XspecT 0.4.0__py3-none-any.whl → 0.5.0__py3-none-any.whl

xspect/xspect-web/public/vite.svg

@@ -0,0 +1 @@
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xspect/xspect-web/src/App.tsx

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+import Header from "@/components/header"
+import Landing from "@/components/landing";
+import Classify from "@/components/classify"
+import Filter from "@/components/filter"
+import Models from "@/components/models"
+import Result from "@/components/result"
+import { BrowserRouter as Router, Routes, Route } from "react-router-dom"
+import ModelDetails from "./components/models-details";
+
+
+function App() {
+  return (
+    <Router basename="/xspect-web">
+      <div className="min-h-screen flex flex-col">
+      <Header />
+        <Routes>
+          <Route path="/classify" element={<Classify />} />
+          <Route path="/filter" element={<Filter />} />
+          <Route path="/models" element={<Models />} />
+          <Route path="/models/:model_slug" element={<ModelDetails />} />
+          <Route path="/result/:classification_uuid" element={<Result />} />
+          <Route path="*" element={<Landing />} />
+        </Routes>
+      </div>
+    </Router>
+  )
+}
+
+export default App

xspect/xspect-web/src/api.tsx

@@ -0,0 +1,62 @@
+import axios from 'axios';
+import { Models, ClassificationResult, ModelMetadata } from '@/types';
+
+export async function getModels(): Promise<Models> {
+    try {
+        const response = await axios.get('/api/list-models');
+        return response.data as Models;
+    } catch (error) {
+        console.error('Error fetching models:', error);
+        throw new Error('Failed to fetch models');
+    }
+}
+
+export async function uploadFile(file: File): Promise<{ filename: string }> {
+    try {
+        const formData = new FormData();
+        formData.append('file', file);
+        const response = await axios.post('/api/upload-file', formData, {
+            headers: {
+                'Content-Type': 'multipart/form-data',
+            },
+        });
+        return response.data as { filename: string };
+    } catch (error) {
+        console.error('Error uploading file:', error);
+        throw new Error('Failed to upload file');
+    }
+}
+
+export async function classify(filename: string, classification_type: string, model: string, step: number): Promise<any> {
+    try {
+        const response = await axios.post(`/api/classify?classification_type=${classification_type}&model=${model}&file=${filename}&step=${step}`);
+        return response.data;
+    } catch (error) {
+        console.error('Error classifying file:', error);
+        throw new Error('Failed to classify file');
+    }
+}
+
+export async function getClassificationResult(classification_uuid: string): Promise<ClassificationResult> {
+    try {
+        const response = await axios.get(`/api/classification-result`, {
+            params: { uuid: classification_uuid },
+        });
+        return response.data as ClassificationResult;
+    } catch (error) {
+        console.error('Error fetching classification result:', error);
+        throw new Error('Failed to fetch classification result');
+    }
+}
+
+export async function getModelMetadata(modelSlug: string): Promise<ModelMetadata> {
+    try {
+        const response = await axios.get(`/api/model-metadata`, {
+            params: { model_slug: modelSlug },
+        });
+        return response.data as ModelMetadata;
+    } catch (error) {
+        console.error('Error fetching model metadata:', error);
+        throw new Error('Failed to fetch model metadata');
+    }
+}

xspect/xspect-web/src/assets/react.svg

@@ -0,0 +1 @@
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xspect/xspect-web/src/components/classification-form.tsx

@@ -0,0 +1,284 @@
+import { zodResolver } from "@hookform/resolvers/zod"
+import { useForm } from "react-hook-form"
+import { z } from "zod"
+import { Button } from "@/components/ui/button"
+import { Switch } from "@/components/ui/switch"
+import { Input } from "@/components/ui/input"
+import {
+    Form,
+    FormControl,
+    FormDescription,
+    FormField,
+    FormItem,
+    FormLabel,
+    FormMessage,
+} from "@/components/ui/form"
+import {
+    Select,
+    SelectContent,
+    SelectItem,
+    SelectTrigger,
+    SelectValue,
+} from "@/components/ui/select"
+import { classify, getModels, uploadFile } from "../api"
+import {
+    FileUpload,
+    FileUploadDropzone,
+    FileUploadItem,
+    FileUploadItemDelete,
+    FileUploadItemMetadata,
+    FileUploadItemPreview,
+    FileUploadItemProgress,
+    FileUploadList,
+    FileUploadTrigger,
+} from "@/components/ui/file-upload";
+import { Upload, X } from "lucide-react";
+import { useState, useCallback, useEffect } from "react"
+import { useNavigate } from "react-router-dom"
+
+const FormSchema = z.object({
+    input_file: z.string().min(1, "Please upload a file"),
+    classification_type: z.enum([
+        "Genus",
+        "Species",
+        "MLST",
+    ]),
+    model: z.string(),
+    sparse_sampling: z.boolean(),
+    sparse_sampling_step: z.number().min(1).max(500)
+});
+
+export default function ClassificationForm() {
+
+    const [models, setModels] = useState<Record<string, string[]>>({});
+
+    useEffect(() => {
+        getModels()
+            .then((data) => {
+                setModels(data);
+            })
+            .catch((error) => {
+                console.error("Error fetching models:", error);
+            });
+    }, []);
+
+    const navigate = useNavigate()
+
+    const form = useForm<z.infer<typeof FormSchema>>({
+        resolver: zodResolver(FormSchema),
+        defaultValues: {
+            classification_type: "Species",
+            model: undefined,
+            sparse_sampling: false,
+            sparse_sampling_step: 1,
+        },
+    })
+    const [files, setFiles] = useState<File[]>([]);
+
+
+    const onUpload = useCallback(
+        async (
+            files: File[],
+            {
+                onSuccess,
+                onError,
+            }: {
+                onSuccess: (file: File) => void;
+                onError: (file: File, error: Error) => void;
+            },
+        ) => {
+            const file = files[0]
+            try {
+                const { filename } = await uploadFile(file)
+                onSuccess(file)
+                console.log("File uploaded successfully:", filename)
+                form.setValue("input_file", filename)
+            } catch (error) {
+                onError(file, error as Error)
+                console.error("Error uploading file:", error)
+            }
+        },
+        [form]
+    );
+
+    const onFileReject = useCallback((file: File, message: string) => {
+        console.log(message, {
+            description: `"${file.name.length > 20 ? `${file.name.slice(0, 20)}...` : file.name}" has been rejected`,
+        });
+    }, []);
+
+    function onSubmit(data: z.infer<typeof FormSchema>) {
+        classify(data.input_file, data.classification_type, data.model, data.sparse_sampling_step)
+            .then((response) => {
+                console.log("Classification response:", response)
+                navigate(`/result/${response.uuid}`)
+            })
+            .catch((error) => {
+                console.error("Error during classification:", error)
+            });
+    }
+
+    return (
+
+        <Form {...form}>
+            <form onSubmit={form.handleSubmit(onSubmit)} className="space-y-6">
+                <FormField
+                    control={form.control}
+                    name="input_file"
+                    render={({ field }) => (
+                        <FormItem>
+                            <FormLabel>Input File</FormLabel>
+                            <FormControl>
+                                <FileUpload
+                                    value={files}
+                                    onValueChange={setFiles}
+                                    onUpload={onUpload}
+                                    onFileReject={onFileReject}
+                                    maxFiles={1}
+                                    multiple
+                                >
+                                    {files.length === 0 && (
+                                        <FileUploadDropzone>
+                                            <div className="flex flex-col items-center gap-1 text-center">
+                                                <div className="flex items-center justify-center rounded-full border p-2.5">
+                                                    <Upload className="size-6 text-muted-foreground" />
+                                                </div>
+                                                <p className="font-medium text-sm">Drag & drop file here</p>
+                                                <p className="text-muted-foreground text-xs">
+                                                    Or click to browse
+                                                </p>
+                                            </div>
+                                            <FileUploadTrigger asChild>
+                                                <Button variant="outline" size="sm" className="mt-2 w-fit">
+                                                    Browse files
+                                                </Button>
+                                            </FileUploadTrigger>
+                                        </FileUploadDropzone>
+                                    )}
+                                    <FileUploadList>
+                                        {files.map((file, index) => (
+                                            <FileUploadItem key={index} value={file} className="flex-col">
+                                                <div className="flex w-full items-center gap-2">
+                                                    <FileUploadItemPreview />
+                                                    <FileUploadItemMetadata />
+                                                    <FileUploadItemDelete asChild>
+                                                        <Button variant="ghost" size="icon" className="size-7" onClick={() => {
+                                                            setFiles((prev) => prev.filter((_, i) => i !== index));
+                                                            form.setValue("input_file", "")
+                                                        }}>
+                                                            <X />
+                                                        </Button>
+                                                    </FileUploadItemDelete>
+                                                </div>
+                                                <FileUploadItemProgress />
+                                            </FileUploadItem>
+                                        ))}
+                                    </FileUploadList>
+                                </FileUpload>
+                            </FormControl>
+                            <FormDescription>
+                                Upload the file you would like to classify.
+                            </FormDescription>
+                            <FormMessage />
+                        </FormItem>
+                    )}
+                />
+                <FormField
+                    control={form.control}
+                    name="classification_type"
+                    render={({ field }) => (
+                        <FormItem>
+                            <FormLabel>Classification Type</FormLabel>
+                            <FormControl>
+                                <Select defaultValue="Species" onValueChange={(value) => field.onChange(value)}>
+                                    <SelectTrigger className="w-full">
+                                        <SelectValue />
+                                    </SelectTrigger>
+                                    <SelectContent>
+                                        <SelectItem value="Genus">Genus</SelectItem>
+                                        <SelectItem value="Species">Species</SelectItem>
+                                        <SelectItem value="MLST">MLST</SelectItem>
+                                    </SelectContent>
+                                </Select>
+                            </FormControl>
+                            <FormDescription>
+                                Select the type of classification you would like to perform.
+                            </FormDescription>
+                            <FormMessage />
+                        </FormItem>
+                    )}
+                />
+                <FormField
+                    control={form.control}
+                    name="model"
+                    render={({ field }) => (
+                        <FormItem>
+                            <FormLabel>Model</FormLabel>
+                            <FormControl>
+                                <Select onValueChange={field.onChange}>
+                                    <SelectTrigger className="w-full">
+                                        <SelectValue />
+                                    </SelectTrigger>
+                                    <SelectContent>
+                                        {models[form.watch("classification_type")]?.map((model: string) => (
+                                            <SelectItem key={model} value={model}>
+                                                {model}
+                                            </SelectItem>
+                                        ))}
+                                    </SelectContent>
+                                </Select>
+                            </FormControl>
+                            <FormDescription>
+                                Select the model you would like to use for classification.
+                            </FormDescription>
+                            <FormMessage />
+                        </FormItem>
+                    )}
+                />
+                <FormField
+                    control={form.control}
+                    name="sparse_sampling"
+                    render={({ field }) => (
+                        <FormItem className="flex flex-row items-center justify-between pr-2">
+                            <div className="space-y-0.5">
+                                <FormLabel>Sparse Sampling</FormLabel>
+                                <FormDescription>
+                                    Enable sparse sampling for classification.
+                                </FormDescription>
+                            </div>
+                            <FormControl>
+                                <Switch
+                                    checked={field.value}
+                                    onCheckedChange={field.onChange}
+                                />
+                            </FormControl>
+                        </FormItem>
+                    )}
+                />
+                {form.watch("sparse_sampling") && (
+                    <FormField
+                        control={form.control}
+                        name="sparse_sampling_step"
+                        render={({ field }) => (
+                            <FormItem>
+                                <FormLabel>Sparse Sampling Step</FormLabel>
+                                <FormControl>
+                                    <Input
+                                        type="number"
+                                        value={field.value}
+                                        onChange={(e) => field.onChange(Number(e.target.value))}
+                                    />
+                                </FormControl>
+                                <FormDescription>
+                                    Set the step size for sparse sampling.
+                                </FormDescription>
+                                <FormMessage />
+                            </FormItem>
+                        )}
+                    />
+                )}
+                <Button type="submit">Classify</Button>
+            </form>
+        </Form>
+    )
+}

xspect/xspect-web/src/components/classify.tsx

@@ -0,0 +1,18 @@
+import ClassificationForm from "./classification-form";
+import { Separator } from "@/components/ui/separator"
+
+
+
+export default function Classify() {
+
+    return (
+        <main className="flex-1 flex flex-col items-center justify-center p-4">
+            <div className="w-1/2">
+                <h1 className="text-xl font-bold">Classify your data</h1>
+                <p>Upload your data and select a model to classify it.</p>
+                <Separator className="my-4" />
+                <ClassificationForm />
+            </div>
+        </main>
+    )
+}

xspect/xspect-web/src/components/data-table.tsx

@@ -0,0 +1,78 @@
+import {
+  ColumnDef,
+  flexRender,
+  getCoreRowModel,
+  useReactTable,
+} from "@tanstack/react-table"
+
+import {
+  Table,
+  TableBody,
+  TableCell,
+  TableHead,
+  TableHeader,
+  TableRow,
+} from "@/components/ui/table"
+
+interface DataTableProps<TData, TValue> {
+  columns: ColumnDef<TData, TValue>[]
+  data: TData[]
+}
+
+export function DataTable<TData, TValue>({
+  columns,
+  data,
+}: DataTableProps<TData, TValue>) {
+  const table = useReactTable({
+    data,
+    columns,
+    getCoreRowModel: getCoreRowModel(),
+  })
+
+  return (
+    <div className="rounded-md border">
+      <Table>
+        <TableHeader>
+          {table.getHeaderGroups().map((headerGroup) => (
+            <TableRow key={headerGroup.id}>
+              {headerGroup.headers.map((header) => {
+                return (
+                  <TableHead key={header.id}>
+                    {header.isPlaceholder
+                      ? null
+                      : flexRender(
+                          header.column.columnDef.header,
+                          header.getContext()
+                        )}
+                  </TableHead>
+                )
+              })}
+            </TableRow>
+          ))}
+        </TableHeader>
+        <TableBody>
+          {table.getRowModel().rows?.length ? (
+            table.getRowModel().rows.map((row) => (
+              <TableRow
+                key={row.id}
+                data-state={row.getIsSelected() && "selected"}
+              >
+                {row.getVisibleCells().map((cell) => (
+                  <TableCell key={cell.id}>
+                    {flexRender(cell.column.columnDef.cell, cell.getContext())}
+                  </TableCell>
+                ))}
+              </TableRow>
+            ))
+          ) : (
+            <TableRow>
+              <TableCell colSpan={columns.length} className="h-24 text-center">
+                No results.
+              </TableCell>
+            </TableRow>
+          )}
+        </TableBody>
+      </Table>
+    </div>
+  )
+}

xspect/xspect-web/src/components/dropdown-checkboxes.tsx

@@ -0,0 +1,63 @@
+"use client"
+import { DropdownMenuCheckboxItemProps } from "@radix-ui/react-dropdown-menu"
+
+import { Button } from "@/components/ui/button"
+import {
+  DropdownMenu,
+  DropdownMenuCheckboxItem,
+  DropdownMenuContent,
+  DropdownMenuLabel,
+  DropdownMenuSeparator,
+  DropdownMenuTrigger,
+} from "@/components/ui/dropdown-menu"
+import { ChevronDown } from "lucide-react"
+
+type Checked = DropdownMenuCheckboxItemProps["checked"]
+
+interface DropdownCheckboxItem {
+  id: string;
+  label: string;
+  checked: Checked;
+  onCheckedChange: (checked: Checked) => void;
+  disabled?: boolean;
+}
+
+interface DropdownMenuCheckboxesProps {
+  triggerButtonText?: string;
+  labelText?: string;
+  items: DropdownCheckboxItem[];
+  disabled?: boolean;
+}
+
+export function DropdownMenuCheckboxes({
+  triggerButtonText,
+  labelText,
+  items,
+  disabled = false,
+}: DropdownMenuCheckboxesProps) {
+  return (
+    <DropdownMenu>
+      <DropdownMenuTrigger asChild>
+        <Button variant="ghost" disabled={disabled}>{triggerButtonText}<ChevronDown /></Button>
+      </DropdownMenuTrigger>
+      <DropdownMenuContent className="w-56">
+        {labelText && (
+          <>
+            <DropdownMenuLabel>{labelText}</DropdownMenuLabel>
+            <DropdownMenuSeparator />
+          </>
+        )}
+        {items.map((item) => (
+          <DropdownMenuCheckboxItem
+            key={item.id}
+            checked={item.checked}
+            onCheckedChange={item.onCheckedChange}
+            disabled={item.disabled}
+          >
+            {item.label}
+          </DropdownMenuCheckboxItem>
+        ))}
+      </DropdownMenuContent>
+    </DropdownMenu>
+  )
+}

xspect/xspect-web/src/components/dropdown-slider.tsx

@@ -0,0 +1,42 @@
+"use client"
+
+import * as React from "react"
+import { DropdownMenuCheckboxItemProps } from "@radix-ui/react-dropdown-menu"
+
+import { Button } from "@/components/ui/button"
+import {
+  DropdownMenu,
+  DropdownMenuContent,
+  DropdownMenuTrigger,
+} from "@/components/ui/dropdown-menu"
+import { Slider } from "@/components/ui/slider"
+import { ChevronDown } from "lucide-react"
+
+
+interface DropdownMenuSlider {
+  triggerButtonText?: string;
+  value: number;
+  max?: number;
+  step?: number;
+  disabled?: boolean;
+}
+
+export function DropdownMenuSlider({
+  triggerButtonText,
+  value,
+  onValueChange,
+  max,
+  step,
+  disabled = false,
+}: DropdownMenuSlider) {
+  return (
+    <DropdownMenu>
+      <DropdownMenuTrigger asChild>
+        <Button variant="ghost" disabled={disabled}>{triggerButtonText}<ChevronDown /></Button>
+      </DropdownMenuTrigger>
+      <DropdownMenuContent className="w-56">
+        <Slider value={[value]} onValueChange={onValueChange} max={max} step={step} className="my-3" />
+      </DropdownMenuContent>
+    </DropdownMenu>
+  )
+}