Have tol data in sqlite db, and add server script that accesses it

Adapt otol-data-converting script to generate otol.db, add server.py
script that provides access to that db, and adapt the app to query the
server for tol data when needed.

3 files changed, 0 insertions, 480 deletions

diff --git a/data_tol_old/genTestImgs.sh b/data_tol_old/genTestImgs.sh
deleted file mode 100755
index 21b001b..0000000
--- a/data_tol_old/genTestImgs.sh
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/bin/bash
-set -e
-
-#generate tol.json from tol.txt
-cat tolData.txt | ./txtTreeToJSON.py > tolData.json
-
-#reads through tolData.json, gets names, and generates image for each name
-cat tolData.json | \
-	gawk 'match ($0, /"name"\s*:\s*"([^"]*)"/, arr) {print arr[1]}' | \
-	while read; do
-		convert -size 200x200 xc:khaki +repage \
-			-size 150x150  -fill black -background None  \
-			-font Ubuntu-Mono -gravity center caption:"$REPLY" +repage \
-			-gravity Center  -composite -strip ../public/img/"$REPLY".png
-	done
-
diff --git a/data_tol_old/tolData.txt b/data_tol_old/tolData.txt
deleted file mode 100644
index f73a064..0000000
--- a/data_tol_old/tolData.txt
+++ /dev/null
@@ -1,388 +0,0 @@
-Tree of Life
-	Viruses
-		Caudovirales
-		Herpesvirales
-		Ligamenvirales
-		Mononegavirales
-		Nidovirales
-		Picornavirales
-		Tymovirales
-	Archaea
-		Crenarchaeota
-		Euryarchaeota
-	Bacteria
-		Acidobacteria
-		Actinobacteria
-		Aquificae
-		Armatimonadetes
-		Bacteroidetes
-		Caldiserica
-		Chlamydiae
-		Chlorobi
-		Chloroflexi
-		Chrysiogenetes
-		Cyanobacteria
-		Deferribacteres
-		Deinococcus-thermus
-		Dictyoglomi
-		Elusimicrobia
-		Fibrobacteres
-		Firmicutes
-		Fusobacteria
-		Gemmatimonadetes
-		Lentisphaerae
-		Nitrospira
-		Planctomycetes
-		Proteobacteria
-		Spirochaetae
-		Synergistetes
-		Tenericutes
-		Thermodesulfobacteria
-		Thermotogae
-		Verrucomicrobia
-	Eukaryota
-		Diatoms
-		Amoebozoa
-		Plantae
-			Rhodopyhta
-			Viridiplantae
-				Prasinophytes
-				Ulvophyceae
-				Streptophyta
-					Charales
-					Embryophytes
-						Marchantiomorpha
-						Anthocerotophyta
-						Bryophyta
-						Lycopodiopsida
-							Lycopodiidae
-							Selaginellales
-						Polypodiopsida
-							Polypodiidae
-								Polypodiales
-							Equisetidae
-						Spermatopsida
-							Cycads
-							Conifers
-								Taxaceae
-								Cupressaceae
-								Pinaceae
-									Pinus
-									Picea
-									Larix
-									Cedrus
-									Abies
-							Ginkgos
-							Angiosperms
-								Illicium
-								magnoliids
-									Piperales
-										Piperaceae
-									Magnoliales
-										Annonaceae
-										Myristicaceae
-									Laurales
-										Lauraceae
-								Monocotyledons
-									Alismatanae
-									Aranae
-									Liliaceae
-									Asparagales
-										Amaryllidaceae
-										Asparagaceae
-										Asphodelaceae
-										Iridaceae
-										Orchidaceae
-									Dioscoreaceae
-									Arecanae
-										Cocoeae
-										Phoeniceae
-									Zingiberanae
-										Musaceae
-										Strelitziaceae
-										Zingiberaceae
-									Commelinanae
-										Bromeliaceae
-										Cyperaceae
-										Typhaceae
-										Poaceae
-											Zea mays
-											Triticum
-											Bambusoideae
-								eudicots
-									Ranunculales
-										Papaveraceae
-										Ranunculaceae
-									Proteales
-										Proteaceae
-										Nelumbo
-									Core Eudicots
-										Saxifragales
-										Rosids
-											Fabaceae
-												Mimosoideae
-												IRLC (Inverted Repat-lacking clade)
-													Trifolieae
-													Fabeae
-											Rosales
-												Rosaceae
-													Rosa
-													Malus pumila
-												Ulmaceae
-												Urticaceae
-												Moraceae
-												Cannabaceae
-											Fagales
-												Fagaceae
-												Betulaceae
-												Juglandaceae
-											Cucurbitales
-												Cucurbitaceae
-											Malpighiales
-												Salicaceae
-												Violaceae
-												Passifloraceae
-												Erythroxylaceae
-												Rhizophoraceae
-												Euphorbiaceae
-												Linaceae
-												Rafflesiaceae
-											Myrtales
-												Myrtaceae
-												Onagraceae
-												Lythraceae
-											Brassicales
-												Caricaceae
-												Brassicaceae
-											Malvales
-												Core Malvales
-													Malvoideae
-													Bombacoideae
-													Sterculioideae
-													Helicteroideae
-													Byttnerioideae
-											Sapindales
-												Anacardiaceae
-												Burseraceae
-												Meliaceae
-												Rutaceae
-												Sapindaceae
-										Vitaceae
-										Caryophyllales
-											Polygonaceae
-											Droseraceae
-											Nepenthaceae
-											core Caryophyllales
-												Cactaceae
-												Amaranthaceae
-										Asterids
-											Ericales
-												Actinidiaceae
-												Ericaceae
-												Lecythidaceae
-												Sapotaceae
-												Ebenaceae
-												Theaceae
-											Solanales
-												Solanaceae
-												Convolvulaceae
-											Lamiales
-												Oleaceae
-													Fraxinus
-												Bignoniaceae
-												Pedaliaceae
-												Lentibulariaceae
-												Lamiaceae
-											Gentianales
-												Rubiaceae
-											Asterales
-												Campanulaceae
-												Asteraceae
-													Carduoideae
-														Cardueae
-													Cichorioideae
-														Cichorieae
-													Asteroideae
-														Asterodae
-														Helianthodae
-											Apiales
-												Apiaceae
-												Araliaceae
-											Aquifoliaceae
-		Fungi
-			Fungi 1
-				Dikarya
-					Basidiomycota
-						Agaricomycotina
-							Agaricomycetes
-								Agaricomycetes 1
-									Agaricomycetidae
-										Agaricales
-											Strophariaceae strict-sense
-											Psathyrellaceae
-											Agaricaceae
-											Nidulariaceae
-											Marasmiaceae
-											Physalacriaceae
-											Pleurotaceae
-											Amanitaceae
-											Podoserpula
-										Boletales
-											Serpulaceae
-											Sclerodermataceae
-											Boletaceae
-									Russulales
-									Hymenochaetales
-								Phallomycetidae
-									Geastrales
-									Gomphales
-									Phallales
-								Cantharellales
-								Auriculariales
-							Tremellomycetes
-						Ustilaginomycotina
-						Pucciniomycotina
-							Pucciniomycetes
-								Septobasidiales
-								Pucciniales
-							Mixiomycetes
-							Tritirachiomycetes
-						Entorrhizomycetes
-						Wallemiomycetes
-					Ascomycota
-						Pezizomycotina
-							Pezizomycetes
-							'Leotiomyceta'
-								Eurotiomycetes
-								Geoglossaceae
-								Sordariomycetes
-									Hypocreomycetidae
-									Sordariomycetidae
-								Laboulbeniomycetes
-								Pleosporomycetidae
-						Saccharomycotina
-						Taphrinomycotina
-							Schizosaccharomycetes
-							Pneumocystidiomycetes
-							Taphrinomycetes
-				Glomeromycota
-			Zygomycota
-				Endogonales
-				Mucorales
-			Blastocladiomycota
-			Chytridiomycota
-			Neocallimastigomycota
-			Microsporidia
-		Animalia
-			Porifera
-			Cnidaria
-			Tardigrada
-			Annelida
-			Mollusca
-				Bivalvia
-				Gastropoda
-				Cephalopoda
-			Arthropoda
-				Arachnida
-					Araneae
-					Opiliones
-					Scorpiones
-					Heterostigmata
-				Crustacea
-					Euphausiacea
-					Brachyura
-					Isopoda
-					Cirripedia
-				Insecta
-					Anisoptera
-					Mantodea
-					Cicadoidea
-					Siphonaptera
-					Cucujoidea
-					Phengodidae
-					Drosophilidae
-					Culicidae
-					Lepidoptera
-					Apini
-					Formicidae
-			Deuterostomia
-				Echinodermata
-					Crinoidea
-					Asteroidea
-					Echinoidea
-					Holothuroidea
-				Vertebrata
-					Chondrichthyes
-						Carcharodon carcharias
-						Rhinocodon typus
-						Batoidea
-						Pristidae
-					Actinopterygii
-						Clupeomorpha
-						Xiphias gladius
-						Siluriformes
-						Carassius auratus
-						Tetraodontidae
-						Molidae
-						Gymnotiformes
-						Lophiiformes
-						Exocoetidae
-						'mudskipper'
-						Hippocampus
-						Psudoliparis swirei
-					Sarcopterygii
-					Tetrapoda
-						Amphibia
-							Gymnophiona
-							Caudata
-								Salamandra
-								Cryptobranchidae
-								Ambystomatidae
-							Anura
-						Reptilia
-							Testudines
-							Plesiosauria
-							Chamaeleonidae
-							Serpentes
-							Crocodilia
-							Dinosauria
-								Triceratops
-								Sauropoda
-								Tyrannosauroidea
-								Aves
-									magpie
-									parrot
-									eagle
-									owl
-									swan
-									chicken
-									penguin
-									hummingbird
-						Synapsida
-							monotreme
-							marsupial
-								kangaroo
-								possum
-								wombat
-							rodent
-								mouse
-								beaver
-							rabbit
-							feline
-							canine
-							bear
-							walrus
-							Artiodactyla
-								pig
-								camel
-								deer
-								giraffe
-							horse
-							elephant
-							cetacean
-							armadillo
-							bat
-							monkey
-							gorilla
-							chimpanzee
-							homo sapien
diff --git a/data_tol_old/txtTreeToJSON.py b/data_tol_old/txtTreeToJSON.py
deleted file mode 100755
index 3b77622..0000000
--- a/data_tol_old/txtTreeToJSON.py
+++ /dev/null
@@ -1,76 +0,0 @@
-#!/usr/bin/python3
-
-import sys, re
-
-usageInfo =  f"usage: {sys.argv[0]}\n"
-usageInfo += "Reads, from stdin, tab-indented lines representing trees, and outputs corresponding JSON.\n"
-
-if len(sys.argv) > 1:
-	print(usageInfo, file=sys.stderr)
-	sys.exit(1)
-
-lineNum = 0
-trees = [] #each node is a pair holding a name and an array of child nodes
-nodeList = []
-while True: 
-	#read line
-	line = sys.stdin.readline()
-	if line == "": break
-	line = line.rstrip()
-	lineNum += 1
-	#create node
-	match = re.match(r"^\t*", line)
-	indent = len(match.group())
-	newNode = [line[indent:], []]
-	#add node
-	if indent == len(nodeList): #sibling or new tree
-		if len(nodeList) == 0:
-			nodeList.append(newNode)
-			trees.append(newNode)
-		else:
-			nodeList[-1] = newNode
-			if len(nodeList) == 1:
-				trees[-1][1].append(newNode)
-			else:
-				nodeList[-2][1].append(newNode)
-	elif indent == len(nodeList) + 1: #direct child
-		if len(nodeList) == 0:
-			print(f"ERROR: Child without preceding root (line {lineNum})")
-			sys.exit(1)
-		nodeList.append(newNode)
-		nodeList[-2][1].append(newNode)
-	elif indent < len(nodeList): #ancestor sibling or new tree
-		nodeList = nodeList[:indent]
-		if len(nodeList) == 0:
-			nodeList.append(newNode)
-			trees.append(newNode)
-		else:
-			nodeList[-1] = newNode
-			if len(nodeList) == 1:
-				trees[-1][1].append(newNode)
-			else:
-				nodeList[-2][1].append(newNode)
-	else:
-		print(f"ERROR: Child with invalid relative indent (line {lineNum})")
-		sys.exit(1)
-#print as JSON
-if len(trees) > 1:
-	print("[")
-def printNode(node, indent):
-	if len(node[1]) == 0:
-		print(indent + "{\"name\": \"" + node[0] + "\"}", end="")
-	else:
-		print(indent + "{\"name\": \"" + node[0] + "\", \"children\": [")
-		for i in range(len(node[1])):
-			printNode(node[1][i], indent + "\t")
-			if i < len(node[1])-1:
-				print(",", end="")
-			print()
-		print(indent + "]}", end="")
-for i in range(len(trees)):
-	printNode(trees[i], "")
-	if i < len(trees)-1:
-		print(",", end="")
-	print()
-if len(trees) > 1:
-	print("]")