Make backend dev server script serve the image files

Previously, image files in backend/data/img were moved to, or
symlinked from, public/. This needed to be changed before each
build, otherwise vite would end up copying gigabytes of images.

4 files changed, 390 insertions, 0 deletions

diff --git a/backend/tolData/eol/README.md b/backend/tolData/eol/README.md
new file mode 100644
index 0000000..8c527a8
--- /dev/null
+++ b/backend/tolData/eol/README.md
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+This directory holds files obtained from/using the [Encyclopedia of Life](https://eol.org/).
+
+# Name Data Files
+-   vernacularNames.csv <br>
+    Obtained from <https://opendata.eol.org/dataset/vernacular-names> on 24/04/2022 (last updated on 27/10/2020).
+    Contains alternative-name data from EOL.
+
+# Image Metadata Files
+-   imagesList.tgz <br>
+    Obtained from <https://opendata.eol.org/dataset/images-list> on 24/04/2022 (last updated on 05/02/2020).
+    Contains metadata for images from EOL.
+-   imagesList/ <br>
+    Extracted from imagesList.tgz.
+-   genImagesListDb.sh <br>
+    Creates a database, and imports imagesList/*.csv files into it.
+-   imagesList.db <br>
+    Created by running genImagesListDb.sh <br>
+    Tables: <br>
+    -   `images`:
+        `content_id INT PRIMARY KEY, page_id INT, source_url TEXT, copy_url TEXT, license TEXT, copyright_owner TEXT`
+
+# Image Generation Files
+-   downloadImgs.py <br>
+    Used to download image files into imgsForReview/.
+-   reviewImgs.py <br>
+    Used to review images in imgsForReview/, moving acceptable ones into imgs/.
diff --git a/backend/tolData/eol/downloadImgs.py b/backend/tolData/eol/downloadImgs.py
new file mode 100755
index 0000000..96bc085
--- /dev/null
+++ b/backend/tolData/eol/downloadImgs.py
@@ -0,0 +1,147 @@
+#!/usr/bin/python3
+
+import sys, re, os, random
+import sqlite3
+import urllib.parse, requests
+import time
+from threading import Thread
+import signal
+
+usageInfo = f"""
+Usage: {sys.argv[0]}
+
+For some set of EOL IDs, downloads associated images from URLs in
+an image-list database. Uses multiple downloading threads.
+
+May obtain multiple images per ID. The images will get names
+with the form 'eolId1 contentId1.ext1'.
+
+SIGINT causes the program to finish ongoing downloads and exit.
+The program can be re-run to continue downloading. It looks for
+already-downloaded files, and continues after the one with
+highest EOL ID.
+"""
+if len(sys.argv) > 1:
+	print(usageInfo, file=sys.stderr)
+	sys.exit(1)
+# In testing, this downloaded about 70k images, over a few days
+
+imagesListDb = "imagesList.db"
+def getInputEolIds():
+	eolIds = set()
+	dbCon = sqlite3.connect("../data.db")
+	dbCur = dbCon.cursor()
+	for (id,) in dbCur.execute("SELECT id FROM eol_ids"):
+		eolIds.add(id)
+	dbCon.close()
+	return eolIds
+outDir = "imgsForReview/"
+MAX_IMGS_PER_ID = 3
+MAX_THREADS = 5
+POST_DL_DELAY_MIN = 2 # Minimum delay in seconds to pause after download before starting another (for each thread)
+POST_DL_DELAY_MAX = 3
+LICENSE_REGEX = r"cc-by((-nc)?(-sa)?(-[234]\.[05])?)|cc-publicdomain|cc-0-1\.0|public domain"
+
+print("Getting input EOL IDs")
+eolIds = getInputEolIds()
+print("Getting EOL IDs to download for")
+# Get IDs from images-list db
+imgDbCon = sqlite3.connect(imagesListDb)
+imgCur = imgDbCon.cursor()
+imgListIds = set()
+for (pageId,) in imgCur.execute("SELECT DISTINCT page_id FROM images"):
+	imgListIds.add(pageId)
+# Get set intersection, and sort into list
+eolIds = eolIds.intersection(imgListIds)
+eolIds = sorted(eolIds)
+print(f"Result: {len(eolIds)} EOL IDs")
+
+print("Checking output directory")
+if not os.path.exists(outDir):
+	os.mkdir(outDir)
+print("Finding next ID to download for")
+nextIdx = 0
+fileList = os.listdir(outDir)
+ids = [int(filename.split(" ")[0]) for filename in fileList]
+if len(ids) > 0:
+	ids.sort()
+	nextIdx = eolIds.index(ids[-1]) + 1
+if nextIdx == len(eolIds):
+	print("No IDs left. Exiting...")
+	sys.exit(0)
+
+print("Starting download threads")
+numThreads = 0
+threadException = None # Used for ending main thread after a non-main thread exception
+# Handle SIGINT signals
+interrupted = False
+oldHandler = None
+def onSigint(sig, frame):
+	global interrupted
+	interrupted = True
+	signal.signal(signal.SIGINT, oldHandler)
+oldHandler = signal.signal(signal.SIGINT, onSigint)
+# Function for threads to execute
+def downloadImg(url, outFile):
+	global numThreads, threadException
+	try:
+		data = requests.get(url)
+		with open(outFile, 'wb') as file:
+			file.write(data.content)
+		time.sleep(random.random() * (POST_DL_DELAY_MAX - POST_DL_DELAY_MIN) + POST_DL_DELAY_MIN)
+	except Exception as e:
+		print(f"Error while downloading to {outFile}: {str(e)}", file=sys.stderr)
+		threadException = e
+	numThreads -= 1
+# Manage downloading
+for idx in range(nextIdx, len(eolIds)):
+	eolId = eolIds[idx]
+	# Get image urls
+	imgDataList = []
+	ownerSet = set() # Used to get images from different owners, for variety
+	exitLoop = False
+	query = "SELECT content_id, copy_url, license, copyright_owner FROM images WHERE page_id = ?"
+	for (contentId, url, license, copyrightOwner) in imgCur.execute(query, (eolId,)):
+		if url.startswith("data/"):
+			url = "https://content.eol.org/" + url
+		urlParts = urllib.parse.urlparse(url)
+		extension = os.path.splitext(urlParts.path)[1]
+		if len(extension) <= 1:
+			print(f"WARNING: No filename extension found in URL {url}", file=sys.stderr)
+			continue
+		# Check image-quantity limit
+		if len(ownerSet) == MAX_IMGS_PER_ID:
+			break
+		# Check for skip conditions
+		if re.fullmatch(LICENSE_REGEX, license) == None:
+			continue
+		if len(copyrightOwner) > 100: # Avoid certain copyrightOwner fields that seem long and problematic
+			continue
+		if copyrightOwner in ownerSet:
+			continue
+		ownerSet.add(copyrightOwner)
+		# Determine output filename
+		outPath = f"{outDir}{eolId} {contentId}{extension}"
+		if os.path.exists(outPath):
+			print(f"WARNING: {outPath} already exists. Skipping download.")
+			continue
+		# Check thread limit
+		while numThreads == MAX_THREADS:
+			time.sleep(1)
+		# Wait for threads after an interrupt or thread-exception
+		if interrupted or threadException != None:
+			print("Waiting for existing threads to end")
+			while numThreads > 0:
+				time.sleep(1)
+			exitLoop = True
+			break
+		# Perform download
+		print(f"Downloading image to {outPath}")
+		numThreads += 1
+		thread = Thread(target=downloadImg, args=(url, outPath), daemon=True)
+		thread.start()
+	if exitLoop:
+		break
+# Close images-list db
+print("Finished downloading")
+imgDbCon.close()
diff --git a/backend/tolData/eol/genImagesListDb.sh b/backend/tolData/eol/genImagesListDb.sh
new file mode 100755
index 0000000..87dd840
--- /dev/null
+++ b/backend/tolData/eol/genImagesListDb.sh
@@ -0,0 +1,12 @@
+#!/bin/bash
+set -e
+
+# Combine CSV files into one, skipping header lines
+cat imagesList/media_*_{1..58}.csv | tail -n +2 > imagesList.csv
+# Create database, and import the CSV file
+sqlite3 imagesList.db <<END
+CREATE TABLE images (
+	content_id INT PRIMARY KEY, page_id INT, source_url TEXT, copy_url TEXT, license TEXT, copyright_owner TEXT);
+.mode csv
+.import 'imagesList.csv' images
+END
diff --git a/backend/tolData/eol/reviewImgs.py b/backend/tolData/eol/reviewImgs.py
new file mode 100755
index 0000000..ecdf7ab
--- /dev/null
+++ b/backend/tolData/eol/reviewImgs.py
@@ -0,0 +1,205 @@
+#!/usr/bin/python3
+
+import sys, re, os, time
+import sqlite3
+import tkinter as tki
+from tkinter import ttk
+import PIL
+from PIL import ImageTk, Image, ImageOps
+
+usageInfo = f"""
+Usage: {sys.argv[0]}
+
+Provides a GUI for reviewing images. Looks in a for-review directory for
+images named 'eolId1 contentId1.ext1', and, for each EOL ID, enables the user to
+choose an image to keep, or reject all. Also provides image rotation.
+Chosen images are placed in another directory, and rejected ones are deleted.
+"""
+if len(sys.argv) > 1:
+	print(usageInfo, file=sys.stderr)
+	sys.exit(1)
+
+imgDir = "imgsForReview/"
+outDir = "imgs/"
+extraInfoDbCon = sqlite3.connect("../data.db")
+extraInfoDbCur = extraInfoDbCon.cursor()
+def getExtraInfo(eolId):
+	global extraInfoDbCur
+	query = "SELECT names.alt_name FROM" \
+		" names INNER JOIN eol_ids ON eol_ids.name = names.name" \
+		" WHERE id = ? and pref_alt = 1"
+	row = extraInfoDbCur.execute(query, (eolId,)).fetchone()
+	if row != None:
+		return f"Reviewing EOL ID {eolId}, aka \"{row[0]}\""
+	else:
+		return f"Reviewing EOL ID {eolId}"
+IMG_DISPLAY_SZ = 400
+MAX_IMGS_PER_ID = 3
+IMG_BG_COLOR = (88, 28, 135)
+PLACEHOLDER_IMG = Image.new("RGB", (IMG_DISPLAY_SZ, IMG_DISPLAY_SZ), IMG_BG_COLOR)
+
+print("Checking output directory")
+if not os.path.exists(outDir):
+	os.mkdir(outDir)
+print("Getting input image list")
+imgList = os.listdir(imgDir)
+imgList.sort(key=lambda s: int(s.split(" ")[0]))
+if len(imgList) == 0:
+	print("No input images found")
+	sys.exit(0)
+
+class EolImgReviewer:
+	" Provides the GUI for reviewing images "
+	def __init__(self, root, imgList):
+		self.root = root
+		root.title("EOL Image Reviewer")
+		# Setup main frame
+		mainFrame = ttk.Frame(root, padding="5 5 5 5")
+		mainFrame.grid(column=0, row=0, sticky=(tki.N, tki.W, tki.E, tki.S))
+		root.columnconfigure(0, weight=1)
+		root.rowconfigure(0, weight=1)
+		# Set up images-to-be-reviewed frames
+		self.imgs = [PLACEHOLDER_IMG] * MAX_IMGS_PER_ID # Stored as fields for use in rotation
+		self.photoImgs = list(map(lambda img: ImageTk.PhotoImage(img), self.imgs)) # Image objects usable by tkinter
+			# These need a persistent reference for some reason (doesn't display otherwise)
+		self.labels = []
+		for i in range(MAX_IMGS_PER_ID):
+			frame = ttk.Frame(mainFrame, width=IMG_DISPLAY_SZ, height=IMG_DISPLAY_SZ)
+			frame.grid(column=i, row=0)
+			label = ttk.Label(frame, image=self.photoImgs[i])
+			label.grid(column=0, row=0)
+			self.labels.append(label)
+		# Add padding
+		for child in mainFrame.winfo_children():
+			child.grid_configure(padx=5, pady=5)
+		# Add keyboard bindings
+		root.bind("<q>", self.quit)
+		root.bind("<Key-j>", lambda evt: self.accept(0))
+		root.bind("<Key-k>", lambda evt: self.accept(1))
+		root.bind("<Key-l>", lambda evt: self.accept(2))
+		root.bind("<Key-i>", lambda evt: self.reject())
+		root.bind("<Key-a>", lambda evt: self.rotate(0))
+		root.bind("<Key-s>", lambda evt: self.rotate(1))
+		root.bind("<Key-d>", lambda evt: self.rotate(2))
+		root.bind("<Key-A>", lambda evt: self.rotate(0, True))
+		root.bind("<Key-S>", lambda evt: self.rotate(1, True))
+		root.bind("<Key-D>", lambda evt: self.rotate(2, True))
+		# Initialise images to review
+		self.imgList = imgList
+		self.imgListIdx = 0
+		self.nextEolId = 0
+		self.nextImgNames = []
+		self.rotations = []
+		self.getNextImgs()
+		# For displaying extra info
+		self.numReviewed = 0
+		self.startTime = time.time()
+	def getNextImgs(self):
+		" Updates display with new images to review, or ends program "
+		# Gather names of next images to review
+		for i in range(MAX_IMGS_PER_ID):
+			if self.imgListIdx == len(self.imgList):
+				if i == 0:
+					self.quit()
+					return
+				break
+			imgName = self.imgList[self.imgListIdx]
+			eolId = int(re.match(r"(\d+) (\d+)", imgName).group(1))
+			if i == 0:
+				self.nextEolId = eolId
+				self.nextImgNames = [imgName]
+				self.rotations = [0]
+			else:
+				if self.nextEolId != eolId:
+					break
+				self.nextImgNames.append(imgName)
+				self.rotations.append(0)
+			self.imgListIdx += 1
+		# Update displayed images
+		idx = 0
+		while idx < MAX_IMGS_PER_ID:
+			if idx < len(self.nextImgNames):
+				try:
+					img = Image.open(imgDir + self.nextImgNames[idx])
+					img = ImageOps.exif_transpose(img)
+				except PIL.UnidentifiedImageError:
+					os.remove(imgDir + self.nextImgNames[idx])
+					del self.nextImgNames[idx]
+					del self.rotations[idx]
+					continue
+				self.imgs[idx] = self.resizeImgForDisplay(img)
+			else:
+				self.imgs[idx] = PLACEHOLDER_IMG
+			self.photoImgs[idx] = ImageTk.PhotoImage(self.imgs[idx])
+			self.labels[idx].config(image=self.photoImgs[idx])
+			idx += 1
+		# Restart if all image files non-recognisable
+		if len(self.nextImgNames) == 0:
+			self.getNextImgs()
+			return
+		# Update title
+		firstImgIdx = self.imgListIdx - len(self.nextImgNames) + 1
+		lastImgIdx = self.imgListIdx
+		title = getExtraInfo(self.nextEolId)
+		title += f" (imgs {firstImgIdx} to {lastImgIdx} out of {len(self.imgList)})"
+		self.root.title(title)
+	def accept(self, imgIdx):
+		" React to a user selecting an image "
+		if imgIdx >= len(self.nextImgNames):
+			print("Invalid selection")
+			return
+		for i in range(len(self.nextImgNames)):
+			inFile = imgDir + self.nextImgNames[i]
+			if i == imgIdx: # Move accepted image, rotating if needed
+				outFile = outDir + self.nextImgNames[i]
+				img = Image.open(inFile)
+				img = ImageOps.exif_transpose(img)
+				if self.rotations[i] != 0:
+					img = img.rotate(self.rotations[i], expand=True)
+				img.save(outFile)
+				os.remove(inFile)
+			else: # Delete non-accepted image
+				os.remove(inFile)
+		self.numReviewed += 1
+		self.getNextImgs()
+	def reject(self):
+		" React to a user rejecting all images of a set "
+		for i in range(len(self.nextImgNames)):
+			os.remove(imgDir + self.nextImgNames[i])
+		self.numReviewed += 1
+		self.getNextImgs()
+	def rotate(self, imgIdx, anticlockwise = False):
+		" Respond to a user rotating an image "
+		deg = -90 if not anticlockwise else 90
+		self.imgs[imgIdx] = self.imgs[imgIdx].rotate(deg)
+		self.photoImgs[imgIdx] = ImageTk.PhotoImage(self.imgs[imgIdx])
+		self.labels[imgIdx].config(image=self.photoImgs[imgIdx])
+		self.rotations[imgIdx] = (self.rotations[imgIdx] + deg) % 360
+	def quit(self, e = None):
+		global extraInfoDbCon
+		print(f"Number reviewed: {self.numReviewed}")
+		timeElapsed = time.time() - self.startTime
+		print(f"Time elapsed: {timeElapsed:.2f} seconds")
+		if self.numReviewed > 0:
+			print(f"Avg time per review: {timeElapsed/self.numReviewed:.2f} seconds")
+		extraInfoDbCon.close()
+		self.root.destroy()
+	def resizeImgForDisplay(self, img):
+		" Returns a copy of an image, shrunk to fit in it's frame (keeps aspect ratio), and with a background "
+		if max(img.width, img.height) > IMG_DISPLAY_SZ:
+			if (img.width > img.height):
+				newHeight = int(img.height * IMG_DISPLAY_SZ/img.width)
+				img = img.resize((IMG_DISPLAY_SZ, newHeight))
+			else:
+				newWidth = int(img.width * IMG_DISPLAY_SZ / img.height)
+				img = img.resize((newWidth, IMG_DISPLAY_SZ))
+		bgImg = PLACEHOLDER_IMG.copy()
+		bgImg.paste(img, box=(
+			int((IMG_DISPLAY_SZ - img.width) / 2),
+			int((IMG_DISPLAY_SZ - img.height) / 2)))
+		return bgImg
+# Create GUI and defer control
+print("Starting GUI")
+root = tki.Tk()
+EolImgReviewer(root, imgList)
+root.mainloop()