Bring dev to the recent

demo/gencontrol.py

@@ -0,0 +1,45 @@
+import numpy as np
+import concore
+
+ysp = 3.0
+
+# controller function
+def controller(ym): 
+  if ym[0] < ysp:
+     return 1.01 * ym
+  else:
+     return 0.9 * ym
+
+# main
+concore.default_maxtime(150)
+concore.delay = 0.02
+
+# initial values -- transforms to string including the simtime as the 0th entry in the list
+init_simtime_u = "[0.0, 0.0]"
+init_simtime_ym = "[0.0, 0.0]"
+
+u = np.array([concore.initval(init_simtime_u)]).T
+while(concore.simtime<10):
+    while concore.unchanged():
+        ym = concore.read(concore.iport['SYM'],"ym",init_simtime_ym)
+    ym = np.array([ym]).T
+    #####
+    u = controller(ym)
+    #####
+    print("****"+str(concore.simtime) + ". u="+str(u) + "ym="+str(ym))
+    concore.write(concore.oport['SU'],"u",list(u.T[0]),delta=0)
+
+concore.write(concore.oport['CU'],"u",list(u.T[0]),delta=0)
+
+while(concore.simtime<concore.maxtime):
+    while concore.unchanged():
+        ym = concore.read(concore.iport['PYM'],"ym",init_simtime_ym)
+    ym = np.array([ym]).T
+    #####
+    u = controller(ym)
+    #####
+    print(str(concore.simtime) + ". u="+str(u) + "ym="+str(ym))
+    concore.write(concore.oport['CU'],"u",list(u.T[0]),delta=0)
+
+concore.write(concore.oport['SU'],"u",list(u.T[0]),delta=0)
+print("retry="+str(concore.retrycount))

fri/server/main.py

@@ -1,5 +1,6 @@
 from flask import Flask, request, jsonify, send_file, send_from_directory
 from werkzeug.utils import secure_filename
+import xml.etree.ElementTree as ET
 import os
 import subprocess
 from subprocess import call
@@ -18,6 +19,17 @@
 cors = CORS(app)
 app.config['CORS_HEADERS'] = 'Content-Type'
 
+def check_node_labels(graphml_file):
+    tree = ET.parse(graphml_file)
+    root = tree.getroot()
+    namespace = {'y': 'http://www.yworks.com/xml/graphml'}
+    node_labels = root.findall('.//y:NodeLabel', namespace)
+    for node_label in node_labels:
+        label = node_label.text
+        if label.endswith('.m'):
+            return True
+    return False
+
 # To upload multiple file. For example, /upload/test?apikey=xyz
 @app.route('/upload/<dir>', methods=['POST'])
 def upload(dir):
@@ -65,9 +77,14 @@ def upload(dir):
 # to download /build/<dir>?fetch=<graphml>. For example, /build/test?fetch=sample1&apikey=xyz
 @app.route('/build/<dir>', methods=['POST'])
 def build(dir):
-    graphml_file = request.args.get('fetch')  
+    graphml_file = request.args.get('fetch')
+    params = request.args.get('params')
+    docker = request.args.get('docker')
+    octave = request.args.get('octave')
+    maxtime = request.args.get('maxtime')
     apikey = request.args.get('apikey') 
     out_dir = request.args.get('outdir')
+    output_str = ""
     if(apikey == None):
         dirname = secure_filename(dir)
     else:
@@ -77,35 +94,132 @@ def build(dir):
         dir_path = os.path.abspath(os.path.join(concore_path, graphml_file)) #path for ./build
     else:
         dir_path = os.path.abspath(os.path.join(concore_path, out_dir)) #path for ./build
+
+    dotMCheck = check_node_labels(os.path.abspath(os.path.join(concore_path, makestudy_dir)) + '.graphml')
+    if((dotMCheck == False or octave == 'false') and os.path.isfile(os.path.abspath(os.path.join(concore_path, 'concore.octave')))):
+        if(platform.uname()[0]!='Windows'):
+            proc= call(["rm", "concore.octave"], cwd=concore_path)
+        else:
+            proc= call(["del", "concore.octave"], shell=True, cwd=concore_path)
+
+    if(octave == 'true' and dotMCheck):
+        if(platform.uname()[0]!='Windows'):
+            proc= call(["touch", "concore.octave"], cwd=concore_path)
+        else:
+            proc= open(os.path.abspath(os.path.join(concore_path, 'concore.octave')), 'x')
+
+
     if not os.path.exists(dir_path):
         if(platform.uname()[0]=='Windows'):
             if(out_dir == None or out_dir == ""):
-                proc= call(["makestudy", makestudy_dir], shell=True, cwd=concore_path)
+                if(docker == 'true'):
+                    try:
+                        output_bytes = subprocess.check_output(["makedocker", makestudy_dir], cwd=concore_path, shell=True)
+                        output_str = output_bytes.decode("utf-8")
+                        proc = 0
+                    except subprocess.CalledProcessError as e:
+                        output_str = f"Docker study creation failed with return code {e.returncode} (check duplicate directory)"
+                        proc = 1
+                else:
+                    try:
+                        output_bytes = subprocess.check_output(["makestudy", makestudy_dir], cwd=concore_path, shell=True)
+                        output_str = output_bytes.decode("utf-8")
+                        proc = 0
+                    except subprocess.CalledProcessError as e:
+                        output_str = f"Study creation failed with return code {e.returncode} (check duplicate directory)"
+                        proc = 1
             else:
-                proc= call(["makestudy", makestudy_dir, out_dir], shell=True, cwd=concore_path)
+                if(docker == 'true'):
+                    try:
+                        output_bytes = subprocess.check_output(["makedocker", makestudy_dir, out_dir], cwd=concore_path, shell=True)
+                        output_str = output_bytes.decode("utf-8")
+                        proc = 0
+                    except subprocess.CalledProcessError as e:
+                        output_str = f"Docker study creation failed with return code {e.returncode} (check duplicate directory)"
+                        proc = 1
+                else:
+                    try:
+                        output_bytes = subprocess.check_output(["makestudy", makestudy_dir, out_dir], cwd=concore_path, shell=True)
+                        output_str = output_bytes.decode("utf-8")
+                        proc = 0
+                    except subprocess.CalledProcessError as e:
+                        output_str = f"Study creation failed with return code {e.returncode} (check duplicate directory)"
+                        proc = 1
         else:
             if(out_dir == None or out_dir == ""):
-                proc= call(["./makestudy", makestudy_dir], cwd=concore_path)
+                if(docker == 'true'):
+                    try:
+                        output_bytes = subprocess.check_output(["./makedocker", makestudy_dir], cwd=concore_path)
+                        output_str = output_bytes.decode("utf-8")
+                        proc = 0
+                    except subprocess.CalledProcessError as e:
+                        output_str = f"Docker study creation failed with return code {e.returncode} (check duplicate directory)"
+                        proc = 1
+                else:
+                    try:
+                        output_bytes = subprocess.check_output(["./makestudy", makestudy_dir], cwd=concore_path)
+                        output_str = output_bytes.decode("utf-8")
+                        proc = 0
+                    except subprocess.CalledProcessError as e:
+                        output_str = f"Study creation failed with return code {e.returncode} (check duplicate directory)"
+                        proc = 1
             else:
-                proc= call(["./makestudy", makestudy_dir, out_dir], cwd=concore_path)
+                if(docker == 'true'):
+                    try:
+                        output_bytes = subprocess.check_output(["./makedocker", makestudy_dir, out_dir], cwd=concore_path)
+                        output_str = output_bytes.decode("utf-8")
+                        proc = 0
+                    except subprocess.CalledProcessError as e:
+                        output_str = f"Docker study creation failed with return code {e.returncode} (check duplicate directory)"
+                        proc = 1
+                else:
+                    try:
+                        output_bytes = subprocess.check_output(["./makestudy", makestudy_dir, out_dir], cwd=concore_path)
+                        output_str = output_bytes.decode("utf-8")
+                        proc = 0
+                    except subprocess.CalledProcessError as e:
+                        output_str = f"Study creation failed with return code {e.returncode} (check duplicate directory)"
+                        proc = 1
         if(proc == 0):
             resp = jsonify({'message': 'Directory successfully created'})
             resp.status_code = 201
         else:
             resp = jsonify({'message': 'There is an Error'})
-            resp.status_code = 500   
+            resp.status_code = 500
     if(platform.uname()[0]=='Windows'):
-        call(["build"], cwd=dir_path, shell=True)
+        try:
+            output_bytes = subprocess.check_output("build", cwd=dir_path, shell=True)
+            output_str = output_str + output_bytes.decode("utf-8")
+            resp = jsonify({'message': 'Directory successfully created', 'output': output_str})
+        except subprocess.CalledProcessError as e:
+            output_str = f"Build failed with return code {e.returncode}"
+            resp = jsonify({'message': 'Build Failed', 'output': output_str})
+            resp.status_code = 500
+        if(maxtime != None and maxtime != ''):
+            proc=call(["maxtime", maxtime],shell=True, cwd=dir_path)
+        if(params != None and params != ''):
+            proc=call(["params", params],shell=True, cwd=dir_path)
     else:
-        call(["./build"], cwd=dir_path)  
+        try:
+            output_bytes = subprocess.check_output("./build", cwd=dir_path)
+            output_str = output_str + output_bytes.decode("utf-8")
+            resp = jsonify({'message': 'Directory successfully created', 'output': output_str})
+        except subprocess.CalledProcessError as e:
+            output_str = f"Build failed with return code {e.returncode}"
+            resp = jsonify({'message': 'Build Failed', 'output': output_str})
+            resp.status_code = 500
+        if(maxtime != None and maxtime != ''):
+            proc=call(["./maxtime", maxtime], cwd=dir_path)
+        if(params != None and params != ''):
+            proc=call(["./params", params], cwd=dir_path)
     return resp 
 
 @app.route('/debug/<dir>', methods=['POST'])
 def debug(dir):
     dir_name = secure_filename(dir)
     dir_path = os.path.abspath(os.path.join(concore_path, dir_name))
     if(platform.uname()[0]=='Windows'):
-        proc=call(["debug"],shell=True, cwd=dir_path)
+        proc = call(["debug"],shell=True, cwd=dir_path)
     else:
         proc = call(["./debug"], cwd=dir_path)
     if(proc == 0):
@@ -122,7 +236,7 @@ def run(dir):
     dir_name = secure_filename(dir)
     dir_path = os.path.abspath(os.path.join(concore_path, dir_name))
     if(platform.uname()[0]=='Windows'):
-        proc=call(["run"],shell=True, cwd=dir_path)
+        proc = call(["run"],shell=True, cwd=dir_path)
     else:
         proc = call(["./run"], cwd=dir_path)
     if(proc == 0):
@@ -139,7 +253,7 @@ def stop(dir):
     dir_name = secure_filename(dir)
     dir_path = os.path.abspath(os.path.join(concore_path, dir_name))
     if(platform.uname()[0]=='Windows'):
-        proc=call(["stop"],shell=True, cwd=dir_path)
+        proc = call(["stop"],shell=True, cwd=dir_path)
     else:
         proc = call(["./stop"], cwd=dir_path)
     if(proc == 0):
@@ -154,12 +268,23 @@ def stop(dir):
 
 @app.route('/clear/<dir>', methods=['POST'])
 def clear(dir):
+    unlock = request.args.get('unlock')
+    params = request.args.get('params')
+    maxtime = request.args.get('maxtime')
     dir_name = secure_filename(dir)
     dir_path = os.path.abspath(os.path.join(concore_path, dir_name))
     if(platform.uname()[0]=='Windows'):
-        proc=call(["clear"],shell=True, cwd=dir_path)
+        proc = call(["clear"],shell=True, cwd=dir_path)
+        if(maxtime != None and maxtime != ''):
+            proc = call(["maxtime", maxtime],shell=True, cwd=dir_path)
+        if(params != None and params != ''):
+            proc = call(["params", params],shell=True, cwd=dir_path)
     else:
         proc = call(["./clear"], cwd=dir_path)
+        if(maxtime != None and maxtime != ''):
+            proc = call(["./maxtime", maxtime], cwd=dir_path)
+        if(params != None and params != ''):
+            proc = call(["./params", params], cwd=dir_path)
     if(proc == 0):
         resp = jsonify({'message': 'result deleted'})
         resp.status_code = 201
@@ -191,7 +316,7 @@ def download(dir):
 def destroy(dir):
     dir = secure_filename(dir)
     if(platform.uname()[0]=='Windows'):
-        proc=call(["destroy", dir],shell=True, cwd=concore_path)
+        proc = call(["destroy", dir],shell=True, cwd=concore_path)
     else:
         proc = call(["./destroy", dir], cwd=concore_path)
     if(proc == 0):
@@ -201,7 +326,31 @@ def destroy(dir):
     else:
         resp = jsonify({'message': 'There is an Error'})
         resp.status_code = 500
-        return resp   
+        return resp
+
+@app.route('/library/<dir>', methods=['POST'])
+def library(dir):
+    dir_name = secure_filename(dir)
+    dir_path = os.path.abspath(os.path.join(concore_path, dir_name))
+    filename = request.args.get('filename')
+    library_path = request.args.get('path')
+    proc = 0
+    if (library_path == None or library_path  == ''):
+        library_path = "../tools"
+    if(platform.uname()[0]=='Windows'):
+        proc = subprocess.check_output(["..\library", library_path, filename],shell=True, cwd=dir_path)
+    else:
+        proc = subprocess.check_output(["../library", library_path, filename], cwd=dir_path)
+    if(proc != 0):
+        resp = jsonify({'message': proc.decode("utf-8")})
+        resp.status_code = 201
+        return resp
+    else:
+        resp = jsonify({'message': 'There is an Error'})
+        resp.status_code = 500
+        return resp
+
+
 
 @app.route('/getFilesList/<dir>', methods=['POST'])
 def getFilesList(dir):

humanc/dummy/README.md

@@ -0,0 +1 @@
+# Human cardiac (humanc) models

library

@@ -0,0 +1,36 @@
+#!/bin/bash
+if [ $# = 0 ]
+  then
+    echo "library -- create a link that references "library" program or dir"
+  else
+    tooldir="../tools"
+    if [ $# = 1 ]
+      then
+        filename=$1
+      elif [ $# = 2 ]
+      then
+        tooldir=$1
+        filename=$2
+      else
+        echo "too many args"
+        exit
+    fi
+    if [ -e $filename ]
+     then
+       echo "cannot create library link over existing file"
+       exit
+     fi
+    if [ -d $tooldir ]
+     then
+       if [ -e $tooldir/$filename ]
+         then
+           ln -s $tooldir/$filename $filename
+           echo "library link created"
+         else
+           echo "$filename does not exist in $tooldir"
+       fi
+     else
+       echo "$tooldir does not exist"
+    fi
+fi
+

library.bat

@@ -0,0 +1,25 @@
+@echo off
+if "%2" == "" (
+  if exist "..\tools\%1" (
+    if exist "%1" (
+      echo "cannot create library link over existing file"
+    ) else (
+      echo "mklink %1 ..\tools\%1"
+      mklink "%1" "..\tools\%1"
+    )
+  ) else (
+    echo "..\tools\%1 does not exist"
+  )
+) else (
+  if exist "%1\%2" (
+    if exist "%2" (
+      echo "cannot create library link over existing file"
+    ) else (
+      echo "mklink %2 %1\%2"
+      mklink "%2" "%1\%2"
+    )
+  ) else (
+    echo "%1\%2 does not exist"
+  )
+)
+