fix: fix build speed (#1021) (#1023)

* fix: check if build speed can be improved (#1021)

* feat: added tests for workflows service (#1021)

* refactor: error (#1021)

* fix: early exit on loading workflows (#1021)

* fix: clear json from public api folder prior to copying new json (#1021)

* fix: reuse of page props in workflow inputs view (#1021)

---------

Co-authored-by: Fran McDade <[email protected]>

Author: frano-m

.gitignore

@@ -36,8 +36,12 @@ backend/**/.env
 # Playwright test artifacts
 /test-results
 /tests/screenshots
+/playwright-report
 
 # python
 venv
 __pycache__
-playwright-report/
+
+
+## public api
+/public/api

app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/GTFStep/hooks/UseUCSCFiles/hook.ts

@@ -1,17 +1,14 @@
 import { useEffect, useState } from "react";
-import { BRCDataCatalogGenome } from "../../../../../../../../../../../../../apis/catalog/brc-analytics-catalog/common/entities";
 import { parseUCSCFilesResult } from "./utils";
 import { UCSC_FILES_ENDPOINT } from "./constants";
 import { UseUCSCFiles } from "./types";
-import { GA2AssemblyEntity } from "../../../../../../../../../../../../../apis/catalog/ga2/entities";
+import { Assembly } from "../../../../../../../../../../../../../views/WorkflowInputsView/types";
 
 const SPECIAL_CASE_ASSEMBLY_LOOKUP: Record<string, string> = {
   "GCF_000001405.40": "hg38",
 } as const;
 
-export const useUCSCFiles = (
-  genome: BRCDataCatalogGenome | GA2AssemblyEntity
-): UseUCSCFiles => {
+export const useUCSCFiles = (genome: Assembly): UseUCSCFiles => {
   const assemblyId =
     SPECIAL_CASE_ASSEMBLY_LOOKUP[genome.accession] ?? genome.accession;
   const [geneModelUrls, setGeneModelUrls] = useState<string[] | undefined>();

app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/SequencingStep/components/ENASequencingData/components/CollectionSummary/components/Alert/hooks/UseRequirementsMatches/hook.ts

@@ -3,12 +3,11 @@ import { ReadRun } from "../../../../../../types";
 import { UseRequirementsMatches } from "./types";
 import { useMemo } from "react";
 import { buildRequirementWarnings } from "./utils";
-import { BRCDataCatalogGenome } from "../../../../../../../../../../../../../../../../../../../apis/catalog/brc-analytics-catalog/common/entities";
-import { GA2AssemblyEntity } from "../../../../../../../../../../../../../../../../../../../apis/catalog/ga2/entities";
+import { Assembly } from "../../../../../../../../../../../../../../../../../../../views/WorkflowInputsView/types";
 
 export const useRequirementsMatches = (
   table: Table<ReadRun>,
-  genome: BRCDataCatalogGenome | GA2AssemblyEntity
+  genome: Assembly
 ): UseRequirementsMatches => {
   const { getSelectedRowModel, initialState } = table;
   const { columnFilters } = initialState;

app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/SequencingStep/components/ENASequencingData/components/CollectionSummary/components/Alert/hooks/UseRequirementsMatches/utils.ts

@@ -1,9 +1,8 @@
 import { ColumnFiltersState, Row } from "@tanstack/react-table";
 import { ReadRun } from "../../../../../../types";
 import { COLUMN_KEY_TO_LABEL } from "./constants";
-import { BRCDataCatalogGenome } from "../../../../../../../../../../../../../../../../../../../apis/catalog/brc-analytics-catalog/common/entities";
-import { GA2AssemblyEntity } from "../../../../../../../../../../../../../../../../../../../apis/catalog/ga2/entities";
 import { LABEL } from "@databiosphere/findable-ui/lib/apis/azul/common/entities";
+import { Assembly } from "../../../../../../../../../../../../../../../../../../../views/WorkflowInputsView/types";
 
 /**
  * Builds warnings for column filter mismatches.
@@ -61,7 +60,7 @@ function buildDataWarnings(
 export function buildRequirementWarnings(
   initialColumnFilters: ColumnFiltersState,
   rows: Row<ReadRun>[],
-  genome: BRCDataCatalogGenome | GA2AssemblyEntity
+  genome: Assembly
 ): string[] {
   if (rows.length === 0) return [];
   const speciesWarnings = buildSpeciesWarnings(rows, genome);
@@ -77,7 +76,7 @@ export function buildRequirementWarnings(
  */
 function buildSpeciesWarnings(
   rows: Row<ReadRun>[],
-  genome: BRCDataCatalogGenome | GA2AssemblyEntity
+  genome: Assembly
 ): string[] {
   const { ncbiTaxonomyId, taxonomicLevelSpecies } = genome;
 

app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/SequencingStep/components/ENASequencingData/hooks/UseENADataByTaxonomyId/hook.ts

@@ -3,13 +3,12 @@ import { UseENADataByTaxonomyId } from "./types";
 import { fetchENAData } from "./request";
 import { useAsync } from "@databiosphere/findable-ui/lib/hooks/useAsync";
 import { isEligible } from "./utils";
-import { BRCDataCatalogGenome } from "../../../../../../../../../../../../../../../apis/catalog/brc-analytics-catalog/common/entities";
-import { GA2AssemblyEntity } from "../../../../../../../../../../../../../../../apis/catalog/ga2/entities";
 import { useConfig } from "@databiosphere/findable-ui/lib/hooks/useConfig";
 import { AppSiteConfig } from "../../../../../../../../../../../../../../../../site-config/common/entities";
+import { Assembly } from "../../../../../../../../../../../../../../../views/WorkflowInputsView/types";
 
 export const useENADataByTaxonomyId = <T>(
-  genome: BRCDataCatalogGenome | GA2AssemblyEntity
+  genome: Assembly
 ): UseENADataByTaxonomyId<T> => {
   const { ncbiTaxonomyId: taxonomyId } = genome;
   const { config } = useConfig();

app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/types.ts

@@ -1,16 +1,13 @@
 import { ComponentType, ReactNode } from "react";
 import { StepProps as MStepProps } from "@mui/material";
-import {
-  BRCDataCatalogGenome,
-  Workflow,
-} from "../../../../../../../../../../apis/catalog/brc-analytics-catalog/common/entities";
+import { Workflow } from "../../../../../../../../../../apis/catalog/brc-analytics-catalog/common/entities";
 import {
   ConfiguredInput,
   OnConfigure,
 } from "../../../../../../../../../../views/WorkflowInputsView/hooks/UseConfigureInputs/types";
 import { Status, OnLaunchGalaxy } from "./hooks/UseLaunchGalaxy/types";
 import { OnContinue, OnEdit } from "../../hooks/UseStepper/types";
-import { GA2AssemblyEntity } from "../../../../../../../../../../apis/catalog/ga2/entities";
+import { Assembly } from "../../../../../../../../../../views/WorkflowInputsView/types";
 
 export interface StepConfig {
   description?: ReactNode;
@@ -27,7 +24,7 @@ export interface StepProps
     Required<Pick<MStepProps, "index" | "active">> {
   configuredInput: ConfiguredInput;
   entryLabel: string;
-  genome: BRCDataCatalogGenome | GA2AssemblyEntity;
+  genome: Assembly;
   onConfigure: OnConfigure;
   onContinue: OnContinue;
   onEdit: OnEdit;

app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/types.ts

@@ -1,20 +1,17 @@
-import {
-  BRCDataCatalogGenome,
-  Workflow,
-} from "../../../../../../../../apis/catalog/brc-analytics-catalog/common/entities";
+import { Workflow } from "../../../../../../../../apis/catalog/brc-analytics-catalog/common/entities";
 import { OnConfigure } from "../../../../../../../../views/WorkflowInputsView/hooks/UseConfigureInputs/types";
 import {
   Status,
   OnLaunchGalaxy,
 } from "./components/Step/hooks/UseLaunchGalaxy/types";
-import { GA2AssemblyEntity } from "../../../../../../../../apis/catalog/ga2/entities";
 import { StepConfig } from "./components/Step/types";
 import { ConfiguredInput } from "../../../../../../../../views/WorkflowInputsView/hooks/UseConfigureInputs/types";
+import { Assembly } from "../../../../../../../../views/WorkflowInputsView/types";
 
 export interface Props {
   configuredInput: ConfiguredInput;
   configuredSteps: StepConfig[];
-  genome: BRCDataCatalogGenome | GA2AssemblyEntity;
+  genome: Assembly;
   onConfigure: OnConfigure;
   onLaunchGalaxy: OnLaunchGalaxy;
   status: Status;

app/components/Entity/components/ConfigureWorkflowInputs/components/Main/types.ts

@@ -1,18 +1,15 @@
-import {
-  BRCDataCatalogGenome,
-  Workflow,
-} from "../../../../../../apis/catalog/brc-analytics-catalog/common/entities";
+import { Workflow } from "../../../../../../apis/catalog/brc-analytics-catalog/common/entities";
 import {
   ConfiguredInput,
   OnConfigure,
 } from "../../../../../../views/WorkflowInputsView/hooks/UseConfigureInputs/types";
-import { GA2AssemblyEntity } from "../../../../../../apis/catalog/ga2/entities";
 import { StepConfig } from "./components/Stepper/components/Step/types";
+import { Assembly } from "../../../../../../views/WorkflowInputsView/types";
 
 export interface Props {
   configuredInput: ConfiguredInput;
   configuredSteps: StepConfig[];
-  genome: BRCDataCatalogGenome | GA2AssemblyEntity;
+  genome: Assembly;
   onConfigure: OnConfigure;
   workflow: Workflow;
 }

app/components/Entity/components/ConfigureWorkflowInputs/components/SideColumn/types.ts

@@ -1,14 +1,11 @@
-import {
-  BRCDataCatalogGenome,
-  Workflow,
-} from "../../../../../../apis/catalog/brc-analytics-catalog/common/entities";
+import { Workflow } from "../../../../../../apis/catalog/brc-analytics-catalog/common/entities";
 import { ConfiguredInput } from "../../../../../../views/WorkflowInputsView/hooks/UseConfigureInputs/types";
-import { GA2AssemblyEntity } from "../../../../../../apis/catalog/ga2/entities";
 import { StepConfig } from "../../../../../../components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/types";
+import { Assembly } from "../../../../../../views/WorkflowInputsView/types";
 
 export interface Props {
   configuredInput: ConfiguredInput;
   configuredSteps: StepConfig[];
-  genome: BRCDataCatalogGenome | GA2AssemblyEntity;
+  genome: Assembly;
   workflow: Workflow;
 }

app/components/Entity/components/ConfigureWorkflowInputs/components/Top/top.tsx

@@ -1,4 +1,4 @@
-import { Props } from "../../../../../../views/WorkflowInputsView/types";
+import { Props } from "./types";
 import { getBreadcrumbs } from "./utils";
 import { BackPageHero } from "@databiosphere/findable-ui/lib/components/Layout/components/BackPage/components/BackPageHero/backPageHero";