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AG-1565 remove druggability #1340

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merged 3 commits into from
Dec 16, 2024
Merged

AG-1565 remove druggability #1340

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2da975a
Update ci.yml
sagely1 Dec 3, 2024
41996e5
Merge pull request #2 from sagely1/sagely1-docker-compose-fix
sagely1 Dec 3, 2024
57fa18a
AG-1565 remove druggability columns
sagely1 Dec 16, 2024
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4 changes: 2 additions & 2 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -215,7 +215,7 @@ jobs:
- name: start database, server, and app
run: |
echo "==> start database and data containers"
docker-compose -f "${{ env.DOCKER_COMPOSE_PATH }}" up -d
docker compose -f "${{ env.DOCKER_COMPOSE_PATH }}" up -d

echo "==> wait for data container to finish seeding database container"
DATA_CONTAINER=$(docker compose -f "${{ env.DOCKER_COMPOSE_PATH }}" ps -a --format '{{.Name}}' mongo-seed)
Expand All @@ -237,7 +237,7 @@ jobs:
pid=$(lsof -i :8080 -t) && kill ${pid}

echo "==> stop database"
docker-compose -f "${{ env.DOCKER_COMPOSE_PATH }}" down
docker compose -f "${{ env.DOCKER_COMPOSE_PATH }}" down

- uses: actions/upload-artifact@v4
if: ${{ !cancelled() }}
Expand Down
4 changes: 2 additions & 2 deletions package.json
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
{
"name": "agora",
"version": "3.4.0",
"version": "3.5.0",
"data-file": "syn13363290",
"data-version": "70",
"data-version": "71",
"private": true,
"scripts": {
"dev": "concurrently --kill-others \"npm:dev:server\" \"npm:dev:app\"",
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30 changes: 0 additions & 30 deletions src/app/features/genes/components/gene-nominated-targets/gene-nominated-targets.component.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -56,21 +56,6 @@ export class GeneNominatedTargetsComponent implements OnInit {
header: 'Pharos Class',
selected: false,
},
{
field: 'sm_druggability_display_value',
header: 'Small Molecule Druggability',
selected: false,
},
{
field: 'safety_rating_display_value',
header: 'Safety Rating',
selected: false,
},
{
field: 'ab_modality_display_value',
header: 'Antibody Modality',
selected: false,
},
];

constructor(private apiService: ApiService) {}
Expand Down Expand Up @@ -138,23 +123,8 @@ export class GeneNominatedTargetsComponent implements OnInit {
de.pharos_class_display_value = de.druggability[0].pharos_class
? de.druggability[0].pharos_class
: 'No value';
de.sm_druggability_display_value =
de.druggability[0].sm_druggability_bucket +
': ' +
de.druggability[0].classification;
de.safety_rating_display_value =
de.druggability[0].safety_bucket +
': ' +
de.druggability[0].safety_bucket_definition;
de.ab_modality_display_value =
de.druggability[0].abability_bucket +
': ' +
de.druggability[0].abability_bucket_definition;
} else {
de.pharos_class_display_value = 'No value';
de.sm_druggability_display_value = 'No value';
de.safety_rating_display_value = 'No value';
de.ab_modality_display_value = 'No value';
}
});

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21 changes: 0 additions & 21 deletions src/app/features/genes/components/gene-similar/gene-similar.component.ts
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Expand Up @@ -45,12 +45,6 @@ export class GeneSimilarComponent implements OnInit {
header: 'Protein Expression Change',
},
{ field: 'pharos_class_display_value', header: 'Pharos Class' },
{
field: 'sm_druggability_display_value',
header: 'Small Molecule Druggability',
},
{ field: 'safety_rating_display_value', header: 'Safety Rating' },
{ field: 'ab_modality_display_value', header: 'Antibody Modality' },
];

gctLink: { [key: string]: string } | undefined;
Expand Down Expand Up @@ -117,23 +111,8 @@ export class GeneSimilarComponent implements OnInit {
de.pharos_class_display_value = de.druggability[0].pharos_class
? de.druggability[0].pharos_class
: 'No value';
de.sm_druggability_display_value =
de.druggability[0].sm_druggability_bucket +
': ' +
de.druggability[0].classification;
de.safety_rating_display_value =
de.druggability[0].safety_bucket +
': ' +
de.druggability[0].safety_bucket_definition;
de.ab_modality_display_value =
de.druggability[0].abability_bucket +
': ' +
de.druggability[0].abability_bucket_definition;
} else {
de.pharos_class_display_value = 'No value';
de.sm_druggability_display_value = 'No value';
de.safety_rating_display_value = 'No value';
de.ab_modality_display_value = 'No value';
}
});

Expand Down
15 changes: 1 addition & 14 deletions src/app/features/genes/components/gene-table/gene-table.component.ts
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Expand Up @@ -116,20 +116,7 @@ export class GeneTableComponent implements OnInit {
} else if (a == null && b == null) {
result = 0;
} else if (typeof a === 'string' && typeof b === 'string') {
// Natural sorting for this score type, which can be >= 10
if (event.field === 'sm_druggability_display_value'
|| event.field === 'safety_rating_display_value'
|| event.field === 'ab_modality_display_value') {
let nA = parseInt(a.split(':')[0], 10);
let nB = parseInt(b.split(':')[0], 10);

nA = !isNaN(nA) ? nA : 999 * event.order;
nB = !isNaN(nB) ? nB : 999 * event.order;

result = nA < nB ? -1 : nA > nB ? 1 : 0;
} else {
result = a.localeCompare(b);
}
result = a.localeCompare(b);
} else {
result = a < b ? -1 : a > b ? 1 : 0;
}
Expand Down
3 changes: 0 additions & 3 deletions src/app/models/genes.ts
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Expand Up @@ -85,9 +85,6 @@ export interface Gene {
similar_genes_network?: SimilarGenesNetwork;

// Similar table (not in mongo document)
ab_modality_display_value?: string;
safety_rating_display_value?: string;
sm_druggability_display_value?: string;
pharos_class_display_value?: string;
is_any_rna_changed_in_ad_brain_display_value?: string;
is_any_protein_changed_in_ad_brain_display_value?: string;
Expand Down
53 changes: 0 additions & 53 deletions tests/nominated-targets.spec.ts
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Expand Up @@ -9,57 +9,4 @@ test.describe('specific viewport block', () => {
// Expect a title "to contain" a substring.
await expect(page).toHaveTitle('Nominated Targets | Candidate genes for AD treatment or prevention');
});

test('has correct sort on druggability columns', async ({ page }) => {
await page.goto('/genes/nominated-targets');

await expect(page.locator('table')).toBeVisible();

await page.locator('#pr_id_3 span').click();

await page.getByLabel('Nominations').click();
await page.getByLabel('Year First Nominated').click();
await page.getByLabel('Nominating Teams').click();
await page.getByLabel('Cohort Study').click();
await page.getByLabel('Small Molecule Druggability').click();
await page.getByLabel('Safety Rating').click();
await page.getByLabel('Antibody Modality').click();

// sort forward on small molecule druggability
await page.getByRole('cell', { name: 'Small Molecule Druggability' }).click();

const row = page.locator('table tr:nth-child(2)');
let cell = row.getByRole('cell').nth(1);
await expect(cell).not.toContainText('No Value');

// sort reverse on small molecule druggability
await page.getByRole('cell', { name: 'Small Molecule Druggability' }).click();

cell = row.getByRole('cell').nth(1);
await expect(cell).not.toContainText('No Value');

// sort forward on safety rating
await page.getByRole('cell', { name: 'Safety Rating' }).click();

cell = row.getByRole('cell').nth(2);
await expect(cell).not.toContainText('No Value');

// sort reverse on safety rating
await page.getByRole('cell', { name: 'Safety Rating' }).click();

cell = row.getByRole('cell').nth(2);
await expect(cell).not.toContainText('No Value');

// sort forward on antibody modality
await page.getByRole('cell', { name: 'Antibody Modality' }).click();

cell = row.getByRole('cell').nth(3);
await expect(cell).not.toContainText('No Value');

// sort reverse on antibody modality
await page.getByRole('cell', { name: 'Antibody Modality' }).click();

cell = row.getByRole('cell').nth(3);
await expect(cell).not.toContainText('No Value');
});
});
7 changes: 0 additions & 7 deletions tests/similar-genes.spec.ts
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Expand Up @@ -20,12 +20,5 @@ test.describe('specific viewport block', () => {

const cell = await page.getByRole('row').nth(1).getByRole('cell').nth(1).innerText();
expect(cell).not.toBe('');


// sort reverse on small molecule druggability
await page.getByRole('cell', { name: 'Nominated Target' }).click();

const cell2 = await page.getByRole('row').nth(1).getByRole('cell').nth(1).innerText();
expect(cell2).not.toBe('');
});
});