NLeSC · jspaaks · Apr 14, 2016
diff --git a/job/magma/__init__.py b/job/magma/__init__.py
@@ -498,7 +498,7 @@ def run_scenario(self, scenario, time_limit=None):
 
 class MsDataEngine(object):
 
-    """ Engine to read MS/MS data """
+    """ Engine to read LC-MS/MS data """
 
     def __init__(self, db_session, ionisation_mode, abs_peak_cutoff, mz_precision, mz_precision_abs,
                  precursor_mz_precision, max_ms_level, call_back_url=None):
@@ -825,7 +825,7 @@ def mass_from_formula(self, form):
 
 class AnnotateEngine(object):
 
-    """ Engine to perform MAGMa annotation of the MS/MS data based candidate molecules present
+    """ Engine to perform MAGMa annotation of the LC-MS/MS data based candidate molecules present
         or retrieved from a chemical database """
 
     def __init__(self, db_session, skip_fragmentation, max_broken_bonds, max_water_losses,
@@ -1301,7 +1301,7 @@ def query_on_mim(self, low, high, charge):
 
     def check_inchi(self, mim, inchikey14):
         """ Function to look up uploaded structures in PubChem based on inchikey. Returns refscore and reference.
-            Only available if PubChem database is installed locally""" 
+            Only available if PubChem database is installed locally"""
         if config.getboolean('magma job', 'structure_database.online'):
             return False
         self.c.execute('SELECT cid,name,refscore FROM molecules WHERE charge IN (-1,0,1) AND mim between ? and ? and inchikey = ?',
@@ -1335,7 +1335,7 @@ def __init__(self, dbfilename='', max_64atoms=False, online=True):
             self.conn = sqlite3.connect(dbfilename)
             self.conn.text_factory = str
             self.c = self.conn.cursor()
-        
+
     def query_online(self, low, high, charge):
         r = requests.post(self.service, data=json.dumps([low, high, charge, True]))
         try:
@@ -1421,7 +1421,7 @@ def export_molecules(self, output_format='sdf', filename=None, columns=None, sor
                     if column[:1] != '_' and column != 'mol' and column != 'metadata' and column != 'fragments' and column != 'smiles':
                         file.write(' ' + column + '=' + str(molecule.__getattribute__(column)).replace(" ","_"))
                 file.write('\n')
-                
+
         file.close()
 
     def export_assigned_molecules(self, filename=None):

diff --git a/job/magma/script/__init__.py b/job/magma/script/__init__.py
@@ -50,7 +50,7 @@ def __init__(self):
         sc = subparsers.add_parser("read_ms_data", help=self.read_ms_data.__doc__, description=self.read_ms_data.__doc__)
         sc.add_argument('-z', '--description', help="Description of the job (default: %(default)s)", default="",type=str)
         # read_ms_data arguments
-        sc.add_argument('ms_data', type=str, help="file with MS/MS data")
+        sc.add_argument('ms_data', type=str, help="file with LC-MS/MS data")
         sc.add_argument('-f', '--ms_data_format', help="MS data input format (default: %(default)s)", default="mzxml", choices=["mzxml", "mass_tree","form_tree_pos","form_tree_neg","mgf"])
         sc.add_argument('-i', '--ionisation_mode', help="Ionisation mode (default: %(default)s)", default="1", choices=["-1", "1"])
         sc.add_argument('-m', '--max_ms_level', help="Maximum MS level to be processsed (default: %(default)s)", default=10,type=int)
@@ -93,7 +93,7 @@ def __init__(self):
         sc = subparsers.add_parser("light", help=self.annotate.__doc__, description=self.light.__doc__)
         sc.add_argument('-z', '--description', help="Description of the job (default: %(default)s)", default="",type=str)
         # annotate arguments
-        sc.add_argument('ms_data', type=str, help="file with MS/MS data")
+        sc.add_argument('ms_data', type=str, help="file with LC-MS/MS data")
         sc.add_argument('-f', '--ms_data_format', help="MS data input format (default: %(default)s)", default="mass_tree", choices=["mass_tree","form_tree_pos","form_tree_neg","mgf"])
         sc.add_argument('-i', '--ionisation_mode', help="Ionisation mode (default: %(default)s)", default="1", choices=["-1", "1"])
         sc.add_argument('-e', '--output_format', help="Output format for ranked compound list (default: %(default)s)", default="smiles", choices=["smiles","sdf"])
@@ -130,7 +130,7 @@ def get_magma_session(self, db, description="",log='warn'):
     def init_db(self,args):
         """Initialize database"""
         return self.get_magma_session(args.db,"")
-    
+
     def light(self, args):
         """
         This option runs all MAGMa components in one go to generate a ranked list of compounds (smiles of SDF) for a single spectrum/spectral tree.

diff --git a/web/magmaweb/static/app/view/scan/UploadFieldSet.js b/web/magmaweb/static/app/view/scan/UploadFieldSet.js
@@ -71,7 +71,7 @@ Ext.define('Esc.magmaweb.view.scan.UploadFieldSet', {
   }, {
     name: 'ms_data_file',
     xtype: 'filefield',
-    emptyText: 'Upload MS/MS data file',
+    emptyText: 'Upload LC-MS/MS data file',
     anchor: '75%'
   }, {
     xtype: 'displayfield',

diff --git a/web/magmaweb/templates/help.mak b/web/magmaweb/templates/help.mak
@@ -16,8 +16,8 @@
                 <h1>MAGMa Help page</h1>
                 <h2 id="home">Home page</h2>
                 The home page enables to run a new MAGMa job. This requires three types of input:
-                <h3 id="msdata">MS Data</h3>
-                MS Data can be imported, either as file or via the text field, as:
+                <h3 id="msdata">LC-MS/MS Data</h3>
+                LC-MS/MS Data can be imported, either as file or via the text field, as:
                 <ul>
                     <li>mzXML: a public dataformat that can be generated with
                         <ul>

diff --git a/web/magmaweb/templates/home.mak b/web/magmaweb/templates/home.mak
@@ -63,7 +63,7 @@ Ext.onReady(function() {
     	margin: 5
     },
     items:[{
-    	title: 'MS Data',
+    	title: 'LC-MS/MS Data',
         xtype : 'uploadmsdatafieldset',
         flex: 1,
         minHeight: 490,