Improved output file names

MDANSE/Src/MDANSE/Framework/Configurators/HDFTrajectoryConfigurator.py

@@ -48,8 +48,11 @@ def configure(self, value):
         self._original_input = value
 
         InputFileConfigurator.configure(self, value)
-
-        inputTraj = IInputData.create("HDFTrajectoryInputData", self["value"])
+        try:
+            inputTraj = IInputData.create("HDFTrajectoryInputData", self["value"])
+        except KeyError:
+            self.error_status = f"Could not use {value} as input trajectory"
+            return
 
         self["hdf_trajectory"] = inputTraj
 

MDANSE/Src/MDANSE/Framework/Configurators/OutputFilesConfigurator.py

@@ -52,6 +52,7 @@ def __init__(self, name, formats=None, **kwargs):
         self._formats = (
             formats if formats is not None else OutputFilesConfigurator._default[-1]
         )
+        self._forbidden_files = []
 
     def configure(self, value):
         """
@@ -98,7 +99,16 @@ def configure(self, value):
 
         self["root"] = root
         self["formats"] = formats
-        self["files"] = ["%s%s" % (root, IFormat.create(f).extension) for f in formats]
+        self["files"] = []
+        for extension in [IFormat.create(f).extension for f in formats]:
+            if extension in root[-len(extension) :]:
+                self["files"].append(root)
+            else:
+                self["files"].append(root + extension)
+        for file in self["files"]:
+            if os.path.abspath(file) in self._forbidden_files:
+                self.error_status = f"File {file} is either open or being written into. Please pick another name."
+                return
 
         self["value"] = self["files"]
         self["log_level"] = logs

MDANSE/Src/MDANSE/Framework/Configurators/OutputStructureConfigurator.py

@@ -51,6 +51,7 @@ def __init__(self, name, formats=None, **kwargs):
         IConfigurator.__init__(self, name, **kwargs)
 
         self._formats = [fmt for fmt in ioformats if ioformats[fmt].can_write]
+        self._forbidden_files = []
 
     def configure(self, value):
         """
@@ -87,6 +88,9 @@ def configure(self, value):
         self["root"] = root
         self["format"] = format
         self["file"] = root
+        if os.path.abspath(self["file"]) in self._forbidden_files:
+            self.error_status = f"File {self['file']} is either open or being written into. Please pick another name."
+            return
         self["log_level"] = logs
         if logs == "no logs":
             self["write_logs"] = False

MDANSE/Src/MDANSE/Framework/Configurators/OutputTrajectoryConfigurator.py

@@ -54,6 +54,7 @@ def __init__(self, name, format=None, **kwargs):
         self._format = "MDTFormat"
         self._dtype = np.float64
         self._compression = "none"
+        self._forbidden_files = []
 
     def configure(self, value: tuple):
         self._original_input = value
@@ -95,6 +96,9 @@ def configure(self, value: tuple):
         if not self["extension"] in temp_name[-5:]:  # capture most extension lengths
             temp_name += self["extension"]
         self["file"] = temp_name
+        if os.path.abspath(self["file"]) in self._forbidden_files:
+            self.error_status = f"File {self['file']} is either open or being written into. Please pick another name."
+            return
         self["dtype"] = self._dtype
         self["compression"] = self._compression
         self["log_level"] = logs

MDANSE/Src/MDANSE/Framework/Converters/DCD.py

@@ -275,6 +275,8 @@ class DCD(Converter):
     Converts a DCD trajectory to a HDF trajectory.
     """
 
+    label = "DCD"
+
     settings = collections.OrderedDict()
     settings["pdb_file"] = (
         "InputFileConfigurator",

MDANSE/Src/MDANSE/Framework/Converters/VASP.py

@@ -34,7 +34,7 @@ class VASP(Converter):
     Converts a VASP trajectory to a HDF trajectory.
     """
 
-    label = "VASP (>=5)"
+    label = "VASP v5"
 
     settings = collections.OrderedDict()
     settings["xdatcar_file"] = (

MDANSE/Src/MDANSE/Framework/Jobs/Infrared.py

@@ -26,7 +26,7 @@ class Infrared(IJob):
 
     enabled = True
 
-    label = "Dipole AutoCorrelation Function"
+    label = "Infrared Spectrum"
 
     category = (
         "Analysis",

MDANSE/Src/MDANSE/Framework/Session/CurrentSession.py

@@ -35,7 +35,7 @@ def load_session(self, fname: str):
 class SessionSettings(AbstractSession):
     def __init__(self):
         super().__init__()
-        self.main_path = "."
+        self.main_path = os.path.abspath(".")
 
     def create_structured_project(self):
         self.relative_paths = {

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/AseInputFileWidget.py

@@ -13,6 +13,8 @@
 #    You should have received a copy of the GNU General Public License
 #    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 #
+import os
+
 from qtpy.QtWidgets import QLineEdit, QPushButton, QFileDialog, QComboBox
 from qtpy.QtCore import Slot
 from ase.io.formats import filetype
@@ -37,10 +39,10 @@ def __init__(self, *args, **kwargs):
             parent = kwargs.get("parent", None)
             self.default_path = parent.default_path
         except KeyError:
-            self.default_path = "."
+            self.default_path = os.path.abspath(".")
             LOG.error("KeyError in InputFileWidget - can't get default path.")
         except AttributeError:
-            self.default_path = "."
+            self.default_path = os.path.abspath(".")
             LOG.error("AttributeError in InputFileWidget - can't get default path.")
         default_value = kwargs.get("default", "")
         if self._tooltip:

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/InputFileWidget.py

@@ -33,29 +33,19 @@ def __init__(self, *args, file_dialog=QFileDialog.getOpenFileName, **kwargs):
         else:
             default_value = ""
         parent = kwargs.get("parent", None)
+        self._parent = parent
         if parent is not None:
             self._job_name = parent._job_name
             self._settings = parent._settings
         try:
-            paths_group = self._settings.group("paths")
-            try:
-                self.default_path = paths_group.get(self._job_name)
-            except KeyError:
-                paths_group.add(
-                    self._job_name,
-                    ".",
-                    f"The filesystem path recently used by {self._job_name}",
-                )
-                self.default_path = "."
+            parent = kwargs.get("parent", None)
+            self.default_path = parent._default_path
+        except KeyError:
+            self.default_path = os.path.abspath(".")
+            LOG.error("KeyError in OutputFilesWidget - can't get default path.")
         except AttributeError:
-            try:
-                self.default_path = parent.default_path
-            except KeyError:
-                self.default_path = "."
-                LOG.error("KeyError in InputFileWidget - can't get default path.")
-            except AttributeError:
-                self.default_path = "."
-                LOG.error("AttributeError in InputFileWidget - can't get default path.")
+            self.default_path = os.path.abspath(".")
+            LOG.error("AttributeError in OutputFilesWidget - can't get default path.")
         default_value = kwargs.get("default", "")
         if self._tooltip:
             self._tooltip_text = self._tooltip
@@ -95,15 +85,10 @@ def valueFromDialog(self):
         This will start a FileDialog, take the resulting path,
         and emit a signal to update the value show by the GUI.
         """
-        paths_group = self._settings.group("paths")
-        try:
-            self.default_path = paths_group.get(self._job_name)
-        except:
-            LOG.warning(f"session.get_path failed for {self._job_name}")
         new_value = self._file_dialog(
             self.parent(),  # the parent of the dialog
             "Load file",  # the label of the window
-            self.default_path,  # the initial search path
+            self._parent._default_path,  # the initial search path
             self._qt_file_association,  # text string specifying the file name filter.
         )
         if new_value is not None and new_value[0]:
@@ -113,7 +98,8 @@ def valueFromDialog(self):
                 LOG.info(
                     f"Settings path of {self._job_name} to {os.path.split(new_value[0])[0]}"
                 )
-                paths_group.set(self._job_name, os.path.split(new_value[0])[0])
+                if self._parent is not None:
+                    self._parent._default_path = os.path.split(new_value[0])[0]
             except:
                 LOG.error(
                     f"session.set_path failed for {self._job_name}, {os.path.split(new_value[0])[0]}"

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/OutputFilesWidget.py

@@ -13,8 +13,6 @@
 #    You should have received a copy of the GNU General Public License
 #    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 #
-import glob
-import itertools
 import os
 import os.path
 
@@ -35,18 +33,30 @@ def __init__(self, *args, **kwargs):
         super().__init__(*args, layout_type="QGridLayout", **kwargs)
         default_value = self._configurator.default
         try:
-            parent = kwargs.get("parent", None)
-            self.default_path = parent.default_path
+            self._parent = kwargs.get("parent", None)
+            self.default_path = self._parent._default_path
         except KeyError:
-            self.default_path = "."
+            self.default_path = os.path.abspath(".")
             LOG.error("KeyError in OutputFilesWidget - can't get default path.")
         except AttributeError:
-            self.default_path = "."
+            self.default_path = os.path.abspath(".")
             LOG.error("AttributeError in OutputFilesWidget - can't get default path.")
+        else:
+            self._session = self._parent._parent_tab._session
+        try:
+            self._parent = kwargs.get("parent", None)
+            jobname = str(self._parent._job_instance.label).replace(" ", "")
+            guess_name = os.path.join(self.default_path, jobname + "_result1")
+        except:
+            guess_name = default_value[0]
+            LOG.error("It was not possible to get the job name from the parent")
+        while os.path.exists(guess_name + ".mda"):
+            prefix, number = guess_name.split("_result")
+            guess_name = prefix + "_result" + str(1 + int(number))
         self.file_association = "Output file name (*)"
         self._value = default_value
-        self._field = QLineEdit(default_value[0], self._base)
-        self._field.setPlaceholderText(default_value[0])
+        self._field = QLineEdit(guess_name, self._base)
+        self._field.setPlaceholderText(guess_name)
         self.type_box = CheckableComboBox(self._base)
         self.type_box.addItems(self._configurator.formats)
         self.type_box.set_default("MDAFormat")
@@ -92,6 +102,10 @@ def file_dialog(self):
         This will start a FileDialog, take the resulting path,
         and emit a signal to update the value show by the GUI.
         """
+        try:
+            self.default_path = self._parent._default_path
+        except AttributeError:
+            self.default_path = os.path.abspath(".")
         new_value = QFileDialog.getSaveFileName(
             self._base,  # the parent of the dialog
             "Save files",  # the label of the window
@@ -102,44 +116,13 @@ def file_dialog(self):
             self._field.setText(new_value[0])
             self.updateValue()
 
-    @staticmethod
-    def _get_unique_filename(directory, basename):
-        filesInDirectory = [
-            os.path.join(directory, e)
-            for e in itertools.chain(
-                glob.iglob(os.path.join(directory, "*")),
-                glob.iglob(os.path.join(directory, ".*")),
-            )
-            if os.path.isfile(os.path.join(directory, e))
-        ]
-        basenames = [os.path.splitext(f)[0] for f in filesInDirectory]
-
-        initialPath = path = os.path.join(directory, basename)
-        comp = 1
-        while True:
-            if path in basenames:
-                path = "%s(%d)" % (initialPath, comp)
-                comp += 1
-                continue
-            return path
-
     def get_widget_value(self):
+        self._configurator._forbidden_files = self._session.reserved_filenames()
         filename = self._field.text()
         if len(filename) < 1:
             filename = self._default_value[0]
 
         formats = self.type_box.checked_values()
         log_level = self.logs_combo.currentText()
 
-        return (filename, formats, log_level)
-
-    def set_data(self, datakey):
-        basename = "%s_%s" % (
-            os.path.splitext(os.path.basename(datakey))[0],
-            self._parent.type,
-        )
-        trajectoryDir = os.path.dirname(datakey)
-
-        path = OutputFilesWidget._get_unique_filename(trajectoryDir, basename)
-
-        self._filename.SetValue(path)
+        return (os.path.abspath(filename), formats, log_level)

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/OutputStructureWidget.py

@@ -13,8 +13,6 @@
 #    You should have received a copy of the GNU General Public License
 #    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 #
-import glob
-import itertools
 import os
 import os.path
 
@@ -37,17 +35,24 @@ def __init__(self, *args, **kwargs):
             parent = kwargs.get("parent", None)
             self.default_path = parent.default_path
         except KeyError:
-            self.default_path = "."
+            self.default_path = os.path.abspath(".")
             LOG.error("KeyError in OutputTrajectoryWidget - can't get default path.")
         except AttributeError:
-            self.default_path = "."
+            self.default_path = os.path.abspath(".")
             LOG.error(
                 "AttributeError in OutputTrajectoryWidget - can't get default path."
             )
+        try:
+            parent = kwargs.get("parent", None)
+            jobname = str(parent._job_instance.label).replace(" ", "")
+            guess_name = os.path.join(self.default_path, "POSCAR")
+        except:
+            guess_name = default_value[0]
+            LOG.error("It was not possible to get the job name from the parent")
         self.file_association = "Output file name (*)"
         self._value = default_value
-        self._field = QLineEdit(default_value[0], self._base)
-        self._field.setPlaceholderText(default_value[0])
+        self._field = QLineEdit(guess_name, self._base)
+        self._field.setPlaceholderText(guess_name)
         self.format_box = QComboBox(self._base)
         self.format_box.addItems(self._configurator._formats)
         self.format_box.setCurrentText(default_value[1])
@@ -108,31 +113,10 @@ def file_dialog(self):
             self._field.setText(new_value[0])
             self.updateValue()
 
-    @staticmethod
-    def _get_unique_filename(directory, basename):
-        filesInDirectory = [
-            os.path.join(directory, e)
-            for e in itertools.chain(
-                glob.iglob(os.path.join(directory, "*")),
-                glob.iglob(os.path.join(directory, ".*")),
-            )
-            if os.path.isfile(os.path.join(directory, e))
-        ]
-        basenames = [os.path.splitext(f)[0] for f in filesInDirectory]
-
-        initialPath = path = os.path.join(directory, basename)
-        comp = 1
-        while True:
-            if path in basenames:
-                path = "%s(%d)" % (initialPath, comp)
-                comp += 1
-                continue
-            return path
-
     def get_widget_value(self):
         filename = self._field.text()
         if len(filename) < 1:
             filename = self._default_value[0]
         format = self.format_box.currentText()
         log_level = self.logs_combo.currentText()
-        return (filename, format, log_level)
+        return (os.path.abspath(filename), format, log_level)