feat!: use latest object schemas and dependency releases (#293)

* build!: updating to vrs 2.0 models

* update pydantic-to-ts2 and update models

* wip: updating models, making variable casing consistent, converting descriptors

* fix: utilities requests

* fix: response model casing

* wip: updating models

* bug fixes

* updating models and fixing validation

* pass around formatted fusion to reduce repeated code

* fixing demo data

* specifying fusion type since null param gets dropped and fusor can't infer the type

* fixing tests and updating data with new models, bug fixes

* bug fixes for input elements

* pin latest fusor

* update dependencies

* fix clientification of demos

* fix formatting in docstrings

* fix type handling of failed lookup

* fix up gene lookup api

* fix tx utils bug

* fix bug where region and strand were incorrect in templated sequence, fix regulatory element missing field, pin pydantic version

* removing console logs

* fix: bug where error messages no longer displayed on summary page

* fixing tests and adjusting variable casing

* add reusable function for checking valid sequence locations

* add reusable function for checking valid sequence locations

* fixing nomenclature bugs

* fixing nomenclature bugs

* DOn't bother w/ semver checks (out of control of this app) and use proper fixture mode

* add assertion notes

* stash changes

* stash

* fix a few fixtures

* sequence util fixes

* minor rearrange

* fix int/str problem

* commit this

* catch static files error

* validation tests

* fix reg element URL

* remove todos

* review comments

---------

Co-authored-by: James Stevenson <james.stevenson@nationwidechildrens.org>

README.md

@@ -30,7 +30,7 @@ source venv/bin/activate
 python3 -m pip install -e ".[dev,tests]"  # make sure to include the extra dependencies!
 ```
 
-Acquire two sets of static assets and place all of them within the `server/curation/data` directory:
+Acquire two sets of static assets and place all of them within the `server/src/curfu/data` directory:
 
 1. Gene autocomplete files, providing legal gene search terms to the client autocomplete component. One file each is used for entity types `aliases`, `assoc_with`, `xrefs`, `prev_symbols`, `labels`, and `symbols`. Each should be named according to the pattern `gene_<type>_<YYYYMMDD>.tsv`. These can be regenerated with the shell command `curfu_devtools genes`.
 
@@ -39,7 +39,7 @@ Acquire two sets of static assets and place all of them within the `server/curat
 Your data/directory should look something like this:
 
 ```
-server/curfu/data
+server/src/curfu/data
 ├── domain_lookup_2022-01-20.tsv
 ├── gene_aliases_suggest_20211025.tsv
 ├── gene_assoc_with_suggest_20211025.tsv

client/src/components/Pages/Assay/Assay.tsx

@@ -61,52 +61,52 @@ export const Assay: React.FC<Props> = () => {
 
   // initialize field values
   const [fusionDetection, setFusionDetection] = useState(
-    fusion?.assay?.fusion_detection !== undefined
-      ? fusion?.assay?.fusion_detection
+    fusion?.assay?.fusionDetection !== undefined
+      ? fusion?.assay?.fusionDetection
       : null
   );
 
   const [assayName, setAssayName] = useState(
-    fusion?.assay?.assay_name !== undefined ? fusion?.assay?.assay_name : ""
+    fusion?.assay?.assayName !== undefined ? fusion?.assay?.assayName : ""
   );
 
   const [assayId, setAssayId] = useState(
-    fusion?.assay?.assay_id !== undefined ? fusion?.assay?.assay_id : ""
+    fusion?.assay?.assayId !== undefined ? fusion?.assay?.assayId : ""
   );
 
   const [methodUri, setMethodUri] = useState(
-    fusion?.assay?.method_uri !== undefined ? fusion?.assay?.method_uri : ""
+    fusion?.assay?.methodUri !== undefined ? fusion?.assay?.methodUri : ""
   );
 
   const handleEvidenceChange = (event: FormEvent<HTMLInputElement>) => {
     const evidence_value = event.currentTarget.value;
-    if (fusion?.assay?.fusion_detection !== evidence_value) {
+    if (fusion?.assay?.fusionDetection !== evidence_value) {
       setFusionDetection(evidence_value);
       const assay = JSON.parse(JSON.stringify(fusion.assay));
-      assay["fusion_detection"] = evidence_value;
+      assay["fusionDetection"] = evidence_value;
       setFusion({ ...fusion, assay: assay });
     }
   };
 
   const propertySetterMap = {
-    assayName: [setAssayName, "assay_name"],
-    assayId: [setAssayId, "assay_id"],
-    methodUri: [setMethodUri, "method_uri"],
+    assayName: [setAssayName, "assayName"],
+    assayId: [setAssayId, "assayId"],
+    methodUri: [setMethodUri, "methodUri"],
   };
 
   // live update fields
   useEffect(() => {
-    if (fusion?.assay?.fusion_detection !== fusionDetection) {
-      setFusionDetection(fusion?.assay?.fusion_detection);
+    if (fusion?.assay?.fusionDetection !== fusionDetection) {
+      setFusionDetection(fusion?.assay?.fusionDetection);
     }
-    if (fusion?.assay?.assay_name !== assayName) {
-      setAssayName(fusion?.assay?.assay_name);
+    if (fusion?.assay?.assayName !== assayName) {
+      setAssayName(fusion?.assay?.assayName);
     }
-    if (fusion?.assay?.assay_id !== assayId) {
-      setAssayId(fusion?.assay?.assay_id);
+    if (fusion?.assay?.assayId !== assayId) {
+      setAssayId(fusion?.assay?.assayId);
     }
-    if (fusion?.assay?.method_uri !== methodUri) {
-      setMethodUri(fusion?.assay?.method_uri);
+    if (fusion?.assay?.methodUri !== methodUri) {
+      setMethodUri(fusion?.assay?.methodUri);
     }
   }, [fusion]);
 

client/src/components/Pages/CausativeEvent/CausativeEvent.tsx

@@ -28,18 +28,18 @@ export const CausativeEvent: React.FC<Props> = () => {
   const { fusion, setFusion } = useContext(FusionContext);
 
   const [eventType, setEventType] = useState<string>(
-    fusion.causative_event?.event_type || ""
+    fusion.causativeEvent?.eventType || ""
   );
   const [eventDescription, setEventDescription] = useState<string>(
-    fusion.causative_event?.event_type || ""
+    fusion.causativeEvent?.eventType || ""
   );
 
   /**
    * Ensure that causative event object exists for getter/setter purposes
    */
   const ensureEventInitialized = () => {
-    if (!fusion.causative_event) {
-      setFusion({ ...fusion, causative_event: {} });
+    if (!fusion.causativeEvent) {
+      setFusion({ ...fusion, causativeEvent: {} });
     }
   };
 
@@ -56,8 +56,8 @@ export const CausativeEvent: React.FC<Props> = () => {
     if (eventType !== value) {
       setEventType(value);
     }
-    const newCausativeEvent = { event_type: value, ...fusion.causative_event };
-    setFusion({ causative_event: newCausativeEvent, ...fusion });
+    const newCausativeEvent = { eventType: value, ...fusion.causativeEvent };
+    setFusion({ causativeEvent: newCausativeEvent, ...fusion });
   };
 
   /**
@@ -72,10 +72,10 @@ export const CausativeEvent: React.FC<Props> = () => {
       setEventDescription(value);
     }
     const newCausativeEvent = {
-      event_description: value,
-      ...fusion.causative_event,
+      eventDescription: value,
+      ...fusion.causativeEvent,
     };
-    setFusion({ causative_event: newCausativeEvent, ...fusion });
+    setFusion({ causativeEvent: newCausativeEvent, ...fusion });
   };
 
   return (

client/src/components/Pages/Domains/DomainForm/DomainForm.tsx

@@ -35,8 +35,8 @@ const useStyles = makeStyles((theme) => ({
 const DomainForm: React.FC = () => {
   // // TODO: shouldn't be necessary
   useEffect(() => {
-    if (fusion.critical_functional_domains === undefined) {
-      setFusion({ ...fusion, ...{ critical_functional_domains: [] } });
+    if (fusion.criticalFunctionalDomains === undefined) {
+      setFusion({ ...fusion, ...{ criticalFunctionalDomains: [] } });
     }
   }, []);
 
@@ -65,7 +65,7 @@ const DomainForm: React.FC = () => {
 
   const handleAdd = () => {
     const domainParams = domainOptions[gene].find(
-      (domainOption: DomainParams) => domainOption.interpro_id == domain
+      (domainOption: DomainParams) => domainOption.interproId == domain
     );
     getFunctionalDomain(domainParams, status as DomainStatus, gene).then(
       (response) => {
@@ -74,11 +74,11 @@ const DomainForm: React.FC = () => {
             domain_id: uuid(),
             ...response.domain,
           };
-          const cloneArray = Array.from(fusion["critical_functional_domains"]);
+          const cloneArray = Array.from(fusion["criticalFunctionalDomains"]);
           cloneArray.push(newDomain);
           setFusion({
             ...fusion,
-            ...{ critical_functional_domains: cloneArray },
+            ...{ criticalFunctionalDomains: cloneArray },
           });
 
           setStatus("default");
@@ -107,11 +107,11 @@ const DomainForm: React.FC = () => {
     if (domainOptions[gene]) {
       const uniqueInterproIds: Set<string> = new Set();
       domainOptions[gene].forEach((domain: DomainParams, index: number) => {
-        if (!uniqueInterproIds.has(domain.interpro_id)) {
-          uniqueInterproIds.add(domain.interpro_id);
+        if (!uniqueInterproIds.has(domain.interproId)) {
+          uniqueInterproIds.add(domain.interproId);
           domainOptionMenuItems.push(
-            <MenuItem key={index} value={domain.interpro_id}>
-              {domain.domain_name}
+            <MenuItem key={index} value={domain.interproId}>
+              {domain.domainName}
             </MenuItem>
           );
         }

client/src/components/Pages/Domains/Main/Domains.tsx

@@ -22,7 +22,7 @@ export const Domain: React.FC<Props> = () => {
   const { fusion, setFusion } = useContext(FusionContext);
 
   const { globalGenes } = useContext(GeneContext);
-  const domains = fusion.critical_functional_domains || [];
+  const domains = fusion.criticalFunctionalDomains || [];
 
   const { colorTheme } = useColorTheme();
   const useStyles = makeStyles(() => ({
@@ -73,14 +73,14 @@ export const Domain: React.FC<Props> = () => {
 
   const handleRemove = (domain: ClientFunctionalDomain) => {
     let cloneArray: ClientFunctionalDomain[] = Array.from(
-      fusion.critical_functional_domains
+      fusion.criticalFunctionalDomains
     );
     cloneArray = cloneArray.filter((obj) => {
       return obj["domain_id"] !== domain["domain_id"];
     });
     setFusion({
       ...fusion,
-      ...{ critical_functional_domains: cloneArray || [] },
+      ...{ criticalFunctionalDomains: cloneArray || [] },
     });
   };
 
@@ -108,7 +108,7 @@ export const Domain: React.FC<Props> = () => {
         avatar={<Avatar>{domain.status === "preserved" ? "P" : "L"}</Avatar>}
         label={
           <React.Fragment>
-            {domainLabelString} <b>{`(${domain.associated_gene.label})`}</b>
+            {domainLabelString} <b>{`(${domain.associatedGene.label})`}</b>
           </React.Fragment>
         }
         onDelete={() => handleRemove(domain)}

client/src/components/Pages/Gene/StructureDiagram/StructureDiagram.tsx

@@ -42,8 +42,8 @@ export const StructureDiagram: React.FC = () => {
         });
 
         const regEls = [];
-        suggestion.regulatory_elements.forEach((el) => {
-          regEls.push(el.gene_descriptor.label);
+        suggestion.regulatoryElements.forEach((el) => {
+          regEls.push(el.gene.label);
         });
 
         return (

client/src/components/Pages/ReadingFrame/ReadingFrame.tsx

@@ -50,19 +50,19 @@ export const ReadingFrame: React.FC<Props> = ({ index }) => {
   };
 
   const [rFramePreserved, setRFramePreserved] = useState(
-    assignRadioValue(fusion.r_frame_preserved)
+    assignRadioValue(fusion.readingFramePreserved)
   );
 
   useEffect(() => {
     if (
-      fusion.r_frame_preserved &&
-      fusion.r_frame_preserved !== rFramePreserved
+      fusion.readingFramePreserved &&
+      fusion.readingFramePreserved !== rFramePreserved
     ) {
-      setRFramePreserved(assignRadioValue(fusion.r_frame_preserved));
+      setRFramePreserved(assignRadioValue(fusion.readingFramePreserved));
     }
 
-    if (fusion.r_frame_preserved === undefined) {
-      setFusion({ ...fusion, r_frame_preserved: null });
+    if (fusion.readingFramePreserved === undefined) {
+      setFusion({ ...fusion, readingFramePreserved: null });
     }
   }, [fusion]);
 
@@ -71,13 +71,13 @@ export const ReadingFrame: React.FC<Props> = ({ index }) => {
     if (value !== rFramePreserved) {
       if (value === "yes") {
         setRFramePreserved("yes");
-        setFusion({ ...fusion, r_frame_preserved: true });
+        setFusion({ ...fusion, readingFramePreserved: true });
       } else if (value === "no") {
         setRFramePreserved("no");
-        setFusion({ ...fusion, r_frame_preserved: false });
+        setFusion({ ...fusion, readingFramePreserved: false });
       } else {
         setRFramePreserved("unspecified");
-        setFusion({ ...fusion, r_frame_preserved: null });
+        setFusion({ ...fusion, readingFramePreserved: null });
       }
     }
   };