SBML export / import implemented

xstreck1 · xstreck1 · commit fe340888b726 · 2017-04-15T17:51:31.000+02:00
diff --git a/javascript/common/tremppi.js b/javascript/common/tremppi.js
@@ -654,7 +654,7 @@ tremppi = {
         var file = $('#fileSelect')[0].files[0];
         if (typeof file === 'undefined')
         {
-            tremppi.logError("No file selected");
+            tremppi.log("No file selected", 'error');
         } else {
             data.append('file', file);
             var oReq = new XMLHttpRequest();
@@ -664,7 +664,7 @@ tremppi = {
                     tremppi.log("Project uploaded. " + oReq.responseText);
                     location.reload(true);
                 } else {
-                    tremppi.logError("Error " + oReq.responseText + " occurred when trying to upload the project.");
+                    tremppi.log("Error " + oReq.responseText + " occurred when trying to upload the project.", 'error');
                 }
             };
             oReq.send(data);
@@ -676,7 +676,7 @@ tremppi = {
         var file = $('#fileSelect')[0].files[0];
         if (typeof file === 'undefined')
         {
-            tremppi.logError("No file selected");
+            tremppi.log("No file selected", 'error');
         } else {
             data.append('file', file);
             var oReq = new XMLHttpRequest();
@@ -686,7 +686,7 @@ tremppi = {
                     tremppi.log("Project imported. " + oReq.responseText);
                     location.reload(true);
                 } else {
-                    tremppi.logError("Error " + oReq.responseText + " occurred when trying to import the project.");
+                    tremppi.log("Error " + oReq.responseText + " occurred when trying to import the project.", 'error');
                 }
             };
             oReq.send(data);
diff --git a/python/tremppi/db2sbml.py b/python/tremppi/db2sbml.py
@@ -195,6 +195,48 @@ def writeDBModelToSBML(database_path, sbml_output_path, modelRow=1):
         return 1
     libsbml.writeSBML(document, sbml_output_path)
 
+    conn.close()
+
+
+def database_to_editor(comps, regs):
+
+    model_root = { 'nodes' : [], 'edges' : [] }
+
+    id = 0
+    nodeIds = {}
+    for comp_name, comp_max  in comps:
+        nodeIds[comp_name] = 'n' + str(id)
+        model_root['nodes'].append(
+            {
+                'data' :
+                {
+                    'Name' : comp_name,
+                    'MaxActivity': str(comp_max),
+                    'Label' : comp_name + ':' + str(comp_max),
+                    'id' : nodeIds[comp_name]
+                }
+            }
+        )
+        id += 1
+
+
+    id = 0
+    for source, threshold, target  in regs:
+        model_root['edges'].append(
+            {
+                'data' :
+                {
+                    'source' : nodeIds[source],
+                    'target' : nodeIds[target],
+                    'Threshold': str(threshold),
+                    'Label': 'Free',
+                    'id' : 'e' + str(id)
+                }
+            }
+        )
+        id += 1
+
+    return model_root
 
 #writeDBModelToSBML('./data/databases/bacteriophage.sqlite', './data/sbml/db2sbml_output.sbml', modelRow=3)
 #writeDBModelToSBML('./data/databases/modelDB.sqlite', './data/sbml/db2sbml_output.sbml', modelRow=1)
diff --git a/python/tremppi/query_responses.py b/python/tremppi/query_responses.py
@@ -18,6 +18,8 @@
 import sys
 import zipfile
 import shutil
+import sqlite3
+import json
 from os import replace, remove, makedirs, pathsep
 from os.path import dirname, join, basename, exists, split, commonprefix
 
@@ -30,8 +32,9 @@
 from .header import last_page_filename, data_folder, database_file, configure_filename, system
 from .project_files import write_projects, delete_project, save_file, get_log_data, is_project_folder
 from .server_errors import InvalidUsage, Conflict
-from .db2sbml import writeDBModelToSBML
+from .db2sbml import writeDBModelToSBML, database_to_editor
 from .sbml2db import writeSBMLToDBModel
+from .database_reader import read_regulations, read_components
 
 def wrong_get(app, url):
     raise InvalidUsage('unknown GET command ' + request.args['command'])
@@ -255,9 +258,16 @@ def importSBML(app, url):
 
     try:
         writeSBMLToDBModel(join(target_folder, data_folder, database_file), sbml_file)
+        with sqlite3.connect(join(target_folder, data_folder, database_file)) as conn:
+            comps = read_components(conn)
+            regs = read_regulations(conn)
+            json_root = database_to_editor(comps, regs)
+            json_string = json.dumps(json_root)
+        with open(join(target_folder, data_folder, 'editor.json'), "w+") as editor_file:
+            editor_file.write(json_string)
     except:
         shutil.rmtree(target_folder)
-        raise InvalidUsage('Failed to convert the file ' + file.filename)
+        raise InvalidUsage('Failed to convert the file ' + file.filename + ' error: ' + sys.exc_info()[0])
 
     write_projects(app.projects_path())
     return 'import successful'
diff --git a/python/tremppi/sbml2db.py b/python/tremppi/sbml2db.py
@@ -347,6 +347,7 @@ def writeSBMLToDBModel(database_path, sbml_input_path, use_species_name_attribut
     c.execute('INSERT INTO Parametrizations VALUES ({0})'.format(target_value_string))
 
     conn.commit()
+    conn.close()
     return(0)
 
 #end writeSBMLToDBModel
