_table
#manualTableName=MANUAL_table
# Database
db.userName=DEV_JENKINS
db.password=123
db.tnsName=OMOPCA
# Build bootstrap action
startUpdate.description=Start Update
# Fast recreate phase (SQL-based)
fastRecreate.description=Fast Recreate
fastRecreate.sqlFileName=00.fast_recreate_schema.sql
#fastRecreate.sqlFileName=mock/00.mock_fast_recreate_schema.sql
fastRecreate.logFileName=fast_recreate.log
fastRecreate.streamLogFileName=fast_recreate_stream.log
fastRecreate.streamErrFileName=fast_recreate_stream.err
# Create source file phase (SQL-based)
createSourceTable.description=Create Source Table
createSourceTable.sqlFileName=01.create_source_tables.sql
# This mock file should be used only when real data import is skipped
#createSourceTable.sqlFileName=mock/01.mock_create_source_tables.sql
createSourceTable.logFileName=create_source_table.log
createSourceTable.streamLogFileName=create_source_table_stream.log
createSourceTable.streamErrFileName=create_source_table_stream.err
# Download vocabulary update package phase
downloadUpdatePack.description=Download Update Packages
# LOINC login
downloadUpdatePack.loinc.loginUrl=https://loinc.org/wp-login.php
downloadUpdatePack.loinc.username=ddymshyts
downloadUpdatePack.loinc.password=LoincPass123
# UMLS login
# The "loginUrl" below is not used currently. Authentication can be done by usage of "fileUrl" below
#downloadUpdatePack.umls.loginUrl=https://utslogin.nlm.nih.gov/cas/login
downloadUpdatePack.umls.username=Ddymshyts
downloadUpdatePack.umls.password=UMLSPass123!
# 'Full Set' package
downloadUpdatePack.fullSet.description='Full Set' package
downloadUpdatePack.fullSet.fileUrl=https://loinc.org/download/loinc-table-file-csv/
downloadUpdatePack.fullSet.fileName=LOINC_X_Text.zip
# 'Multiaxial Hierarchy' package
downloadUpdatePack.multiaxialHierarchy.description='Multiaxial Hierarchy' package
downloadUpdatePack.multiaxialHierarchy.fileUrl= https://loinc.org/download/loinc-multiaxial-hierarchy/
downloadUpdatePack.multiaxialHierarchy.fileName=LOINC_X_MULTI-AXIAL_HIERARCHY.zip
# 'Panels and Forms' package
downloadUpdatePack.panelsForms.description='Panels and Forms' package
downloadUpdatePack.panelsForms.fileUrl=https://loinc.org/download/loinc-panels-and-forms/
downloadUpdatePack.panelsForms.fileName=LOINC_X_PanelsAndForms.zip
# 'CT Expression Association' package
downloadUpdatePack.expressionAssociation.description='Express Association' package
downloadUpdatePack.expressionAssociation.fileUrl=https://loinc.org/download/loincsnomed-ct-expression-association-and-map-sets-file-technology-preview-rf2-format/
downloadUpdatePack.expressionAssociation.fileName=SnomedCT_LOINC_AlphaPhase3_INT_X.zip
# 'CPT Mappings' package
downloadUpdatePack.cptMappings.description='CPT Mappings' package
downloadUpdatePack.cptMappings.fileUrl=https://utslogin.nlm.nih.gov/cas/login?service=https://download.nlm.nih.gov/umls/kss/mappings/LNC215_TO_CPT2005/LNC215_TO_CPT2005_MAPPINGS.zip
downloadUpdatePack.cptMappings.fileName=LNCX_TO_CPTX_MAPPINGS.zip
# Extract phase
extractFiles.description=Extract
# Covert phase
convertData.description=Convert from XLS to CSV
# Source file names should be used from "Download" section
# downloadUpdatePack.fullSet.fileName ('Full Set')
# downloadUpdatePack.multiaxialHierarchy.fileName ('Multiaxial Hierarchy')
# downloadUpdatePack.panelsForms.fileName ('Panels and Forms')
# downloadUpdatePack.expressionAssociation.fileName ('CT Expression Association')
# downloadUpdatePack.cptMappings.fileName ('CPT Mappings')
convertData.panelsForms.answers.destFileName=loinc_answers.txt
convertData.panelsForms.forms.destFileName=loinc_forms.txt
convertData.panelsForms.expressionAssociation.srcFileName=Full/Refset/Content/xder2_sscccRefset_LOINCExpressionAssociationFull_INT_20170131.txt
convertData.panelsForms.expressionAssociation.destFileName=xder2_sscccRefset_LOINCExpressionAssociationFull_INT.txt
# Import data phase
importData.description=Import
# 'Full Set' package
importData.fullSet.description=Import 'Full Set' tables
importData.fullSet.loinc.controlFileName=LOINC.CTL
importData.fullSet.loinc.dataFileName=loinc.csv
importData.fullSet.loinc.logFileName=loinc.log
importData.fullSet.loinc.discardFileName=loinc.dsc
importData.fullSet.loinc.badFileName=loinc.bad
importData.fullSet.loinc.streamLogFileName=loinc_stream.log
importData.fullSet.loinc.streamErrorFileName=loinc_stream.err
#
importData.fullSet.mapTo.controlFileName=MAP_TO.CTL
importData.fullSet.mapTo.dataFileName=map_to.csv
importData.fullSet.mapTo.logFileName=map_to.log
importData.fullSet.mapTo.discardFileName=map_to.dsc
importData.fullSet.mapTo.badFileName=map_to.bad
importData.fullSet.mapTo.streamLogFileName=map_to_stream.log
importData.fullSet.mapTo.streamErrorFileName=map_to_stream.err
#
importData.fullSet.sourceOrganization.controlFileName=SOURCE_ORGANIZATION.CTL
importData.fullSet.sourceOrganization.dataFileName=source_organization.csv
importData.fullSet.sourceOrganization.logFileName=source_organization.log
importData.fullSet.sourceOrganization.discardFileName=source_organization.dsc
importData.fullSet.sourceOrganization.badFileName=source_organization.bad
importData.fullSet.sourceOrganization.streamLogFileName=source_organization_stream.log
importData.fullSet.sourceOrganization.streamErrorFileName=source_organization_stream.err
# 'Multiaxial Hierarchy' package
importData.multiaxialHierarchy.description=Import 'Multiaxial Hierarchy' tables
importData.multiaxialHierarchy.controlFileName=loinc_hierarchy.ctl
importData.multiaxialHierarchy.dataFileName=LOINC_2.56_MULTI-AXIAL_HIERARCHY.CSV
importData.multiaxialHierarchy.logFileName=loinc_hierarchy.log
importData.multiaxialHierarchy.discardFileName=loinc_hierarchy.dsc
importData.multiaxialHierarchy.badFileName=loinc_hierarchy.bad
importData.multiaxialHierarchy.streamLogFileName=loinc_hierarchy_stream.log
importData.multiaxialHierarchy.streamErrorFileName=loinc_hierarchy_stream.err
# 'Panels and Forms' package
importData.panelsForms.answers.description=Import 'Panels and Forms' tables
importData.panelsForms.answers.controlFileName=LOINC_ANSWERS.CTL
importData.panelsForms.answers.dataFileName=loinc_answers.txt
importData.panelsForms.answers.logFileName=loinc_answers.log
importData.panelsForms.answers.discardFileName=loinc_answers.dsc
importData.panelsForms.answers.badFileName=loinc_answers.bad
importData.panelsForms.answers.streamLogFileName=loinc_answers_stream.log
importData.panelsForms.answers.streamErrorFileName=loinc_answers_stream.err
#
importData.panelsForms.forms.controlFileName=loinc_forms.ctl
importData.panelsForms.forms.dataFileName=loinc_forms.txt
importData.panelsForms.forms.logFileName=loinc_forms.log
importData.panelsForms.forms.discardFileName=loinc_forms.dsc
importData.panelsForms.forms.badFileName=loinc_forms.bad
importData.panelsForms.forms.streamLogFileName=loinc_forms_stream.log
importData.panelsForms.forms.streamErrorFileName=loinc_forms_stream.err
# 'Expression Association' package
importData.expressionAssociation.description=Import 'Expression Association' tables
importData.expressionAssociation.controlFileName=xder2_sscccRefset_LOINCExpressionAssociationFull_INT.ctl
importData.expressionAssociation.dataFileName=xder2_sscccRefset_LOINCExpressionAssociationFull_INT.txt
importData.expressionAssociation.logFileName=xder2_sscccRefset_LOINCExpressionAssociationFull_INT.log
importData.expressionAssociation.discardFileName=xder2_sscccRefset_LOINCExpressionAssociationFull_INT.dsc
importData.expressionAssociation.badFileName=xder2_sscccRefset_LOINCExpressionAssociationFull_INT.bad
importData.expressionAssociation.streamLogFileName=xder2_sscccRefset_LOINCExpressionAssociationFull_INT_stream.log
importData.expressionAssociation.streamErrorFileName=xder2_sscccRefset_LOINCExpressionAssociationFull_INT_stream.err
# 'CPT Mappings' package
importData.cptMappings.description=Import 'CPT Mappings' tables
importData.cptMappings.controlFileName=CPT_MRSMAP.ctl
importData.cptMappings.dataFileName=MRSMAP.RRF
importData.cptMappings.logFileName=CPT_MRSMAP.log
importData.cptMappings.discardFileName=CPT_MRSMAP.dsc
importData.cptMappings.badFileName=CPT_MRSMAP.bad
importData.cptMappings.streamLogFileName=CPT_MRSMAP_stream.log
importData.cptMappings.streamErrorFileName=CPT_MRSMAP_stream.err
# 'LOINC Class' table
importData.loincClass.description=Import'LOINC Class' table
importData.loincClass.provided=true
importData.loincClass.controlFileName=loinc_class.ctl
importData.loincClass.dataFileName=loinc_class.csv
importData.loincClass.logFileName=loinc_class.log
importData.loincClass.discardFileName=loinc_class.dsc
importData.loincClass.badFileName=loinc_class.bad
importData.loincClass.streamLogFileName=loinc_class.log
importData.loincClass.streamErrorFileName=loinc_class.err
# Load stage phase (SQL-based)
loadStage.description=Load Stage
loadStage.sqlFileName=03.load_stage.sql
#loadStage.sqlFileName=mock/03.mock_load_stage.sql
loadStage.logFileName=load_stage.log
loadStage.streamLogFileName=load_stage_stream.log
loadStage.streamErrFileName=load_stage_stream.err
# Generic update phase (SQL-based)
genericUpdate.description=Generic Update
genericUpdate.sqlFileName=04.generic_update.sql
#genericUpdate.sqlFileName=mock/04.mock_generic_update.sql
genericUpdate.logFileName=generic_update.log
genericUpdate.streamLogFileName=generic_update_stream.log
genericUpdate.streamErrFileName=generic_update_stream.err
# Check update results phase (SQL-based)
checkUpdateResults.description=Check Update Results
checkUpdateResults.sqlFileName=05.update_results.sql
#checkUpdateResults.sqlFileName=mock/05.mock_update_results.sql
checkUpdateResults.logFileName=check_update_results.log
checkUpdateResults.streamLogFileName=check_update_results_stream.log
checkUpdateResults.streamErrFileName=check_update_results_stream.err