Update and fix GUI for databases

Author: RJMW

beams/annotation.py

@@ -306,7 +306,7 @@ def annotate_adducts(source, db_out, ppm, lib, add=False):
     if isinstance(source, nx.classes.digraph.DiGraph):
         source = list(source.subgraph(c) for c in nx.weakly_connected_components(source))
 
-    if isinstance(source, list) and isinstance(source[0], nx.classes.digraph.DiGraph):
+    if isinstance(source, list) and len(source) > 0 and isinstance(source[0], nx.classes.digraph.DiGraph):
         for i, graph in enumerate(source):
             for assignment in _annotate_pairs_from_graph(graph, lib_pairs=lib_pairs, ppm=ppm):
                 cursor.execute("""INSERT OR REPLACE into adduct_pairs (peak_id_a, peak_id_b, label_a, label_b, ppm_error)
@@ -349,7 +349,7 @@ def annotate_isotopes(source, db_out, ppm, lib):
     if isinstance(source, nx.classes.digraph.DiGraph):
         source = list(source.subgraph(c) for c in nx.weakly_connected_components(source))
 
-    if isinstance(source, list) and isinstance(source[0], nx.classes.digraph.DiGraph):
+    if isinstance(source, list) and len(source) > 0 and isinstance(source[0], nx.classes.digraph.DiGraph):
 
         for graph in source:
 
@@ -359,7 +359,7 @@ def annotate_isotopes(source, db_out, ppm, lib):
 
                 y = abundances[assignment["label_a"]]['abundance'] * peaklist[assignment["peak_id_b"]]["intensity"]
                 x = abundances[assignment["label_b"]]['abundance'] * peaklist[assignment["peak_id_a"]]["intensity"]
-            
+
                 if x == 0.0 or y == 0.0:
                     atoms = None
                 else:
@@ -412,7 +412,7 @@ def annotate_oligomers(source, db_out, ppm, lib, maximum=2):
     if isinstance(source, nx.classes.digraph.DiGraph):
         source = list(source.subgraph(c) for c in nx.weakly_connected_components(source))
 
-    if isinstance(source, list) and isinstance(source[0], nx.classes.digraph.DiGraph):
+    if isinstance(source, list) and len(source) > 0 and isinstance(source[0], nx.classes.digraph.DiGraph):
 
         for graph in source:
 
@@ -679,7 +679,7 @@ def annotate_compounds(peaklist, lib_adducts, ppm, db_out, db_name, db_in=""):
                 conn_local = sqlite3.connect(os.path.join(path_dbs, db_local))
                 cursor_local = conn_local.cursor()
                 cursor_local.execute("SELECT name FROM sqlite_master WHERE type='table'")
-                if (db_name, ) not in cursor_local.fetchall():
+                if (db_name.strip(".sqlite"), ) not in cursor_local.fetchall():
                     raise ValueError("Database {} not available".format(db_name))
                 break
         if conn_local is None:

beams/grouping.py

@@ -29,7 +29,7 @@ def group_features(df, db_out, max_rt_diff=5.0, coeff_thres=0.7, pvalue_thres=1.
     graph = statistics.correlation_graphs(df_coeffs, df)
     sub_graphs = list(graph.subgraph(c) for c in nx.weakly_connected_components(graph))
     for i in range(len(sub_graphs)):
-        sub_graphs[i].graph["group_id"] = i + 1 # not stored in output - place holder
+        sub_graphs[i].graph["groupid"] = i + 1 # not stored in output - place holder
         sub_graph_edges = []
         # sort edges
         edges = sorted(sub_graphs[i].edges(data=True), key=lambda e: (e[0], e[1]))

beams/gui.py

@@ -10,6 +10,7 @@
 from PyQt5 import QtCore, QtGui, QtWidgets
 from beams.qt import form
 import sqlite3
+from collections import OrderedDict
 
 
 class BeamsApp(QtWidgets.QMainWindow, form.Ui_MainWindow):
@@ -51,7 +52,7 @@ def __init__(self, parent=None):
         self.checkBox_mz_digits.clicked.connect(self.create_summary)
         self.checkBox_convert_rt.clicked.connect(self.create_summary)
 
-        self.add_databases()
+        self.db_names = self.add_databases()
 
         self.pushButton_start.clicked.connect(self.run)  # When the button is pressed
 
@@ -134,15 +135,15 @@ def source_peak_patterns(self):
     def source_compounds(self):
         if self.checkBox_filename_reference.isChecked():
             self.listWidget_databases.setEnabled(False)
-            self.listWidget_categories.setEnabled(False)
+            # self.listWidget_categories.setEnabled(False)
             self.label_databases.setEnabled(False)
             self.pushButton_filename_reference.setEnabled(True)
             self.lineEdit_filename_reference.setEnabled(True)
         else:
             self.label_databases.setEnabled(True)
             self.listWidget_databases.setEnabled(True)
-            self.label_categories.setEnabled(False)
-            self.listWidget_categories.setEnabled(False)
+            # self.label_categories.setEnabled(False)
+            # self.listWidget_categories.setEnabled(False)
             self.pushButton_filename_reference.setEnabled(False)
             self.lineEdit_filename_reference.setEnabled(False)
 
@@ -208,7 +209,7 @@ def annotate_molecular_formulae(self):
     def annotate_compounds(self):
         if not self.checkBox_annotate_compounds.isChecked():
             self.listWidget_databases.setEnabled(False)
-            self.listWidget_categories.setEnabled(False)
+            # self.listWidget_categories.setEnabled(False)
             self.label_databases.setEnabled(False)
             self.checkBox_filename_reference.setEnabled(False)
             self.pushButton_filename_reference.setEnabled(False)
@@ -249,21 +250,29 @@ def create_summary(self):
                 self.spinBox_mz_digits.setEnabled(False)
 
     def add_databases(self):
-        path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data')
-        dbs = [fn for fn in os.listdir(path) if fn.endswith('.sqlite')]
-        conn = sqlite3.connect(os.path.join(path, dbs[0]))
+
+        path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data', 'databases')
+
+        list_databases = OrderedDict()
+        with open(os.path.join(path, "compound_databases.txt"), "r") as inp:
+           keys = inp.readline().strip().split("\t")
+           for line in inp:
+               line = line.split("\t")
+               if os.path.isfile(os.path.join(path, line[keys.index("filename_sqlite")])):
+                    list_databases[line[keys.index("filename_sqlite")]] = line[keys.index("description")]
+        conn = sqlite3.connect(os.path.join(path, list_databases.keys()[0]))
         cursor = conn.cursor()
         cursor.execute("""SELECT name FROM sqlite_master where type='table'""")
         db_names = [str(name[0]) for name in cursor.fetchall()]
-        for i, db in enumerate(dbs[1:]):
+        for i, db in enumerate(list_databases.keys()[1:]):
             cursor.execute("ATTACH DATABASE ? AS db?", (os.path.join(path, dbs[i+1]), i, ))
             cursor.execute("""SELECT name FROM db?.sqlite_master where type='table'""", (i, ))
             db_names.extend([str(name[0]) for name in cursor.fetchall()])
         self.listWidget_databases.setSelectionMode(QtWidgets.QListWidget.MultiSelection)
-        for db_name in db_names:
-            item = QtWidgets.QListWidgetItem(db_name)
+        for description in list_databases.values():
+            item = QtWidgets.QListWidgetItem(description)
             self.listWidget_databases.addItem(item)
-        return db_names
+        return dict((v, k) for k, v in list_databases.iteritems())
 
     def run(self):
 
@@ -331,6 +340,7 @@ def run(self):
                         QtWidgets.QMessageBox.critical(None, "Select file", "Provide a valid filename for adducts", QtWidgets.QMessageBox.Ok)
                 else:
                     QtWidgets.QMessageBox.critical(None, "Select file", "Provide a valid filename for adducts or 'Use default'", QtWidgets.QMessageBox.Ok)
+
                 annotation.annotate_adducts(inp, db_out=self.lineEdit_sql_database.text(), ppm=self.doubleSpinBox_ppm_error.value(), lib=lib)
                 print("Done")
 
@@ -435,13 +445,12 @@ def run(self):
                 QtWidgets.QMessageBox.critical(None, "Select file", "Provide a valid filename for adducts", QtWidgets.QMessageBox.Ok)
 
             if self.checkBox_filename_reference.isChecked():
-                annotation.annotate_compounds(df, lib_adducts=lib, ppm=self.doubleSpinBox_ppm_error.value(), db_out=self.lineEdit_sql_database.text(), db_in=self.lineEdit_filename_reference.text(), db_name=None)
+                annotation.annotate_compounds(df, lib_adducts=lib, ppm=self.doubleSpinBox_ppm_error.value(),
+                                              db_out=self.lineEdit_sql_database.text(), db_name=None, db_in=self.lineEdit_filename_reference.text())
             else:
-                path = 'data/BEAMS_DB.sqlite'
-                path_db = os.path.join(os.path.dirname(os.path.abspath(__file__)), path)
-                print(path_db)
                 for db_name in self.listWidget_databases.selectedItems():
-                    annotation.annotate_compounds(df, lib_adducts=lib, ppm=self.doubleSpinBox_ppm_error.value(), db_out=self.lineEdit_sql_database.text(), db_in=path_db, db_name=db_name.text())
+                    annotation.annotate_compounds(df, lib_adducts=lib, ppm=self.doubleSpinBox_ppm_error.value(),
+                                                  db_out=self.lineEdit_sql_database.text(), db_name=self.db_names[db_name.text()].strip(".sqlite"))
             print("Done")
             print
 

beams/qt/databases.py

@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'form.ui'
 #
-# Created by: PyQt5 UI code generator 5.10.1
+# Created by: PyQt5 UI code generator 5.10
 #
 # WARNING! All changes made in this file will be lost!
 
@@ -12,7 +12,7 @@ class Ui_MainWindow(object):
     def setupUi(self, MainWindow):
         MainWindow.setObjectName("MainWindow")
         MainWindow.setEnabled(True)
-        MainWindow.resize(795, 842)
+        MainWindow.resize(795, 835)
         MainWindow.setAnimated(False)
         self.centralwidget = QtWidgets.QWidget(MainWindow)
         self.centralwidget.setObjectName("centralwidget")
@@ -331,34 +331,26 @@ def setupUi(self, MainWindow):
         self.checkBox_annotate_compounds.setObjectName("checkBox_annotate_compounds")
         self.lineEdit_filename_reference = QtWidgets.QLineEdit(self.groupBox_annotate_compounds)
         self.lineEdit_filename_reference.setEnabled(False)
-        self.lineEdit_filename_reference.setGeometry(QtCore.QRect(410, 59, 161, 20))
+        self.lineEdit_filename_reference.setGeometry(QtCore.QRect(410, 70, 161, 20))
         self.lineEdit_filename_reference.setText("")
         self.lineEdit_filename_reference.setReadOnly(True)
         self.lineEdit_filename_reference.setObjectName("lineEdit_filename_reference")
         self.pushButton_filename_reference = QtWidgets.QPushButton(self.groupBox_annotate_compounds)
         self.pushButton_filename_reference.setEnabled(False)
-        self.pushButton_filename_reference.setGeometry(QtCore.QRect(580, 57, 71, 23))
+        self.pushButton_filename_reference.setGeometry(QtCore.QRect(580, 69, 71, 23))
         self.pushButton_filename_reference.setMinimumSize(QtCore.QSize(63, 23))
         self.pushButton_filename_reference.setObjectName("pushButton_filename_reference")
         self.checkBox_filename_reference = QtWidgets.QCheckBox(self.groupBox_annotate_compounds)
         self.checkBox_filename_reference.setEnabled(True)
-        self.checkBox_filename_reference.setGeometry(QtCore.QRect(410, 37, 251, 17))
+        self.checkBox_filename_reference.setGeometry(QtCore.QRect(410, 50, 251, 17))
         self.checkBox_filename_reference.setChecked(False)
         self.checkBox_filename_reference.setObjectName("checkBox_filename_reference")
         self.listWidget_databases = QtWidgets.QListWidget(self.groupBox_annotate_compounds)
-        self.listWidget_databases.setGeometry(QtCore.QRect(10, 50, 171, 91))
+        self.listWidget_databases.setGeometry(QtCore.QRect(10, 50, 381, 91))
         self.listWidget_databases.setObjectName("listWidget_databases")
-        self.listWidget_categories = QtWidgets.QListWidget(self.groupBox_annotate_compounds)
-        self.listWidget_categories.setEnabled(False)
-        self.listWidget_categories.setGeometry(QtCore.QRect(200, 50, 171, 91))
-        self.listWidget_categories.setObjectName("listWidget_categories")
         self.label_databases = QtWidgets.QLabel(self.groupBox_annotate_compounds)
         self.label_databases.setGeometry(QtCore.QRect(10, 30, 71, 16))
         self.label_databases.setObjectName("label_databases")
-        self.label_categories = QtWidgets.QLabel(self.groupBox_annotate_compounds)
-        self.label_categories.setEnabled(False)
-        self.label_categories.setGeometry(QtCore.QRect(200, 30, 71, 16))
-        self.label_categories.setObjectName("label_categories")
         self.groupBox_create_summary = QtWidgets.QGroupBox(self.centralwidget)
         self.groupBox_create_summary.setGeometry(QtCore.QRect(20, 657, 761, 101))
         self.groupBox_create_summary.setTitle("")
@@ -443,7 +435,7 @@ def setupUi(self, MainWindow):
         self.checkBox_convert_rt.raise_()
         MainWindow.setCentralWidget(self.centralwidget)
         self.menubar = QtWidgets.QMenuBar(MainWindow)
-        self.menubar.setGeometry(QtCore.QRect(0, 0, 795, 21))
+        self.menubar.setGeometry(QtCore.QRect(0, 0, 795, 22))
         self.menubar.setObjectName("menubar")
         self.menuAdd_example_data = QtWidgets.QMenu(self.menubar)
         self.menuAdd_example_data.setObjectName("menuAdd_example_data")
@@ -514,7 +506,6 @@ def retranslateUi(self, MainWindow):
         self.pushButton_filename_reference.setText(_translate("MainWindow", "Browse..."))
         self.checkBox_filename_reference.setText(_translate("MainWindow", "Reference file"))
         self.label_databases.setText(_translate("MainWindow", "Databases"))
-        self.label_categories.setText(_translate("MainWindow", "Categories"))
         self.pushButton_summary_filename.setText(_translate("MainWindow", "Save as..."))
         self.label_summary_filename.setText(_translate("MainWindow", "Summary:"))
         self.checkBox_mz_digits.setText(_translate("MainWindow", "Number of digits m/z:"))