Basic Name Search API Endpoint

backend/src/server.py

@@ -35,6 +35,30 @@ def get_all_entries():
  log.error(e)
 
 
+@app.get("/search-entries/{query:str}", response_model=list[ProteinEntry] | None)
+def search_entries(query: str):
+ """Gets a list of protein entries by a search string
+ Returns: list[ProteinEntry] if found | None if not found
+ """
+ with Database() as db:
+ try:
+ entries_sql = db.execute_return(
+ """SELECT name, length, mass FROM proteins
+ WHERE name ILIKE \'%{}%\'""".format(query)
+ )
+ log.warn("log test")
+ log.warn(entries_sql)
+
+ # if we got a result back
+ if entries_sql is not None:
+ return [
+ ProteinEntry(name=name, length=length, mass=mass)
+ for name, length, mass in entries_sql
+ ]
+ except Exception as e:
+ log.error(e)
+
+
 @app.get("/protein-entry/{protein_name:str}", response_model=ProteinEntry | None)
 def get_protein_entry(protein_name: str):
  """Get a single protein entry by its id

frontend/src/openapi/models/EditBody.ts

@@ -8,4 +8,3 @@ export type EditBody = {
  newName: string;
  newContent?: (string | null);
 };
-

frontend/src/openapi/models/HTTPValidationError.ts

@@ -8,4 +8,3 @@ import type { ValidationError } from './ValidationError';
 export type HTTPValidationError = {
  detail?: Array<ValidationError>;
 };
-

frontend/src/openapi/models/ProteinEntry.ts

@@ -9,4 +9,3 @@ export type ProteinEntry = {
  mass: number;
  content?: (string | null);
 };
-

frontend/src/openapi/models/UploadBody.ts

@@ -8,4 +8,3 @@ export type UploadBody = {
  content: string;
  pdbFileBase64: string;
 };
-

frontend/src/openapi/models/ValidationError.ts

@@ -8,4 +8,3 @@ export type ValidationError = {
  msg: string;
  type: string;
 };
-

frontend/src/openapi/services/DefaultService.ts

@@ -16,7 +16,7 @@ export class DefaultService {
  /**
  * Get All Entries
  * Gets all protein entries from the database
-  * Returns: list[ProteinEntry] if found | None if not found
+ * Returns: list[ProteinEntry] if found | None if not found
  * @returns any Successful Response
  * @throws ApiError
  */
@@ -27,17 +27,40 @@ export class DefaultService {
  });
  }
 
+ /**
+ * Search Entries
+ * Gets a list of protein entries by a search string
+ * Returns: list[ProteinEntry] if found | None if not found
+ * @param query 
+ * @returns any Successful Response
+ * @throws ApiError
+ */
+ public static searchEntries(
+query: string,
+): CancelablePromise<(Array<ProteinEntry> | null)> {
+ return __request(OpenAPI, {
+ method: 'GET',
+ url: '/search-entries/{query}',
+ path: {
+ 'query': query,
+ },
+ errors: {
+ 422: `Validation Error`,
+ },
+ });
+ }
+
  /**
  * Get Protein Entry
  * Get a single protein entry by its id
-  * Returns: ProteinEntry if found | None if not found
- * @param proteinName
+ * Returns: ProteinEntry if found | None if not found
+ * @param proteinName 
  * @returns any Successful Response
  * @throws ApiError
  */
  public static getProteinEntry(
- proteinName: string,
- ): CancelablePromise<(ProteinEntry | null)> {
+proteinName: string,
+): CancelablePromise<(ProteinEntry | null)> {
  return __request(OpenAPI, {
  method: 'GET',
  url: '/protein-entry/{protein_name}',
@@ -52,13 +75,13 @@ export class DefaultService {
 
  /**
  * Delete Protein Entry
- * @param proteinName
+ * @param proteinName 
  * @returns any Successful Response
  * @throws ApiError
  */
  public static deleteProteinEntry(
- proteinName: string,
- ): CancelablePromise<any> {
+proteinName: string,
+): CancelablePromise<any> {
  return __request(OpenAPI, {
  method: 'DELETE',
  url: '/protein-entry/{protein_name}',
@@ -73,13 +96,13 @@ export class DefaultService {
 
  /**
  * Upload Protein Entry
- * @param requestBody
+ * @param requestBody 
  * @returns any Successful Response
  * @throws ApiError
  */
  public static uploadProteinEntry(
- requestBody: UploadBody,
- ): CancelablePromise<(UploadError | null)> {
+requestBody: UploadBody,
+): CancelablePromise<(UploadError | null)> {
  return __request(OpenAPI, {
  method: 'POST',
  url: '/protein-upload',
@@ -93,13 +116,13 @@ export class DefaultService {
 
  /**
  * Edit Protein Entry
- * @param requestBody
+ * @param requestBody 
  * @returns any Successful Response
  * @throws ApiError
  */
  public static editProteinEntry(
- requestBody: EditBody,
- ): CancelablePromise<(UploadError | null)> {
+requestBody: EditBody,
+): CancelablePromise<(UploadError | null)> {
  return __request(OpenAPI, {
  method: 'PUT',
  url: '/protein-edit',

frontend/src/routes/searchtest/[query]/+page.svelte

@@ -0,0 +1,101 @@
+<!--THIS IS ONLY A TEST FILE, IT OUGHT TO BE DELETED!!!-->
+<script lang="ts">
+ import { onMount } from "svelte";
+ import { goto } from "$app/navigation";
+ import { Backend } from "$lib/backend";
+ import type { ProteinEntry } from "$lib/backend";
+ import { humanReadableProteinName, numberWithCommas } from "$lib/format";
+ import {
+ Table,
+ TableBody,
+ TableBodyCell,
+ TableBodyRow,
+ TableHead,
+ TableHeadCell,
+ } from "flowbite-svelte";
+ import { Tabs, TabItem } from "flowbite-svelte";
+ import { Card, Button, Toggle } from "flowbite-svelte";
+
+ export let data;
+ // at some point, this should be change to request from the backend
+ let allEntries: ProteinEntry[] | null = null;
+ onMount(async () => {
+ console.log("Requesting", data.query, "info from backend");
+ // calls get_all_entries() from backend
+ // to generate this Backend object run `./run.sh gen_api` for newly created server functions
+ allEntries = await Backend.searchEntries(data.query);
+ console.log(allEntries);
+ });
+</script>
+
+<!-- akin to <head /> in html -->
+<svelte:head>
+ <title>Home</title>
+</svelte:head>
+
+<section>
+ <Tabs style="underline" contentClass="bg-none p-5">
+ <TabItem open title="Table">
+ <Table>
+ <TableHead>
+ <TableHeadCell>Protein name</TableHeadCell>
+ <TableHeadCell>Length</TableHeadCell>
+ <TableHeadCell>Mass (Da)</TableHeadCell>
+ </TableHead>
+ <TableBody tableBodyClass="divide-y">
+ {#if allEntries}
+ {#each allEntries as entry}
+ <TableBodyRow
+ class="cursor-pointer hover:bg-gray-100"
+ on:click={() => {
+ goto(`/protein/${entry.name}`);
+ }}
+ >
+ <TableBodyCell
+ ><span class="text-primary-700"
+ >{humanReadableProteinName(entry.name)}</span
+ ></TableBodyCell
+ >
+ <TableBodyCell>{entry.length}</TableBodyCell>
+ <TableBodyCell>{numberWithCommas(entry.mass)}</TableBodyCell>
+ </TableBodyRow>
+ {/each}
+ {/if}
+ </TableBody>
+ </Table>
+ </TabItem>
+ <TabItem title="Gallery">
+ <div class="entries">
+ {#if allEntries}
+ {#each allEntries as entry}
+ <Card
+ class="hover:shadow-lg cursor-pointer"
+ title="Click to see {entry.name}"
+ on:click={() => goto(`/protein/${entry.name}`)}
+ >
+ <div class="name text-primary-700">
+ {humanReadableProteinName(entry.name)}
+ </div>
+ <div class="description">
+ Length: {entry.length}, Mass (Da): {numberWithCommas(
+ entry.mass
+ )}
+ </div>
+ </Card>
+ {/each}
+ {/if}
+ </div>
+ </TabItem>
+ </Tabs>
+</section>
+
+<style>
+ .entries {
+ display: flex;
+ flex-wrap: wrap;
+ gap: 20px;
+ }
+ .name {
+ font-size: 1.5em;
+ }
+</style>

frontend/src/routes/searchtest/[query]/+page.ts

@@ -0,0 +1,7 @@
+/**
+ * This scrapes the data from the route
+ * ie. /protein/your_mom -> { proteinName: "your_mom" }
+ */
+export function load({ params }) {
+ return { query: params.query };
+}