diff --git a/job/magma/__init__.py b/job/magma/__init__.py index 6cb7511..b273267 100644 --- 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 index 0f14396..4845c53 100644 --- 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 index 5e47273..42b023e 100644 --- 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 index 0201766..a67d773 100644 --- a/web/magmaweb/templates/help.mak +++ b/web/magmaweb/templates/help.mak @@ -16,8 +16,8 @@

MAGMa Help page

Home page

The home page enables to run a new MAGMa job. This requires three types of input: -

MS Data

- MS Data can be imported, either as file or via the text field, as: +

LC-MS/MS Data

+ LC-MS/MS Data can be imported, either as file or via the text field, as: