[CHORE] It's true and false now, Morty.

hms-dbmi · Sep 25, 2024 · 20833f1 · 20833f1
1 parent 83058b9
commit 20833f1
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Showing 7 changed files with 65 additions and 65 deletions.
diff --git a/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptRepository.java b/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptRepository.java
@@ -22,7 +22,7 @@ public class ConceptRepository {
         WITH allow_filtering AS (
             SELECT
                 concept_node.concept_node_id AS concept_node_id,
-                (string_agg(concept_node_meta.value, ' ') NOT LIKE '%yes%') AS allowFiltering
+                (string_agg(concept_node_meta.value, ' ') NOT LIKE '%true%') AS allowFiltering
             FROM
                 concept_node
                 JOIN concept_node_meta ON

diff --git a/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardRepository.java b/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardRepository.java
@@ -56,17 +56,17 @@ public List<Map<String, String>> getHackyBDCRows() {
                     dataset.abbreviation AS abbreviation,
                     dataset.full_name AS name,
                     CASE
-                        WHEN consent.variable_count > -1 THEN consent.variable_count
+                        WHEN consent.variable_count > -1 THEN consent.variable_count::text
                         ELSE 'N/A'
                         END
                         AS clinvars,
                     CASE
-                        WHEN consent.participant_count > -1 THEN consent.participant_count
+                        WHEN consent.participant_count > -1 THEN consent.participant_count::text
                         ELSE 'N/A'
                         END
                         AS participants,
                     CASE
-                        WHEN consent.sample_count > -1 THEN consent.sample_count
+                        WHEN consent.sample_count > -1 THEN consent.sample_count::text
                         ELSE 'N/A'
                         END
                         AS samples,

diff --git a/src/main/resources/application-bdc.properties b/src/main/resources/application-bdc.properties
@@ -7,4 +7,4 @@ server.port=80
 
 dashboard.enable.extra_details=true
 
-filtering.unfilterable_concepts=stigmatizing
+filtering.unfilterable_concepts=stigmatized
diff --git a/src/main/resources/application.properties b/src/main/resources/application.properties
@@ -11,4 +11,4 @@ dashboard.nonmeta-columns=abbreviation,name
 dashboard.enable.extra_details=true
 dashboard.enable.bdc_hack=true
 
-filtering.unfilterable_concepts=stigmatizing
+filtering.unfilterable_concepts=stigmatized
diff --git a/src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptRepositoryTest.java b/src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptRepositoryTest.java
@@ -160,20 +160,20 @@ void shouldGetMetaForMultipleConcepts() {
         Map<Concept, Map<String, String>> actual = subject.getConceptMetaForConcepts(concepts);
         Map<Concept, Map<String, String>> expected = Map.of(
             new ConceptShell("\\phs000007\\pht000022\\phv00004260\\FM219\\", "phs000007"), Map.of(
-                "unique_identifier", "no",
-                "stigmatizing", "no",
-                "bdc_open_access", "yes",
+                "unique_identifier", "false",
+                "stigmatizing", "false",
+                "bdc_open_access", "true",
                 "values", "[0, 1]",
                 "description", "# 12 OZ CUPS OF CAFFEINATED COLA / DAY",
-                "free_text", "no"
+                "free_text", "true"
             ),
             new ConceptShell("\\phs000007\\pht000033\\phv00008849\\D080\\", "phs000007"), Map.of(
-                "unique_identifier", "no",
-                "stigmatizing", "no",
-                "bdc_open_access", "yes",
+                "unique_identifier", "false",
+                "stigmatizing", "false",
+                "bdc_open_access", "true",
                 "values", "[0, 5]",
                 "description", "# 12 OZ CUPS OF CAFFEINATED COLA/DAY",
-                "free_text", "no"
+                "free_text", "false"
             )
         );
         Assertions.assertEquals(expected, actual);

diff --git a/src/test/resources/application.properties b/src/test/resources/application.properties
@@ -11,4 +11,4 @@ dashboard.nonmeta-columns=abbreviation,name
 dashboard.enable.extra_details=true
 dashboard.enable.bdc_hack=false
 
-filtering.unfilterable_concepts=stigmatizing
+filtering.unfilterable_concepts=stigmatized
diff --git a/src/test/resources/seed.sql b/src/test/resources/seed.sql
@@ -423,81 +423,81 @@ COPY public.concept_node_meta (concept_node_meta_id, concept_node_id, key, value
 37	225	description	Including living and deceased, were any of {SP's/your} close biological that is, blood relatives including father, mother, sisters or brothers, ever told by a health professional that they had a heart attack or angina (an-gi-na) before the age of 50?
 38	225	values	Yes
 39	229	description	# 12 OZ CUPS OF CAFFEINATED COLA / DAY
-41	229	stigmatizing	no
-42	229	unique_identifier	no
-43	229	free_text	no
-44	229	bdc_open_access	yes
+41	229	stigmatizing	false
+42	229	unique_identifier	false
+43	229	free_text	false
+44	229	bdc_open_access	true
 45	232	description	# 12 OZ CUPS OF CAFFEINATED COLA / DAY
-47	232	stigmatizing	no
-48	232	unique_identifier	no
-49	232	free_text	no
-50	232	bdc_open_access	yes
+47	232	stigmatizing	false
+48	232	unique_identifier	false
+49	232	free_text	false
+50	232	bdc_open_access	true
 51	235	description	# 12 OZ CUPS OF CAFFEINATED COLA/DAY
-53	235	stigmatizing	no
-54	235	unique_identifier	no
-55	235	free_text	no
-56	235	bdc_open_access	yes
+53	235	stigmatizing	false
+54	235	unique_identifier	false
+55	235	free_text	false
+56	235	bdc_open_access	true
 57	239	description	Most recent occupation (A)
 58	239	values	ACCOUNTANT
 59	241	description	Age
-61	241	stigmatizing	no
-62	241	unique_identifier	no
-63	241	free_text	no
-64	241	bdc_open_access	yes
+61	241	stigmatizing	false
+62	241	unique_identifier	false
+63	241	free_text	false
+64	241	bdc_open_access	true
 65	242	description	% of time in artifacts
-67	242	stigmatizing	no
-68	242	unique_identifier	no
-69	242	free_text	no
-70	242	bdc_open_access	yes
+67	242	stigmatizing	false
+68	242	unique_identifier	false
+69	242	free_text	false
+70	242	bdc_open_access	true
 71	244	description	Patient age at transplant, years
 72	244	values	42
-73	244	stigmatizing	no
-74	244	unique_identifier	no
-75	244	free_text	no
-76	244	bdc_open_access	yes
+73	244	stigmatizing	false
+74	244	unique_identifier	false
+75	244	free_text	false
+76	244	bdc_open_access	true
 77	244	hct status	pre-hct
 78	244	computed variable	yes
 79	245	description	Race (regrouped)
 80	245	values	Not Reported
-81	245	stigmatizing	no
-82	245	unique_identifier	no
-83	245	free_text	no
-84	245	bdc_open_access	yes
+81	245	stigmatizing	false
+82	245	unique_identifier	false
+83	245	free_text	false
+84	245	bdc_open_access	true
 85	246	description	Transplant Number
 86	246	values	1
-87	246	stigmatizing	yes
-88	246	unique_identifier	no
-89	246	free_text	no
-90	246	bdc_open_access	no
+87	246	stigmatizing	true
+88	246	unique_identifier	false
+89	246	free_text	false
+90	246	bdc_open_access	false
 91	246	hct status	pre-hct
 92	246	computed variable	yes
 93	248	description	Participant's age (category)
 94	248	values	21
-95	248	stigmatizing	no
-96	248	unique_identifier	no
-97	248	free_text	no
-98	248	bdc_open_access	yes
+95	248	stigmatizing	false
+96	248	unique_identifier	false
+97	248	free_text	false
+98	248	bdc_open_access	true
 99	249	description	Smoker status
-100	249	values	yes
-101	249	stigmatizing	no
-102	249	unique_identifier	no
-103	249	free_text	no
-104	249	bdc_open_access	yes
+100	249	values	true
+101	249	stigmatizing	false
+102	249	unique_identifier	false
+103	249	free_text	false
+104	249	bdc_open_access	true
 105	253	description	(AFC) Reason for ending future contact: Withdrew consent for future nuMoM2b contact
 106	253	values	No
-107	253	unique_identifier	no
-108	253	free_text	no
-109	253	bdc_open_access	yes
+107	253	unique_identifier	false
+108	253	free_text	false
+109	253	bdc_open_access	true
 110	255	description	(V5A) Which of the following problems have a doctor or health care professional told you that you have with your kidney?: Other - Specify Field
 111	255	values	infection
-112	255	unique_identifier	no
-113	255	free_text	yes
-114	255	bdc_open_access	no
+112	255	unique_identifier	false
+113	255	free_text	true
+114	255	bdc_open_access	false
 115	258	description	(T01) Are you currently prescribed medication for your high blood pressure?
 116	258	values	Yes
-117	258	unique_identifier	no
-118	258	free_text	no
-119	258	bdc_open_access	yes
+117	258	unique_identifier	false
+118	258	free_text	false
+119	258	bdc_open_access	true
 120	266	description	Genotype array
 121	266	values	TRUE
 122	267	description	Low coverage WGS
Original file line number	Diff line number	Diff line change
Expand Up		@@ -7,4 +7,4 @@ server.port=80

		dashboard.enable.extra_details=true

		filtering.unfilterable_concepts=stigmatizing
		filtering.unfilterable_concepts=stigmatized