From e873b902ad5a137053d9d590e3cd15ca45bcefd9 Mon Sep 17 00:00:00 2001
From: ansengarvin <45224464+ansengarvin@users.noreply.github.com>
Date: Tue, 28 Nov 2023 15:22:43 -0800
Subject: [PATCH 1/2] feat: protein basic name search endpoint

---
 backend/src/server.py | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/backend/src/server.py b/backend/src/server.py
index fc74b0b2..f6415f39 100644
--- a/backend/src/server.py
+++ b/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 LIKE %%%s%""",
+                [query]
+            )
+            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

From 12f6ed626930ad9733a010f1d87940e6a140b86d Mon Sep 17 00:00:00 2001
From: ansengarvin <45224464+ansengarvin@users.noreply.github.com>
Date: Tue, 28 Nov 2023 16:19:24 -0800
Subject: [PATCH 2/2] Fixed endpoint for search functionality. Created test
 page at /searchtest/[query] to test search.

---
 backend/src/server.py                         |   4 +-
 frontend/src/openapi/models/EditBody.ts       |   1 -
 .../src/openapi/models/HTTPValidationError.ts |   1 -
 frontend/src/openapi/models/ProteinEntry.ts   |   1 -
 frontend/src/openapi/models/UploadBody.ts     |   1 -
 .../src/openapi/models/ValidationError.ts     |   1 -
 .../src/openapi/services/DefaultService.ts    |  51 ++++++---
 .../routes/searchtest/[query]/+page.svelte    | 101 ++++++++++++++++++
 .../src/routes/searchtest/[query]/+page.ts    |   7 ++
 9 files changed, 147 insertions(+), 21 deletions(-)
 create mode 100644 frontend/src/routes/searchtest/[query]/+page.svelte
 create mode 100644 frontend/src/routes/searchtest/[query]/+page.ts

diff --git a/backend/src/server.py b/backend/src/server.py
index f6415f39..684a75d8 100644
--- a/backend/src/server.py
+++ b/backend/src/server.py
@@ -44,9 +44,9 @@ def search_entries(query: str):
         try:
             entries_sql = db.execute_return(
                 """SELECT name, length, mass FROM proteins
-                WHERE name LIKE %%%s%""",
-                [query]
+                WHERE name ILIKE \'%{}%\'""".format(query)
             )
+            log.warn("log test")
             log.warn(entries_sql)
 
             # if we got a result back
diff --git a/frontend/src/openapi/models/EditBody.ts b/frontend/src/openapi/models/EditBody.ts
index 0c7f5aac..aa1acdab 100644
--- a/frontend/src/openapi/models/EditBody.ts
+++ b/frontend/src/openapi/models/EditBody.ts
@@ -8,4 +8,3 @@ export type EditBody = {
     newName: string;
     newContent?: (string | null);
 };
-
diff --git a/frontend/src/openapi/models/HTTPValidationError.ts b/frontend/src/openapi/models/HTTPValidationError.ts
index c0bcc87c..e218a9f3 100644
--- a/frontend/src/openapi/models/HTTPValidationError.ts
+++ b/frontend/src/openapi/models/HTTPValidationError.ts
@@ -8,4 +8,3 @@ import type { ValidationError } from './ValidationError';
 export type HTTPValidationError = {
     detail?: Array<ValidationError>;
 };
-
diff --git a/frontend/src/openapi/models/ProteinEntry.ts b/frontend/src/openapi/models/ProteinEntry.ts
index 6f42077b..0e5a3142 100644
--- a/frontend/src/openapi/models/ProteinEntry.ts
+++ b/frontend/src/openapi/models/ProteinEntry.ts
@@ -9,4 +9,3 @@ export type ProteinEntry = {
     mass: number;
     content?: (string | null);
 };
-
diff --git a/frontend/src/openapi/models/UploadBody.ts b/frontend/src/openapi/models/UploadBody.ts
index 1ec03121..43f1d50c 100644
--- a/frontend/src/openapi/models/UploadBody.ts
+++ b/frontend/src/openapi/models/UploadBody.ts
@@ -8,4 +8,3 @@ export type UploadBody = {
     content: string;
     pdbFileBase64: string;
 };
-
diff --git a/frontend/src/openapi/models/ValidationError.ts b/frontend/src/openapi/models/ValidationError.ts
index 18997ec7..0a3e90e9 100644
--- a/frontend/src/openapi/models/ValidationError.ts
+++ b/frontend/src/openapi/models/ValidationError.ts
@@ -8,4 +8,3 @@ export type ValidationError = {
     msg: string;
     type: string;
 };
-
diff --git a/frontend/src/openapi/services/DefaultService.ts b/frontend/src/openapi/services/DefaultService.ts
index 3d0cf8bf..b2f66a1a 100644
--- a/frontend/src/openapi/services/DefaultService.ts
+++ b/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',
diff --git a/frontend/src/routes/searchtest/[query]/+page.svelte b/frontend/src/routes/searchtest/[query]/+page.svelte
new file mode 100644
index 00000000..6f9a1623
--- /dev/null
+++ b/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>
diff --git a/frontend/src/routes/searchtest/[query]/+page.ts b/frontend/src/routes/searchtest/[query]/+page.ts
new file mode 100644
index 00000000..1764b7d5
--- /dev/null
+++ b/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 };
+}