update API Framework WebServices for Python3.12

src/APIFramework.py

@@ -12,7 +12,7 @@
 import werkzeug
 import atexit
 import hashlib
-import urllib2
+import urllib.request
 import random
 import string
 import datetime
@@ -191,7 +191,7 @@ def google_analytics_tag_id(self):
         return self._google_analytics_tag_id
 
     def set_google_analytics_tag_id(self, tag):
-        assert type(tag) in [str, unicode]
+        assert type(tag) == str
         self._google_analytics_tag_id = tag
 
     def input_file_folder(self):
@@ -293,7 +293,7 @@ def find_config(self, config_file_name):
     def parse_config(self, config_file_name):
 
         config = configparser.ConfigParser()
-	if hasattr(config,"read_file"):
+        if hasattr(config,"read_file"):
             config.read_file(open(config_file_name))
         else:
             config.readfp(open(config_file_name))
@@ -465,7 +465,7 @@ def random_str(l=20):
 
     @staticmethod
     def str2hash(s):
-        return hashlib.md5(s).hexdigest()
+        return hashlib.md5(s.encode('utf8')).hexdigest()
 
     def submit(self):
         if flask.request.method in ['GET', 'POST']:
@@ -738,14 +738,14 @@ def download_file(self):
     # FLASK helper functions
     def form_task(self, params):
         task = {}
-	task_str = ""
-	for par in self.task_params:
+        task_str = ""
+        for par in self.task_params:
             if par in params:
-	        task[par] = params[par].strip()
+                task[par] = params[par].strip()
             elif self.task_params[par] != None:
                 task[par] = self.task_params[par].strip()
             task_str += "_" + task[par]
-        task["id"] = self.str2hash(task_str.encode("utf-8"))
+        task["id"] = self.str2hash(task_str)
         return task
 
     # @staticmethod
@@ -981,7 +981,7 @@ def task_queue_get(self, task_queue, pid, suicide_queue):
     def get_queue_length(self):
         url = "http://%s:%s/queue_length" % (self.host(), self.port())
 
-        req = urllib2.urlopen(url)
+        req = urllib.request.urlopen(url)
         x = req.read()
 
         return int(x)
@@ -1046,7 +1046,7 @@ def cleanup(self):
 
 
     def terminate_all(self):
-        for i, p in self._deamon_process_pool.items():
+        for i, p in list(self._deamon_process_pool.items()):
             self.output(0, "Worker-%s is terminated" % (i))
             p.terminate()
             del self._deamon_process_pool[i]

src/Application/Converter/Converter.py

@@ -21,7 +21,7 @@ def form_task(self, p):
 
         p["seq"] = p["seq"].strip()
         p["format"] = p["format"].strip()
-        task_str = p["seq"].encode("utf-8") +"_"+ p["format"].encode("utf-8")
+        task_str = p["seq"] +"_"+ p["format"]
         list_id = self.str2hash(task_str)
 
         res["id"] = list_id

src/Application/GlyLookup/GlyLookup.py

@@ -24,7 +24,7 @@ def form_task(self, p):
         res = {}
 
         p["seq"] = p["seq"].strip()
-        task_str = p["seq"].encode("utf-8")
+        task_str = p["seq"]
         list_id = self.str2hash(task_str)
 
         res["id"] = list_id

src/Application/Glymage/Glymage.py

@@ -583,15 +583,14 @@ def getimage():
             elif flask.request.method == "POST":
                 para = flask.request.form
             else:
-                raise RuntimeError
+                return self.error_image(), 404
 
             p = {}
             for k in dict(para).keys():
                 v = para.get(k)
                 if v:
                     p[k] = str(v)
 
-            print >>sys.stderr, p
             query, query_type = "", ""
             if "seq" in p:
                 query = p["seq"].strip()
@@ -617,7 +616,7 @@ def getimage():
                         except pygly.GlycanFormatter.GlycanParseError:
                             pass
                     if not newquery:
-                        raise RuntimeError
+                        return self.error_image(), 404
                     query = newquery
 
             if "acc" in p:
@@ -634,7 +633,7 @@ def getimage():
                 query_type = "task"
 
             if query == "" or query_type == "":
-                raise RuntimeError
+                return self.error_image(), 404
 
             p["notation"] = p.get("notation","snfg").lower()
             if p["notation"] not in ("snfg",):

src/Application/Glymage/image2hash.py

@@ -26,17 +26,17 @@ def s2h(s):
 
 for seqtype in ("wurcs","glycoct"):
     for dirpath, dirnames, filenames in os.walk("./"+seqtype):
-	for f in filenames:
+        for f in filenames:
             acc,extn = f.rsplit('.',1)
-	    if extn != 'txt':
-		continue
+            if extn != 'txt':
+                continue
             if not re.search(r'^G[0-9]{5}[A-Z]{2}$',acc):
-		continue
+                continue
             # print f,acc,extn
             s = open(os.path.join(dirpath,f)).read()
             if seqtype == "wurcs":
                 acc_to_cannonseq[acc] = s
-            h = s2h(s)
+            h = s2h(s.encode())
             seq_hash_to_acc[h] = acc
             if acc not in acc_to_seq_hash:
                 acc_to_seq_hash[acc] = []
@@ -59,11 +59,11 @@ def s2h(s):
             continue
 
         acc,ext = fn.split('.',1)
-        print acc,ext
+        print(acc,ext)
 
         fp = os.path.join(dirpath, fn)
 
-        imgstr = open(fp).read()
+        imgstr = open(fp,'rb').read()
         imgh = s2h(imgstr)
 
 

src/Application/Glymage/link.py

@@ -67,9 +67,9 @@
         except:
             continue
 
-            print src_abs
-            print dst_abs
-            print
+            print(src_abs)
+            print(dst_abs)
+            print()
 
 
     # print shash, notation, display

src/Application/Glymage/makeimages.sh

@@ -12,7 +12,7 @@ function dockerrun() {
   # docker wait $CID
 }
 
-PYSCR="python2 pygly-scripts"
+PYSCR="python3 pygly-scripts"
 SHSCR="pygly-scripts"
 DUMPSEQ="$PYSCR/dumpgtcseq.py"
 ALLIMG="$SHSCR/allimg.sh"
@@ -52,7 +52,7 @@ dockerrun $JSONMOTIF /work/snfg/compact
 
 CURDIR=`pwd`
 rm -rf image/hash
-( cd work; python2 $CURDIR/image2hash.py ../image/hash )
+( cd work; python3.12 $CURDIR/image2hash.py ../image/hash )
 rm -rf image/snfg
-python2 $CURDIR/link.py
+python3.12 $CURDIR/link.py
 ( cd image; tar czf image.tgz hash snfg error.png error.json imageinfo.tsv shash2acc.tsv cannonseq.tsv )

src/Application/MotifMatch/MotifMatch.py

@@ -168,7 +168,7 @@ def pre_start(self, worker_para):
             site = worker_para["glycomotif_version"]
         assert site in ["", "dev", "test"]
 
-        gm = pygly.GlycanResource.GlycoMotif()
+        gm = pygly.GlycanResource.GlycoMotif(usecache=False)
         gm.endpt = "https://glycomotif.glyomics.org/glycomotif"+site+"/sparql/query"
 
         wp = WURCS20Format()