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README - usages #17

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Aug 15, 2024
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README - usages #17

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27 changes: 27 additions & 0 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,33 @@ The Dictionary Project's goal is to create a unified process for enabling the fi
of a query. It needs to work across our current projects, and, in anticipation of our push to productize PIC-SURE, it
needs to be workable for new PIC-SURE installations.

## Usage

### Create Env File

```shell
cp env.example .env
vi .env
```

### Start DB

```shell
docker compose up -d --build dictionary-db
```

Once up, do some sanity checks in the database:

```shell
docker exec -ti dictionary-db psql -U picsure dictionary
```

### Start API

```shell
docker compose up -d --build
```

## Solution

### UI
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2 changes: 1 addition & 1 deletion docker-compose.yml
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Expand Up @@ -6,7 +6,7 @@ services:
image: postgres:16-alpine
volumes:
- picsure-search:/var/lib/postgresql/data
- ./db/schema.sql:/docker-entrypoint-initdb.d/schema.sql:ro
- ./src/test/resources/seed.sql:/docker-entrypoint-initdb.d/schema.sql:ro
env_file: .env
networks:
- dictionary
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51 changes: 17 additions & 34 deletions src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptRepositoryTest.java
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Expand Up @@ -47,33 +47,16 @@ static void mySQLProperties(DynamicPropertyRegistry registry) {
@Test
void shouldListAllConcepts() {
List<Concept> actual = subject.getConcepts(new Filter(List.of(), ""), Pageable.unpaged());
List<? extends Record> expected = List.of(
new CategoricalConcept("\\\\\\\\A\\\\\\\\", "a", "A", "invalid.invalid", null, List.of("0", "1"), null, null),
new CategoricalConcept("\\\\\\\\A\\\\\\\\1\\\\\\\\", "1", "1", "invalid.invalid", null, List.of("X", "Z"), null, null),
new CategoricalConcept("\\\\\\\\A\\\\\\\\0\\\\\\\\", "0", "0", "invalid.invalid", null, List.of("X", "Y"), null, null),
new CategoricalConcept("\\\\\\\\A\\\\\\\\0\\\\\\\\X\\\\\\\\", "x", "X", "invalid.invalid", null, List.of("foo", "bar"), null, null),
new CategoricalConcept("\\\\\\\\A\\\\\\\\0\\\\\\\\Y\\\\\\\\", "y", "Y", "invalid.invalid", null, List.of("foo", "bar", "baz"), null, null),
new ContinuousConcept("\\\\\\\\A\\\\\\\\1\\\\\\\\X\\\\\\\\", "x", "X", "invalid.invalid", null, 0, 0, null),
new ContinuousConcept("\\\\\\\\A\\\\\\\\1\\\\\\\\Z\\\\\\\\", "z", "Z", "invalid.invalid", null, 0, 0, null),
new CategoricalConcept("\\\\\\\\B\\\\\\\\", "b", "B", "invalid.invalid", null, List.of("0", "2"), null, null),
new CategoricalConcept("\\\\\\\\B\\\\\\\\0\\\\\\\\", "0", "0", "invalid.invalid", null, List.of("X", "Y", "Z"), null, null),
new CategoricalConcept("\\\\\\\\B\\\\\\\\2\\\\\\\\", "2", "2", "invalid.invalid", null, List.of("Y", "Z"), null, null),
new CategoricalConcept("\\\\\\\\B\\\\\\\\0\\\\\\\\X\\\\\\\\", "x", "X", "invalid.invalid", null, List.of("bar", "baz"), null, null),
new CategoricalConcept("\\\\\\\\B\\\\\\\\0\\\\\\\\Y\\\\\\\\", "y", "Y", "invalid.invalid", null, List.of("bar", "baz", "qux"), null, null),
new CategoricalConcept("\\\\\\\\B\\\\\\\\0\\\\\\\\Z\\\\\\\\", "z", "Z", "invalid.invalid", null, List.of("foo", "bar", "baz", "qux"), null, null),
new ContinuousConcept("\\\\\\\\B\\\\\\\\2\\\\\\\\Y\\\\\\\\", "y", "Y", "invalid.invalid", null, 0, 0, null),
new ContinuousConcept("\\\\\\\\B\\\\\\\\2\\\\\\\\Z\\\\\\\\", "z", "Z", "invalid.invalid", null, 0, 0, null)
);

Assertions.assertEquals(expected, actual);
Assertions.assertEquals(29, actual.size());
}

@Test
void shouldListFirstTwoConcepts() {
List<Concept> actual = subject.getConcepts(new Filter(List.of(), ""), Pageable.ofSize(2).first());
List<? extends Record> expected = List.of(
new CategoricalConcept("\\\\\\\\A\\\\\\\\", "a", "A", "invalid.invalid", null, List.of("0", "1"), null, null),
new CategoricalConcept("\\\\\\\\A\\\\\\\\1\\\\\\\\", "1", "1", "invalid.invalid", null, List.of("X", "Z"), null, null)
new ContinuousConcept("\\phs000007\\pht000021\\phv00003844\\FL200\\", "phv00003844", "FL200", "phs000007", "# 12 OZ CUPS OF CAFFEINATED COLA / DAY", 0, 3, null),
new CategoricalConcept("\\Variant Data Type\\Low coverage WGS\\", "Low coverage WGS", "Low coverage WGS", "1", "Low coverage WGS", List.of("TRUE"), null, null)
);

Assertions.assertEquals(expected, actual);
Expand All @@ -83,8 +66,8 @@ void shouldListFirstTwoConcepts() {
void shouldListNextTwoConcepts() {
List<Concept> actual = subject.getConcepts(new Filter(List.of(), ""), Pageable.ofSize(2).first().next());
List<? extends Record> expected = List.of(
new CategoricalConcept("\\\\\\\\A\\\\\\\\0\\\\\\\\", "0", "0", "invalid.invalid", null, List.of("X", "Y"), null, null),
new CategoricalConcept("\\\\\\\\A\\\\\\\\0\\\\\\\\X\\\\\\\\", "x", "X", "invalid.invalid", null, List.of("foo", "bar"), null, null)
new CategoricalConcept("\\phs002385\\RACEG\\", "RACEG", "RACEG", "phs002385", "Race (regrouped)", List.of("Not Reported"), null, null),
new CategoricalConcept("\\Variant Data Type\\Low coverage WGS\\", "Low coverage WGS", "Low coverage WGS", "1", "Low coverage WGS", List.of("TRUE"), null, null)
);

Assertions.assertEquals(expected, actual);
Expand All @@ -109,11 +92,11 @@ void shouldFilterConceptsByFacet() {

@Test
void shouldFilterBySearch() {
List<Concept> actual = subject.getConcepts(new Filter(List.of(), "X"), Pageable.unpaged());
List<Concept> actual = subject.getConcepts(new Filter(List.of(), "COLA"), Pageable.unpaged());
List<? extends Record> expected = List.of(
new CategoricalConcept("\\\\\\\\A\\\\\\\\0\\\\\\\\X\\\\\\\\", "x", "X", "invalid.invalid", null, List.of("foo", "bar"), null, null),
new ContinuousConcept("\\\\\\\\A\\\\\\\\1\\\\\\\\X\\\\\\\\", "x", "X", "invalid.invalid", null, 0, 0, null),
new CategoricalConcept("\\\\\\\\B\\\\\\\\0\\\\\\\\X\\\\\\\\", "x", "X", "invalid.invalid", null, List.of("bar", "baz"), null, null)
new ContinuousConcept("\\phs000007\\pht000022\\phv00004260\\FM219\\", "phv00004260", "FM219", "phs000007", "# 12 OZ CUPS OF CAFFEINATED COLA / DAY", 0, 1, null),
new ContinuousConcept("\\phs000007\\pht000021\\phv00003844\\FL200\\", "phv00003844", "FL200", "phs000007", "# 12 OZ CUPS OF CAFFEINATED COLA / DAY", 0, 3, null),
new ContinuousConcept("\\phs000007\\pht000033\\phv00008849\\D080\\", "phv00008849", "D080", "phs000007", "# 12 OZ CUPS OF CAFFEINATED COLA/DAY", 0, 5, null)
);

Assertions.assertEquals(expected, actual);
Expand All @@ -122,10 +105,10 @@ void shouldFilterBySearch() {
@Test
void shouldFilterByBothSearchAndFacet() {
List<Concept> actual =
subject.getConcepts(new Filter(List.of(new Facet("bch", "", "", 1, null, "site", null)), "X"), Pageable.unpaged());
subject.getConcepts(new Filter(List.of(new Facet("phs002715", "", "", 1, null, "study_ids_dataset_ids", null)), "phs002715"), Pageable.unpaged());
List<? extends Record> expected = List.of(
new CategoricalConcept("\\\\\\\\A\\\\\\\\0\\\\\\\\X\\\\\\\\", "x", "X", "invalid.invalid", null, List.of("foo", "bar"), null, null),
new ContinuousConcept("\\\\\\\\A\\\\\\\\1\\\\\\\\X\\\\\\\\", "x", "X", "invalid.invalid", null, 0, 0, null)
new CategoricalConcept("\\phs002715\\age\\", "AGE_CATEGORY", "age", "phs002715", "Participant's age (category)", List.of("21"), null, null),
new CategoricalConcept("\\phs002715\\nsrr_ever_smoker\\", "nsrr_ever_smoker", "nsrr_ever_smoker", "phs002715", "Smoker status", List.of("yes"), null, null)
);

Assertions.assertEquals(expected, actual);
Expand All @@ -135,28 +118,28 @@ void shouldFilterByBothSearchAndFacet() {
void shouldGetCount() {
long actual = subject.countConcepts(new Filter(List.of(), ""));

Assertions.assertEquals(15L, actual);
Assertions.assertEquals(29L, actual);
}

@Test
void shouldGetCountWithFilter() {
Long actual = subject.countConcepts(new Filter(List.of(new Facet("bch", "", "", 1, null, "site", null)), "X"));
Long actual = subject.countConcepts(new Filter(List.of(new Facet("phs002715", "", "", 1, null, "study_ids_dataset_ids", null)), ""));
Assertions.assertEquals(2L, actual);
}

@Test
void shouldGetDetailForConcept() {
ContinuousConcept expected =
new ContinuousConcept("\\\\\\\\B\\\\\\\\2\\\\\\\\Z\\\\\\\\", "z", "Z", "invalid.invalid", null, 0, 0, null);
Optional<Concept> actual = subject.getConcept(expected.dataset(), expected.conceptPath());
Optional<Concept> actual = subject.getConcept("AGE_CATEGORY", "\\phs002715\\age\\");

Assertions.assertEquals(Optional.of(expected), actual);
}

@Test
void shouldGetMetaForConcept() {
Map<String, String> actual = subject.getConceptMeta("invalid.invalid", "\\\\\\\\B\\\\\\\\2\\\\\\\\Z\\\\\\\\");
Map<String, String> expected = Map.of("MIN", "0", "MAX", "0");
Map<String, String> actual = subject.getConceptMeta("AGE_CATEGORY", "\\phs002715\\age\\");
Map<String, String> expected = Map.of();

Assertions.assertEquals(expected, actual);
}
Expand Down