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-rw-r--r--.gitignore7
-rw-r--r--backend/data/eol/README.md0
-rw-r--r--backend/data/otol/README.md0
-rwxr-xr-xbackend/data/otolToSqlite.py (renamed from data_otol/namedTreeToJSON.py)129
-rwxr-xr-xbackend/server.py142
-rwxr-xr-xdata_tol_old/genTestImgs.sh16
-rw-r--r--data_tol_old/tolData.txt388
-rwxr-xr-xdata_tol_old/txtTreeToJSON.py76
-rw-r--r--src/App.vue110
-rw-r--r--src/components/SearchModal.vue37
-rw-r--r--vite.config.js5
11 files changed, 343 insertions, 567 deletions
diff --git a/.gitignore b/.gitignore
index 7f8c994..2357fe7 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,8 +2,7 @@ rem.not
package-lock.json
node_modules/
dist/
-src/tolData.json
public/img/
-data_tol_old/img/
-data_tol_old/tolData.json
-data_otol/
+backend/data/otol
+backend/data/otol.db
+backend/data/eol
diff --git a/backend/data/eol/README.md b/backend/data/eol/README.md
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/backend/data/eol/README.md
diff --git a/backend/data/otol/README.md b/backend/data/otol/README.md
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/backend/data/otol/README.md
diff --git a/data_otol/namedTreeToJSON.py b/backend/data/otolToSqlite.py
index 30b8033..187e224 100755
--- a/data_otol/namedTreeToJSON.py
+++ b/backend/data/otolToSqlite.py
@@ -1,11 +1,13 @@
#!/usr/bin/python3
-import sys, re, json
+import sys, re, json, sqlite3
+import os.path
usageInfo = f"usage: {sys.argv[0]}\n"
usageInfo += "Reads labelled_supertree_ottnames.tre & annotations.json (from an Open Tree of Life release), \n"
-usageInfo += "and prints a JSON object, which maps node names to objects of the form \n"
-usageInfo += "{\"children\": [name1, ...], \"parent\": name1, \"tips\": int1, \"pSupport\": bool1}, which holds \n"
+usageInfo += "and creates an sqlite database otol.db, which holds entries of the form (name text, data text).\n"
+usageInfo += "Each row holds a tree-of-life node name, and a JSON string with the form \n"
+usageInfo += "{\"children\": [name1, ...], \"parent\": name1, \"tips\": int1, \"pSupport\": bool1}, holding \n"
usageInfo += "child names, a parent name or null, descendant 'tips', and a phylogeny-support indicator\n"
usageInfo += "\n"
usageInfo += "This script was adapted to handle Open Tree of Life version 13.4.\n"
@@ -25,12 +27,20 @@ if len(sys.argv) > 1:
print(usageInfo, file=sys.stderr)
sys.exit(1)
-nodeMap = {} # The JSON object to output
+treeFile = "otol/labelled_supertree_ottnames.tre"
+annFile = "otol/annotations.json"
+dbFile = "otol.db"
+nodeMap = {} # Maps node names to node objects
idToName = {} # Maps node IDs to names
-# Parse labelled_supertree_ottnames.tre
+# Check for existing db
+if os.path.exists(dbFile):
+ print("ERROR: Existing {} file".format(dbFile), file=sys.stderr)
+ sys.exit(1)
+
+# Parse treeFile
data = None
-with open("labelled_supertree_ottnames.tre") as file:
+with open(treeFile) as file:
data = file.read()
dataIdx = 0
def parseNewick():
@@ -67,6 +77,13 @@ def parseNewick():
for childName in childNames:
tips += nodeMap[childName]["tips"]
# Add node to nodeMap
+ if name in nodeMap: # Turns out the names might not actually be unique
+ count = 2
+ name2 = name + " [" + str(count) + "]"
+ while name2 in nodeMap:
+ count += 1
+ name2 = name + " [" + str(count) + "]"
+ name = name2
nodeMap[name] = {
"n": name, "id": id, "children": childNames, "parent": None, "tips": tips, "pSupport": False
}
@@ -112,6 +129,7 @@ def parseNewickName():
name = name[:-1]
dataIdx = end
# Convert to [name, id]
+ name = name.lower()
if name.startswith("mrca"):
return [name, name]
elif name[0] == "'":
@@ -127,29 +145,63 @@ def parseNewickName():
return [match.group(1).replace("_", " "), match.group(2)]
rootName = parseNewick()
-# Parse annotations.json
+# Parse annFile
data = None
-with open("annotations.json") as file:
+with open(annFile) as file:
data = file.read()
obj = json.loads(data)
nodeAnnsMap = obj['nodes']
-# Do some more postprocessing on each node
-def convertMrcaName(name):
- """Given an mrca* name, returns an expanded version with the form [name1 + name2]"""
- match = re.fullmatch(r"mrca(ott\d+)(ott\d+)", name)
- if match == None:
- print("ERROR: Invalid name \"{}\"".format(name), file=sys.stderr)
- else:
- subName1 = match.group(1)
- subName2 = match.group(2)
- if subName1 not in idToName:
- print("ERROR: MRCA name \"{}\" sub-name \"{}\" not found".format(subName1), file=sys.stderr)
- elif subName2 not in idToName:
- print("ERROR: MRCA name \"{}\" sub-name \"{}\" not found".format(subName2), file=sys.stderr)
- else:
- return "[{} + {}]".format(idToName[subName1], idToName[subName2])
-namesToSwap = [] # Will hold [oldName, newName] pairs, for renaming nodes in nodeMap
+# Change mrca* names
+def applyMrcaNameConvert(name, namesToSwap):
+ """
+ Given an mrca* name, makes namesToSwap map it to an expanded version with the form [childName1 + childName2].
+ May recurse on child nodes with mrca* names.
+ Also returns the name of the highest-tips child (used when recursing).
+ """
+ node = nodeMap[name]
+ childNames = node["children"]
+ if len(childNames) < 2:
+ print("WARNING: MRCA node \"{}\" has less than 2 children".format(name), file=sys.stderr)
+ return name
+ # Get 2 children with most tips
+ childTips = []
+ for n in childNames:
+ childTips.append(nodeMap[n]["tips"])
+ maxTips = max(childTips)
+ maxIdx = childTips.index(maxTips)
+ childTips[maxIdx] = 0
+ maxTips2 = max(childTips)
+ maxIdx2 = childTips.index(maxTips2)
+ #
+ childName1 = node["children"][maxIdx]
+ childName2 = node["children"][maxIdx2]
+ if childName1.startswith("mrca"):
+ childName1 = applyMrcaNameConvert(childName1, namesToSwap)
+ if childName2.startswith("mrca"):
+ childName2 = applyMrcaNameConvert(childName2, namesToSwap)
+ # Create composite name
+ namesToSwap[name] = "[{} + {}]".format(childName1, childName2)
+ return childName1
+namesToSwap = {} # Maps mrca* names to replacement names
+for node in nodeMap.values():
+ name = node["n"]
+ if (name.startswith("mrca") and name not in namesToSwap):
+ applyMrcaNameConvert(name, namesToSwap)
+for [oldName, newName] in namesToSwap.items():
+ nodeMap[newName] = nodeMap[oldName]
+ del nodeMap[oldName]
+for node in nodeMap.values():
+ parentName = node["parent"]
+ if (parentName in namesToSwap):
+ node["parent"] = namesToSwap[parentName]
+ childNames = node["children"]
+ for i in range(len(childNames)):
+ childName = childNames[i]
+ if (childName in namesToSwap):
+ childNames[i] = namesToSwap[childName]
+
+# Add annotations data, and delete certain fields
for node in nodeMap.values():
# Set has-support value using annotations
id = node["id"]
@@ -158,24 +210,19 @@ for node in nodeMap.values():
supportQty = len(nodeAnns["supported_by"]) if "supported_by" in nodeAnns else 0
conflictQty = len(nodeAnns["conflicts_with"]) if "conflicts_with" in nodeAnns else 0
node["pSupport"] = supportQty > 0 and conflictQty == 0
- # Change mrca* names
- name = node["n"]
- if (name.startswith("mrca")):
- namesToSwap.append([name, convertMrcaName(name)])
- parentName = node["parent"]
- if (parentName != None and parentName.startswith("mrca")):
- node["parent"] = convertMrcaName(parentName)
- childNames = node["children"]
- for i in range(len(childNames)):
- if (childNames[i].startswith("mrca")):
- childNames[i] = convertMrcaName(childNames[i])
+ # Root node gets support
+ if node["parent"] == None:
+ node["pSupport"] = True
# Delete some no-longer-needed fields
del node["n"]
del node["id"]
-# Finish mrca* renamings
-for [oldName, newName] in namesToSwap:
- nodeMap[newName] = nodeMap[oldName]
- del nodeMap[oldName]
-# Output JSON
-print(json.dumps(nodeMap))
+# Create db
+con = sqlite3.connect(dbFile)
+cur = con.cursor()
+cur.execute("CREATE TABLE nodes (name TEXT PRIMARY KEY, data TEXT)")
+for name in nodeMap.keys():
+ cur.execute("INSERT INTO nodes VALUES (?, ?)", (name, json.dumps(nodeMap[name])))
+cur.execute("CREATE UNIQUE INDEX nodes_idx on nodes(name)")
+con.commit()
+con.close()
diff --git a/backend/server.py b/backend/server.py
new file mode 100755
index 0000000..2ff7e74
--- /dev/null
+++ b/backend/server.py
@@ -0,0 +1,142 @@
+#!/usr/bin/python3
+
+import sys, re, sqlite3, json
+from http.server import HTTPServer, BaseHTTPRequestHandler
+import urllib.parse
+
+hostname = "localhost"
+port = 8000
+dbFile = "data/otol.db"
+tolnodeReqDepth = 2
+ # For a /tolnode/name1 request, respond with name1's node, and descendent nodes in a subtree to some depth
+ # A depth of 0 means only respond with one node
+
+usageInfo = f"usage: {sys.argv[0]}\n"
+usageInfo += "Starts a server that listens for GET requests to " + hostname + ":" + str(port) + "/tolnode/name1,\n"
+usageInfo += "and responds with JSON representing an object mapping names to node objects.\n"
+usageInfo += "Normally, the response includes node name1, and child nodes up to depth " + str(tolnodeReqDepth) + ".\n"
+usageInfo += "\n"
+usageInfo += "A query section ?type=type1 can be used to affect the result.\n"
+usageInfo += "If type1 is 'children', the operation acts on node name1's children, and the results combined.\n"
+usageInfo += "If type1 is 'chain', the response includes nodes from name1 up to the root, and their direct children.\n"
+
+dbCon = sqlite3.connect(dbFile)
+def lookupName(name):
+ cur = dbCon.cursor()
+ cur.execute("SELECT name, data FROM nodes WHERE name = ?", (name,))
+ row = cur.fetchone()
+ return row[1] if row != None else None
+#def lookupNameLike(name):
+# cur = dbCon.cursor()
+# found = False
+# cur.execute("SELECT name, data FROM nodes WHERE name like ?", ("%{}%".format(name),))
+# rows = cur.fetchall()
+# if len(rows) == 0:
+# return None
+# else:
+# jsonStr = "{"
+# for i in range(len(rows)):
+# jsonStr += json.dumps(rows[i][0]) + ":" + rows[i][1]
+# if i < len(njList) - 1:
+# jsonStr += ","
+# jsonStr += "}"
+# return jsonFromNameJsonList(rows)
+
+class DbServer(BaseHTTPRequestHandler):
+ def do_GET(self):
+ # Parse URL
+ urlParts = urllib.parse.urlparse(self.path)
+ path = urllib.parse.unquote(urlParts.path)
+ queryDict = urllib.parse.parse_qs(urlParts.query)
+ # Check first element of path
+ match = re.match(r"/([^/]+)/(.+)", path)
+ if match != None:
+ reqType = match.group(1)
+ if reqType == "tolnode":
+ name = match.group(2)
+ # Check query string
+ if "type" not in queryDict:
+ nodeJson = lookupName(name)
+ if nodeJson != None:
+ results = []
+ getResultsUntilDepth(name, nodeJson, tolnodeReqDepth, results)
+ self.respondJson(nodeResultsToJSON(results))
+ return
+ elif queryDict["type"][0] == "children":
+ nodeJson = lookupName(name)
+ if nodeJson != None:
+ obj = json.loads(nodeJson)
+ results = []
+ for childName in obj["children"]:
+ nodeJson = lookupName(childName)
+ if nodeJson != None:
+ getResultsUntilDepth(childName, nodeJson, tolnodeReqDepth, results)
+ self.respondJson(nodeResultsToJSON(results))
+ return
+ elif queryDict["type"][0] == "chain":
+ results = []
+ ranOnce = False
+ while True:
+ jsonResult = lookupName(name)
+ if jsonResult == None:
+ if ranOnce:
+ print("ERROR: Parent-chain node {} not found".format(name), file=sys.stderr)
+ break
+ results.append([name, jsonResult])
+ obj = json.loads(jsonResult)
+ # Add children
+ if not ranOnce:
+ ranOnce = True
+ else:
+ internalFail = False
+ for childName in obj["children"]:
+ jsonResult = lookupName(childName)
+ if jsonResult == None:
+ print("ERROR: Parent-chain-child node {} not found".format(name), file=sys.stderr)
+ internalFail = True
+ break
+ results.append([childName, jsonResult])
+ if internalFail:
+ break
+ # Check if root
+ if obj["parent"] == None:
+ self.respondJson(nodeResultsToJSON(results))
+ return
+ else:
+ name = obj["parent"]
+ self.send_response(404)
+ self.end_headers()
+ self.end_headers()
+ def respondJson(self, jsonStr):
+ self.send_response(200)
+ self.send_header("Content-type", "application/json")
+ self.end_headers()
+ self.wfile.write(jsonStr.encode("utf-8"))
+def getResultsUntilDepth(name, nodeJson, depth, results):
+ """Given a node [name, nodeJson] pair, adds child node pairs to 'results', up until 'depth'"""
+ results.append([name, nodeJson])
+ if depth > 0:
+ obj = json.loads(nodeJson)
+ for childName in obj["children"]:
+ childJson = lookupName(childName)
+ if childJson != None:
+ getResultsUntilDepth(childName, childJson, depth-1, results)
+def nodeResultsToJSON(results):
+ """Given a list of [name, nodeJson] pairs, returns a representative JSON string"""
+ jsonStr = "{"
+ for i in range(len(results)):
+ jsonStr += json.dumps(results[i][0]) + ":" + results[i][1]
+ if i < len(results) - 1:
+ jsonStr += ","
+ jsonStr += "}"
+ return jsonStr
+
+server = HTTPServer((hostname, port), DbServer)
+print("Server started at http://{}:{}".format(hostname, port))
+try:
+ server.serve_forever()
+except KeyboardInterrupt:
+ pass
+server.server_close()
+dbCon.close()
+print("Server stopped")
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("]")
diff --git a/src/App.vue b/src/App.vue
index cb2b1f4..f1e6e2a 100644
--- a/src/App.vue
+++ b/src/App.vue
@@ -39,9 +39,8 @@ function getReverseAction(action: Action): Action | null {
}
// Get tree-of-life data
-import data from './tolData.json';
-let tolMap: TolMap = data;
-const rootName = "[Elaeocarpus williamsianus + Brunellia mexicana]";
+const rootName = "cellular organisms";
+const tolMap: TolMap = {[rootName]: new TolNode()};
// Configurable options
const defaultLytOpts: LayoutOptions = {
@@ -117,6 +116,8 @@ export default defineComponent({
height: document.documentElement.clientHeight,
resizeThrottled: false,
resizeDelay: 50, //ms (increasing to 100 seems to cause resize-skipping when opening browser mobile-view)
+ // Other
+ excessTolNodeThreshold: 1000, // Threshold where excess tolMap entries are removed (done on tile collapse)
};
},
computed: {
@@ -173,15 +174,32 @@ export default defineComponent({
methods: {
// For tile expand/collapse events
onLeafClick(layoutNode: LayoutNode){
- let success = tryLayout(this.activeRoot, this.tileAreaPos, this.tileAreaDims, this.lytOpts, {
- allowCollapse: false,
- chg: {type: 'expand', node: layoutNode, tolMap: this.tolMap},
- layoutMap: this.layoutMap
- });
- if (!success){
- layoutNode.failFlag = !layoutNode.failFlag; // Triggers failure animation
+ let doExpansion = () => {
+ let success = tryLayout(this.activeRoot, this.tileAreaPos, this.tileAreaDims, this.lytOpts, {
+ allowCollapse: false,
+ chg: {type: 'expand', node: layoutNode, tolMap: this.tolMap},
+ layoutMap: this.layoutMap
+ });
+ if (!success){
+ layoutNode.failFlag = !layoutNode.failFlag; // Triggers failure animation
+ }
+ return success;
+ };
+ // Check if data for node-to-expand exists, getting from server if needed
+ let tolNode = this.tolMap[layoutNode.name];
+ if (tolNode.children[0] in this.tolMap == false){
+ return fetch('/tolnode/' + layoutNode.name + '?type=children')
+ .then(response => response.json())
+ .then(obj => {
+ Object.getOwnPropertyNames(obj).forEach(key => {this.tolMap[key] = obj[key]});
+ doExpansion();
+ })
+ .catch(error => {
+ console.log('ERROR loading tolnode data', error);
+ });
+ } else {
+ return new Promise((resolve, reject) => resolve(doExpansion()));
}
- return success;
},
onNonleafClick(layoutNode: LayoutNode){
let success = tryLayout(this.activeRoot, this.tileAreaPos, this.tileAreaDims, this.lytOpts, {
@@ -191,6 +209,19 @@ export default defineComponent({
});
if (!success){
layoutNode.failFlag = !layoutNode.failFlag; // Triggers failure animation
+ } else {
+ // Clear out excess nodes when a threshold is reached
+ let tolNodeNames = Object.getOwnPropertyNames(this.tolMap)
+ let extraNodes = tolNodeNames.length - this.layoutMap.size;
+ if (extraNodes > this.excessTolNodeThreshold){
+ for (let n of tolNodeNames){
+ if (!this.layoutMap.has(n)){
+ delete this.tolMap[n];
+ }
+ }
+ let numRemovedNodes = tolNodeNames.length - Object.getOwnPropertyNames(this.tolMap).length;
+ console.log(`Cleaned up tolMap (removed ${numRemovedNodes} out of ${tolNodeNames.length})`);
+ }
}
return success;
},
@@ -271,26 +302,27 @@ export default defineComponent({
return;
}
// Attempt tile-expand
- let success = this.onLeafClick(layoutNode);
- if (success){
- setTimeout(() => this.expandToNode(name), this.uiOpts.tileChgDuration);
- return;
- }
- // Attempt expand-to-view on ancestor just below activeRoot
- if (layoutNode == this.activeRoot){
- console.log('Unable to complete search (not enough room to expand active root)');
- // Note: Only happens if screen is significantly small or node has significantly many children
- this.modeRunning = false;
- return;
- }
- while (true){
- if (layoutNode.parent! == this.activeRoot){
- break;
+ this.onLeafClick(layoutNode).then(success => {
+ if (success){
+ setTimeout(() => this.expandToNode(name), this.uiOpts.tileChgDuration);
+ return;
}
- layoutNode = layoutNode.parent!;
- }
- this.onNonleafClickHeld(layoutNode);
- setTimeout(() => this.expandToNode(name), this.uiOpts.tileChgDuration);
+ // Attempt expand-to-view on ancestor just below activeRoot
+ if (layoutNode == this.activeRoot){
+ console.log('Unable to complete search (not enough room to expand active root)');
+ // Note: Only happens if screen is significantly small or node has significantly many children
+ this.modeRunning = false;
+ return;
+ }
+ while (true){
+ if (layoutNode.parent! == this.activeRoot){
+ break;
+ }
+ layoutNode = layoutNode.parent!;
+ }
+ this.onNonleafClickHeld(layoutNode);
+ setTimeout(() => this.expandToNode(name), this.uiOpts.tileChgDuration);
+ });
},
// For auto-mode events
onPlayIconClick(){
@@ -385,7 +417,9 @@ export default defineComponent({
this.setLastFocused(node.parent!);
break;
case 'expand':
- this.autoPrevActionFail = !this.onLeafClick(node);
+ this.onLeafClick(node)
+ .then(success => this.autoPrevActionFail = !success)
+ .catch(error => this.autoPrevActionFail = true);
break;
case 'collapse':
this.autoPrevActionFail = !this.onNonleafClick(node);
@@ -457,6 +491,20 @@ export default defineComponent({
window.addEventListener('keyup', this.onKeyUp);
tryLayout(this.activeRoot, this.tileAreaPos, this.tileAreaDims, this.lytOpts,
{allowCollapse: true, layoutMap: this.layoutMap});
+ // Get initial tol node data
+ fetch('/tolnode/' + rootName)
+ .then(response => response.json())
+ .then(obj => {
+ Object.getOwnPropertyNames(obj).forEach(key => {this.tolMap[key] = obj[key]});
+ this.layoutTree = initLayoutTree(this.tolMap, this.layoutTree.name, 0);
+ this.activeRoot = this.layoutTree;
+ this.layoutMap = initLayoutMap(this.layoutTree);
+ tryLayout(this.activeRoot, this.tileAreaPos, this.tileAreaDims, this.lytOpts,
+ {allowCollapse: true, layoutMap: this.layoutMap});
+ })
+ .catch(error => {
+ console.log('ERROR loading initial tolnode data', error);
+ });
},
unmounted(){
window.removeEventListener('resize', this.onResize);
diff --git a/src/components/SearchModal.vue b/src/components/SearchModal.vue
index 22b6896..5accd62 100644
--- a/src/components/SearchModal.vue
+++ b/src/components/SearchModal.vue
@@ -12,21 +12,36 @@ export default defineComponent({
},
methods: {
onCloseClick(evt: Event){
- if (evt.target == this.$el || (this.$refs.searchInput as typeof SearchIcon).$el.contains(evt.target)){
+ if (evt.target == this.$el || (this.$refs.searchIcon as typeof SearchIcon).$el.contains(evt.target)){
this.$emit('search-close');
}
},
onSearchEnter(){
let input = this.$refs.searchInput as HTMLInputElement;
- if (this.tolMap.hasOwnProperty(input.value)){
- this.$emit('search-node', input.value);
- } else {
- input.value = '';
- // Trigger failure animation
- input.classList.remove('animate-red-then-fade');
- input.offsetWidth; // Triggers reflow
- input.classList.add('animate-red-then-fade');
- }
+ // Query server
+ let url = new URL(window.location.href);
+ url.pathname = '/tolnode/' + input.value;
+ fetch(url)
+ .then(response => {
+ // Search successful. Get nodes in parent-chain, add to tolMap, then emit event.
+ url.search = '?type=chain';
+ fetch(url)
+ .then(response => response.json())
+ .then(obj => {
+ Object.getOwnPropertyNames(obj).forEach(key => {this.tolMap[key] = obj[key]});
+ this.$emit('search-node', input.value);
+ })
+ .catch(error => {
+ console.log('ERROR loading tolnode chain', error);
+ });
+ })
+ .catch(error => {
+ input.value = '';
+ // Trigger failure animation
+ input.classList.remove('animate-red-then-fade');
+ input.offsetWidth; // Triggers reflow
+ input.classList.add('animate-red-then-fade');
+ });
},
focusInput(){
(this.$refs.searchInput as HTMLInputElement).focus();
@@ -46,7 +61,7 @@ export default defineComponent({
bg-stone-50 rounded-md shadow shadow-black flex gap-1">
<input type="text" class="block border"
@keyup.enter="onSearchEnter" @keyup.esc="onCloseClick" ref="searchInput"/>
- <search-icon @click.stop="onSearchEnter"
+ <search-icon @click.stop="onSearchEnter" ref="searchIcon"
class="block w-6 h-6 ml-1 hover:cursor-pointer hover:bg-stone-200" />
</div>
</div>
diff --git a/vite.config.js b/vite.config.js
index e1200f9..7b02d3f 100644
--- a/vite.config.js
+++ b/vite.config.js
@@ -3,5 +3,10 @@ import vue from '@vitejs/plugin-vue'
export default defineConfig({
plugins: [vue()],
+ server: {
+ proxy: {
+ '/tolnode': 'http://localhost:8000',
+ }
+ },
//server: {open: true} //open browser when dev server starts
})
generated by cgit v1.2.3 (git 2.39.1) at 2026-04-24 21:32:57 +0000