SCKAN-151 feat: Replace PMID with the sentence/statement ID

backend/composer/api/filtersets.py

@@ -36,7 +36,7 @@ class SentenceFilter(django_filters.FilterSet):
     )
     ordering = django_filters.OrderingFilter(
         fields=(
-            ("pmid", "pmid"),
+            ("id", "id"),
             ("modified_date", "last_edited"),
         ),
     )
@@ -78,7 +78,7 @@ class ConnectivityStatementFilter(django_filters.FilterSet):
     )
     ordering = django_filters.OrderingFilter(
         fields=(
-            ("sentence__pmid", "pmid"),
+            ("id", "id"),
             ("modified_date", "last_edited"),
         ),
     )

frontend/src/apiclient/backend/.openapi-generator/VERSION

@@ -1 +1 @@
-6.2.1
+6.3.0

frontend/src/apiclient/backend/base.ts

@@ -13,10 +13,11 @@
  */
 
 
-import { Configuration } from "./configuration";
+import type { Configuration } from './configuration';
 // Some imports not used depending on template conditions
 // @ts-ignore
-import globalAxios, { AxiosPromise, AxiosInstance, AxiosRequestConfig } from 'axios';
+import type { AxiosPromise, AxiosInstance, AxiosRequestConfig } from 'axios';
+import globalAxios from 'axios';
 
 export const BASE_PATH = "http://localhost".replace(/\/+$/, "");
 
@@ -64,8 +65,8 @@ export class BaseAPI {
  * @extends {Error}
  */
 export class RequiredError extends Error {
-    name: "RequiredError" = "RequiredError";
     constructor(public field: string, msg?: string) {
         super(msg);
+        this.name = "RequiredError"
     }
 }

frontend/src/apiclient/backend/common.ts

@@ -13,9 +13,10 @@
  */
 
 
-import { Configuration } from "./configuration";
-import { RequiredError, RequestArgs } from "./base";
-import { AxiosInstance, AxiosResponse } from 'axios';
+import type { Configuration } from "./configuration";
+import type { RequestArgs } from "./base";
+import type { AxiosInstance, AxiosResponse } from 'axios';
+import { RequiredError } from "./base";
 
 /**
  *
@@ -84,6 +85,7 @@ export const setOAuthToObject = async function (object: any, name: string, scope
 }
 
 function setFlattenedQueryParams(urlSearchParams: URLSearchParams, parameter: any, key: string = ""): void {
+    if (parameter == null) return;
     if (typeof parameter === "object") {
         if (Array.isArray(parameter)) {
             (parameter as any[]).forEach(item => setFlattenedQueryParams(urlSearchParams, item, key));

frontend/src/components/CheckForDuplicates/CheckDuplicatesDialog.tsx

@@ -23,7 +23,7 @@ import AutoComplete from "../AutoComplete";
 
 
 type criteria =
-    | ("pmid" | "-pmid")[]
+    | ("id" | "-id")[]
     | undefined;
 
 export default function CheckDuplicates() {
@@ -71,10 +71,10 @@ export default function CheckDuplicates() {
         } else {
             const {field, sort} = model[0];
             const sortingCriteria = `${field} ${sort}`;
-            if (sortingCriteria === "pmid asc") {
-                ordering = ["pmid"];
-            } else if (sortingCriteria === "pmid desc") {
-                ordering = ["-pmid"];
+            if (sortingCriteria === "id asc") {
+                ordering = ["id"];
+            } else if (sortingCriteria === "id desc") {
+                ordering = ["-id"];
             }
         }
         fetchDuplicates(ordering);
@@ -103,7 +103,6 @@ export default function CheckDuplicates() {
             const {id, sentence, knowledge_statement, state} = statement;
             return {
                 id,
-                pmid: sentence.pmid,
                 knowledge_statement,
                 state,
             };

frontend/src/components/CheckForDuplicates/ResultsGrid.tsx

@@ -5,7 +5,7 @@ import Typography from "@mui/material/Typography";
 import { duplicatesRowsPerPage } from "../../helpers/settings";
 import CustomPagination from "../CustomPagination";
 import {
-  renderPMID,
+  renderID,
   renderStatementState,
   renderTitle,
 } from "../DataGridWidgets/DataGridWidgets";
@@ -19,10 +19,10 @@ export default function ResultsGrid({
 }: any) {
   const columns: GridColDef[] = [
     {
-      field: "pmid",
-      headerName: "PMID",
+      field: "id",
+      headerName: "ID",
       headerClassName: "grid--header",
-      renderCell: renderPMID,
+      renderCell: renderID,
     },
     {
       field: "state",

frontend/src/components/DataGridWidgets/DataGridWidgets.tsx

@@ -8,7 +8,7 @@ import Tag from "../Widgets/Tag"
 import {SentenceStateChip, StatementStateChip} from "../Widgets/StateChip"
 import { Tooltip } from "@mui/material"
 
-export const renderPMID = (params: GridRenderCellParams) => (
+export const renderID = (params: GridRenderCellParams) => (
   <Typography variant="subtitle1" color={vars.darkTextColor}>
     {params.value}
   </Typography>

frontend/src/components/EntityDataGrid.tsx

@@ -11,7 +11,7 @@ import { ConnectivityStatement, Sentence, Tag } from "../apiclient/backend";
 import {
   renderDate,
   renderNote,
-  renderPMID,
+  renderID,
   renderSentenceState,
   renderStatementState,
   renderTag,
@@ -41,7 +41,7 @@ interface DataGridProps {
 }
 
 type criteria =
-  | ("pmid" | "-pmid" | "last_edited" | "-last_edited")[]
+  | ("id" | "-id" | "last_edited" | "-last_edited")[]
   | undefined;
 
 const EntityDataGrid = (props: DataGridProps) => {
@@ -64,12 +64,12 @@ const EntityDataGrid = (props: DataGridProps) => {
       notes: has_notes,
     };
     if (entityType === "sentence") {
-      const { pmid, text } = item;
-      return { ...commonRowProps, pmid, text };
+      const { id, text } = item;
+      return { ...commonRowProps, id, text };
     }
     if (entityType === "statement") {
-      const { sentence, knowledge_statement } = item;
-      return { ...commonRowProps, pmid: sentence.pmid, knowledge_statement };
+      const {  id, knowledge_statement } = item;
+      return { ...commonRowProps, id: id, knowledge_statement };
     }
     return {};
   };
@@ -78,7 +78,7 @@ const EntityDataGrid = (props: DataGridProps) => {
     entityList?.map((item) => generateRowProps(item)) || [];
 
   const columns: GridColDef[] = [
-    { field: "pmid", headerName: "PMID", renderCell: renderPMID },
+    { field: "id", headerName: "ID", renderCell: renderID },
     {
       field: entityType === "sentence" ? "text" : "knowledge_statement",
       headerName:
@@ -145,10 +145,10 @@ const EntityDataGrid = (props: DataGridProps) => {
     } else {
       const { field, sort } = model[0];
       const sortingCriteria = `${field} ${sort}`;
-      if (sortingCriteria === "pmid asc") {
-        ordering = ["pmid"];
-      } else if (sortingCriteria === "pmid desc") {
-        ordering = ["-pmid"];
+      if (sortingCriteria === "id asc") {
+        ordering = ["id"];
+      } else if (sortingCriteria === "id desc") {
+        ordering = ["-id"];
       } else if (sortingCriteria === "last_edited asc") {
         ordering = ["last_edited"];
       } else if (sortingCriteria === "last_edited desc") {

frontend/src/redux/sentenceSlice.ts

@@ -6,7 +6,7 @@ export interface QueryParams {
   limit: number,
   notes: boolean | undefined,
   index: number | undefined,
-  ordering: Array<'-last_edited' | '-pmid' | 'last_edited' | 'pmid'> | undefined,
+  ordering: Array<'-last_edited' | '-id' | 'last_edited' | 'id'> | undefined,
   stateFilter: StateFilter | undefined,
   tagFilter: number[] | undefined,
   title: string | undefined

frontend/src/redux/statementSlice.tsx

@@ -19,7 +19,7 @@ export interface QueryParams {
   notes: boolean | undefined;
   index: number | undefined;
   ordering:
-    | Array<"-last_edited" | "-pmid" | "last_edited" | "pmid">
+    | Array<"-last_edited" | "-id" | "last_edited" | "id">
     | undefined;
   stateFilter: StateFilter | undefined;
   tagFilter: number[] | undefined;

openapi/openapi.yaml

@@ -101,10 +101,10 @@ paths:
           items:
             type: string
             enum:
+            - -id
             - -last_edited
-            - -pmid
+            - id
             - last_edited
-            - pmid
         description: Ordering
         explode: false
         style: form
@@ -893,10 +893,10 @@ paths:
           items:
             type: string
             enum:
+            - -id
             - -last_edited
-            - -pmid
+            - id
             - last_edited
-            - pmid
         description: Ordering
         explode: false
         style: form