tomwer 0.6.0b0__tar.gz → 0.6.0b3__tar.gz

home/payno/.local/share/virtualenvs/tomwer_venv/bin/tomwer

@@ -1,6 +1,6 @@
 #!/home/payno/.local/share/virtualenvs/tomwer_venv/bin/python
-# EASY-INSTALL-ENTRY-SCRIPT: 'tomwer==0.6.0b0','console_scripts','tomwer'
-__requires__ = 'tomwer==0.6.0b0'
+# EASY-INSTALL-ENTRY-SCRIPT: 'tomwer==0.6.0b3','console_scripts','tomwer'
+__requires__ = 'tomwer==0.6.0b3'
 import re
 import sys
 from pkg_resources import load_entry_point
@@ -8,5 +8,5 @@ from pkg_resources import load_entry_point
 if __name__ == '__main__':
     sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0])
     sys.exit(
-        load_entry_point('tomwer==0.6.0b0', 'console_scripts', 'tomwer')()
+        load_entry_point('tomwer==0.6.0b3', 'console_scripts', 'tomwer')()
     )

home/payno/.local/share/virtualenvs/tomwer_venv/lib/python3.7/site-packages/orangecontrib/tomwer/widgets/control/DataListOW.py

@@ -31,8 +31,7 @@ from Orange.widgets import widget, gui
 from silx.gui import qt
 from tomwer.core.utils import logconfig
 from tomwer.gui.control.datalist import GenericDataListDialog
-from tomwer.core.process.scanlist import _ScanList
-from tomwer.core.scan.scanfactory import ScanFactory
+from tomwer.core.process.control.scanlist import _ScanList
 from tomwer.web.client import OWClient
 from tomwer.core.scan.scanbase import TomwerScanBase
 from Orange.widgets.settings import Setting

home/payno/.local/share/virtualenvs/tomwer_venv/lib/python3.7/site-packages/orangecontrib/tomwer/widgets/control/DataListenerOW.py

@@ -33,13 +33,19 @@ from orangecontrib.tomwer.widgets.utils import WidgetLongProcessing
 from Orange.widgets import widget, gui
 from Orange.widgets.widget import Output
 from tomwer.core.scan.scanbase import TomwerScanBase
-from tomwer.core.process.datalistener import DataListener
+from tomwer.core.scan.blissscan import BlissScan
+from tomwer.core.process.control.datalistener import DataListener
 from tomwer.utils import docstring
 from tomwer.synctools.datalistener import DataListenerQThread
 from tomwer.gui.control.datalistener import DataListenerWidget
 from tomwer.synctools.datalistener import MockDataListenerQThread
+from tomwer.synctools.stacks.control.datalistener import DataListenerProcessStack
+from tomwer.core.process.control.datalistener.rpcserver import (
+    send_signal_to_local_rpc_servers,
+)
 from tomwer.web.client import OWClient
 from Orange.widgets import settings
+from signal import SIGTERM, SIGKILL
 import functools
 import logging
 import signal
@@ -94,6 +100,8 @@ class DataListenerOW(widget.OWWidget, OWClient, WidgetLongProcessing, DataListen
         OWClient.__init__(self)
         WidgetLongProcessing.__init__(self)
         DataListener.__init__(self)
+        self._processingStack = DataListenerProcessStack()
+        self._processingStack.sigComputationEnded.connect(self._signal_scan_ready)
         self._widget = DataListenerWidget(parent=self)
         self._mock = False
 
@@ -106,6 +114,7 @@ class DataListenerOW(widget.OWWidget, OWClient, WidgetLongProcessing, DataListen
         self._widget.sigDeactivate.connect(self._deactivated)
         self._widget.sigConfigurationChanged.connect(self._jsonRPCConfigChanged)
         self._widget.sigAcquisitionEnded.connect(self._process_bliss_file_frm_tuple)
+        self._widget.sigServerStopped.connect(self._serverStopped)
 
         # manange server stop when delete directly the widget or stop by Ctr+C
         signal.signal(signal.SIGINT, self.handleSigTerm)
@@ -118,15 +127,13 @@ class DataListenerOW(widget.OWWidget, OWClient, WidgetLongProcessing, DataListen
 
     def _process_bliss_file_frm_tuple(self, t):
         master_file, entry, proposal_file, saving_file = t
-        try:
-            self.process_sample_file(
-                sample_file=master_file,
-                entry=str(entry) + ".1",
-                proposal_file=proposal_file,
-                master_sample_file=saving_file,
-            )
-        except Exception as e:
-            logger.error(e)
+        bliss_scan = BlissScan(
+            master_file=master_file,
+            entry=str(entry) + ".1",
+            proposal_file=proposal_file,
+            saving_file=saving_file,
+        )
+        self._processingStack.add(scan=bliss_scan)
 
     def _activated(self):
         self.activate(True)
@@ -134,28 +141,25 @@ class DataListenerOW(widget.OWWidget, OWClient, WidgetLongProcessing, DataListen
     def _deactivated(self):
         self.activate(False)
 
+    def _serverStopped(self):
+        """
+        Callback when the server is stopped
+        """
+        self.activate(False)
+
     @docstring(DataListener.activate)
     def activate(self, activate=True):
         if activate and not self.is_port_available():
             old = self._widget.blockSignals(True)
             self._widget.activate(activate=False)
             self._widget.blockSignals(old)
-            err = (
-                "port ({port}) of {host} already in use. Maybe an "
-                'other instance of "datalistener" is running in this '
-                "session or another tomwer session. As this widget is "
-                "connecting with bliss we enforce it to be unique. "
-                "If necessary you can hard kill server process ()"
-                "".format(port=self.port, host=self.host)
-            )
-            logger.warning(err)
-            mess = qt.QMessageBox(self)
-            mess.setIcon(qt.QMessageBox.Warning)
-            mess.setText(err)
-            mess.setModal(False)
-            mess.setWindowTitle("Unable to launch two listener in parallel")
-            mess.show()
-            return
+            dialog = _PortOccupyDialog(parent=self, port=self.port, host=self.host)
+            dialog.setModal(False)
+            if dialog.exec_() == qt.QDialog.Accepted:
+                if dialog.retry_connection:
+                    return self.activate(activate=True)
+            else:
+                return
 
         old = self._widget.blockSignals(True)
         self.set_configuration(self._widget.getBlissServerConfiguration())
@@ -165,6 +169,8 @@ class DataListenerOW(widget.OWWidget, OWClient, WidgetLongProcessing, DataListen
         self._widget.blockSignals(old)
 
     def _signal_scan_ready(self, scan):
+        if scan is None:
+            return
         assert isinstance(scan, TomwerScanBase)
         self.Outputs.data_out.send(scan)
 
@@ -219,6 +225,9 @@ class DataListenerOW(widget.OWWidget, OWClient, WidgetLongProcessing, DataListen
         thread.sigScanAdded.connect(
             self._widget._acquisitionUpdated, qt.Qt.DirectConnection
         )
+        thread.sigServerStop.connect(
+            self._widget._serverStopped, qt.Qt.DirectConnection
+        )
         return thread
 
     @docstring(DataListener.delete_listening_thread)
@@ -230,6 +239,7 @@ class DataListenerOW(widget.OWWidget, OWClient, WidgetLongProcessing, DataListen
             self._widget._acquisitionEnded
         )
         self._listening_thread.sigScanAdded.disconnect(self._widget._acquisitionUpdated)
+        self._listening_thread.sigServerStop.disconnect(self._widget._serverStopped)
         DataListener.delete_listening_thread(self)
 
     def _stopServerBeforeclosing(self):
@@ -247,15 +257,66 @@ class DataListenerOW(widget.OWWidget, OWClient, WidgetLongProcessing, DataListen
         return self._widget._historyWindow.scanHistory.model().rowCount()
 
 
-def start_app():
-    listener = DataListenerOW()
-    listener.activate()
-    listener.show()
+class _PortOccupyDialog(qt.QDialog):
+    def __init__(self, parent, port, host):
+        qt.QDialog.__init__(self, parent)
+        self.setLayout(qt.QVBoxLayout())
+        self._retry = False
+        self.port = port
+        self.host = host
+
+        mess = (
+            "port ({port}) of {host} already in use. \n Maybe an other "
+            "instance of `datalistener` is running in this session or "
+            "another tomwer session. \n As this widget is connecting with "
+            "bliss we enforce it to be unique.".format(port=port, host=host)
+        )
+        self.layout().addWidget(qt.QLabel(mess, self))
+        self.setWindowTitle("Unable to launch two listener in parallel")
+
+        types = qt.QDialogButtonBox.Cancel | qt.QDialogButtonBox.Retry
+        self._buttons = qt.QDialogButtonBox(self)
+        self._buttons.setStandardButtons(types)
+        self.layout().addWidget(self._buttons)
+
+        self._sendSIGTERMMsb = qt.QPushButton("send SIGTERM", self)
+        self._sendSIGTERMMsb.setToolTip(
+            "Try to send SIGTERM signal to the "
+            "local tomwer-rpcserver if any "
+            "occupies the reserved port"
+        )
+        self._buttons.addButton(self._sendSIGTERMMsb, qt.QDialogButtonBox.ActionRole)
+        self._sendSIGKILLMsb = qt.QPushButton("send SIGKILL", self)
+        self._sendSIGKILLMsb.setToolTip(
+            "Try to send SIGKILL signal to the "
+            "local tomwer-rpcserver if any "
+            "occupies the reserved port"
+        )
+        self._buttons.addButton(self._sendSIGKILLMsb, qt.QDialogButtonBox.ActionRole)
+
+        # set up
+        # for now we don't want to show "send signal" feature
+        self._sendSIGTERMMsb.hide()
+        self._sendSIGKILLMsb.hide()
+
+        # connect signal / slot
+        self._buttons.button(qt.QDialogButtonBox.Cancel).released.connect(self.reject)
+        self._buttons.button(qt.QDialogButtonBox.Retry).released.connect(
+            self._retry_connect
+        )
+        self._sendSIGTERMMsb.released.connect(self._emitSigterm)
+        self._sendSIGKILLMsb.released.connect(self._emitSigkill)
 
+    @property
+    def retry_connection(self):
+        return self._retry
 
-if __name__ == "__main__":
-    app = qt.QApplication([])
+    def _emitSigterm(self, *args, **kwargs):
+        send_signal_to_local_rpc_servers(SIGTERM, port=self.port)
 
-    start_app()
+    def _emitSigkill(self, *args, **kwargs):
+        send_signal_to_local_rpc_servers(SIGKILL, port=self.port)
 
-    exit(app.exec_())
+    def _retry_connect(self, *args, **kargs):
+        self._retry = True
+        self.accept()

home/payno/.local/share/virtualenvs/tomwer_venv/lib/python3.7/site-packages/orangecontrib/tomwer/widgets/control/DataTransfertOW.py

@@ -33,10 +33,9 @@ from Orange.widgets import settings
 from Orange.widgets.widget import Output, Input
 from silx.gui import qt
 from orangecontrib.tomwer.orange.settings import CallbackSettingsHandler
-from tomwer.core.process.datatransfert import FolderTransfert, logger as FTLogger
+from tomwer.core.process.control.datatransfert import FolderTransfert
 from tomwer.web.client import OWClient
 from tomwer.gui.control.datatransfert import DataTransfertSelector
-from tomwer.core.scan.scanfactory import ScanFactory
 from tomwer.core.scan.scanbase import TomwerScanBase
 
 logger = logging.getLogger(__name__)

home/payno/.local/share/virtualenvs/tomwer_venv/lib/python3.7/site-packages/orangecontrib/tomwer/widgets/control/DataWatcherOW.py

@@ -33,7 +33,7 @@ from Orange.widgets import widget, gui
 from Orange.widgets.settings import Setting
 from Orange.widgets.widget import Output
 from tomwer.core.scan.scanbase import TomwerScanBase
-from tomwer.core.process.datawatcher.datawatcher import _DataWatcher, logger as TDLogger
+from tomwer.core.process.control.datawatcher.datawatcher import _DataWatcher
 from tomwer.gui.control.datawatcher import DataWatcherWidget
 from tomwer.web.client import OWClient
 import functools

home/payno/.local/share/virtualenvs/tomwer_venv/lib/python3.7/site-packages/orangecontrib/tomwer/widgets/control/NXTomomillOW.py

@@ -32,7 +32,7 @@ from Orange.widgets import widget, gui
 from tomwer.gui.control.datalist import BlissHDF5DataListDialog
 from tomwer.core.scan.hdf5scan import HDF5TomoScan
 from tomwer.web.client import OWClient
-from tomwer.core.process.nxtomomill import NxTomomillProcess
+from tomwer.core.process.control.nxtomomill import NxTomomillProcess
 from Orange.widgets.settings import Setting
 from Orange.widgets.widget import Output, Input
 from tomwer.core.scan.scanbase import TomwerScanBase
@@ -330,7 +330,7 @@ class NXTomomillOW(widget.OWWidget, OWClient):
             if not self._userAgreeForOverwrite(output_file_path):
                 return
         try:
-            conv = nxtomomill_converter.h5_to_nx(
+            convs = nxtomomill_converter.h5_to_nx(
                 input_file_path=bliss_scan.master_file,
                 output_file=output_file_path,
                 entries=(bliss_scan.entry,),
@@ -347,14 +347,9 @@ class NXTomomillOW(widget.OWWidget, OWClient):
                 "Conversion error is: %s" % (bliss_scan, e)
             )
         else:
-            if len(conv) != 1:
-                logger.processFailed(
-                    "Something went wrong during file conversion. "
-                    "Unable to process the file {}."
-                    "".format(bliss_scan.master_file)
-                )
-            else:
-                conv_file, conv_entry = conv[0]
+            # in the case of zserie we can have several scan for one entry
+            for conv in convs:
+                conv_file, conv_entry = conv
                 scan_converted = HDF5TomoScan(scan=conv_file, entry=conv_entry)
                 logger.processSucceed(
                     "{} has been translated to {}" "".format(bliss_scan, scan_converted)

home/payno/.local/share/virtualenvs/tomwer_venv/lib/python3.7/site-packages/orangecontrib/tomwer/widgets/control/OldDataValidatorOW.py

@@ -34,7 +34,7 @@ import os
 from silx.gui import qt
 from Orange.widgets import widget, gui
 from Orange.widgets.widget import Output, Input
-from tomwer.core.process.scanvalidator import ScanValidator, logger as SVLogger
+from tomwer.core.process.control.scanvalidator import ScanValidator
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.core.scan.scanfactory import ScanFactory
 from tomwer.gui.qfolderdialog import QScanDialog
@@ -350,6 +350,12 @@ class OldDataValidatorOW(widget.OWWidget, ScanValidator):
     def getNScanToValidate(self):
         return len(self._scansToValidate)
 
+    def close(self) -> bool:
+        if self._memoryReleaser is not None:
+            self._memoryReleaser.exit()
+            self._memoryReleaser = None
+        super().close()
+
 
 class _VerticalLabel(qt.QLabel):
     """Display vertically the given text"""

home/payno/.local/share/virtualenvs/tomwer_venv/lib/python3.7/site-packages/orangecontrib/tomwer/widgets/control/TimerOW.py

@@ -31,7 +31,7 @@ from silx.gui import qt
 from Orange.widgets import widget, gui
 from Orange.widgets.settings import Setting
 from Orange.widgets.widget import Input, Output
-from tomwer.core.process.timer import Timer
+from tomwer.core.process.control.timer import Timer
 from tomwer.core.scan.scanbase import TomwerScanBase
 import logging
 

home/payno/.local/share/virtualenvs/tomwer_venv/lib/python3.7/site-packages/orangecontrib/tomwer/widgets/control/VolumeSymLinkOW.py

@@ -0,0 +1,160 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+
+__authors__ = ["H. Payno"]
+__license__ = "MIT"
+__date__ = "16/11/2020"
+
+
+from silx.gui import qt
+from Orange.widgets import widget, gui
+from tomwer.web.client import OWClient
+from Orange.widgets.settings import Setting
+from Orange.widgets.widget import Output, Input
+from tomwer.core.scan.scanbase import TomwerScanBase
+from tomwer.core.process.control.volumesymlink import OutputType, VolumeSymbolicLink
+import logging
+
+_logger = logging.getLogger(__name__)
+
+
+class VolumeSymLinkOW(widget.OWWidget, OWClient):
+    """
+    link volume reconstructed at proposal file if possible else under
+    the given folder
+    """
+
+    name = "volume symbolic link"
+    id = "orange.widgets.tomwer.control.VolumeSymLinkOW.VolumeSymLinkOW"
+    description = (
+        "create a symbolic link for the latest volume reconstructed on a "
+        "given folder"
+    )
+    icon = "icons/volumesymlink.svg"
+    priority = 200
+    category = "esrfWidgets"
+    keywords = [
+        "hdf5",
+        "tomwer",
+        "folder",
+        "volume",
+        "symlink",
+        "tomography",
+        "symbolic link",
+    ]
+
+    want_main_area = True
+    resizing_enabled = True
+    compress_signal = False
+
+    _scans = Setting(list())
+
+    class Inputs:
+        data_in = Input(name="data", type=TomwerScanBase, doc="scan to be process")
+
+    class Outputs:
+        data_out = Output(
+            name="data", type=TomwerScanBase, doc="one scan to be process"
+        )
+
+    def __init__(self, parent=None):
+        widget.OWWidget.__init__(self, parent)
+        OWClient.__init__(self)
+        self._mainWidget = _OutputDir(parent=self)
+        layout = gui.vBox(self.mainArea, self.name).layout()
+        layout.addWidget(self._mainWidget)
+
+    @Inputs.data_in
+    def process(self, scan):
+        if scan is None:
+            return
+        symlink_process = VolumeSymbolicLink()
+        symlink_process.set_properties(
+            {
+                "output_type": self._mainWidget.getOutputType(),
+                "output_folder": self._mainWidget.getOutputFolder(),
+            }
+        )
+        try:
+            scan = symlink_process.process(scan=scan)
+        except Exception as e:
+            _logger.processFailed(
+                "Failed to create symbolic link for {}".format(str(scan))
+            )
+        else:
+            _logger.processSucceed("Create symbolic link for {}".format(str(scan)))
+        self.Outputs.data_out.send(scan)
+
+
+class _OutputDir(qt.QGroupBox):
+    def __init__(self, parent):
+        qt.QGroupBox.__init__(self, parent)
+        self._button_grp = qt.QButtonGroup(self)
+        self._button_grp.setExclusive(True)
+        self.setLayout(qt.QGridLayout())
+        self._oneLevelCB = qt.QRadioButton(OutputType.ONE_LEVEL_UPPER.value, self)
+        self._button_grp.addButton(self._oneLevelCB)
+        self.layout().addWidget(self._oneLevelCB, 1, 0, 1, 3)
+        self._staticOpt = qt.QRadioButton("", self)
+        self._button_grp.addButton(self._staticOpt)
+        self.layout().addWidget(self._staticOpt, 2, 0, 1, 1)
+        self._qleFolder = qt.QLineEdit("", self)
+        self.layout().addWidget(self._qleFolder, 2, 1, 1, 1)
+        self._selectPB = qt.QPushButton("select", self)
+        self.layout().addWidget(self._selectPB, 2, 2, 1, 1)
+
+        # connect signal / slot
+        self._selectPB.released.connect(self._selectFolder)
+        self._qleFolder.editingFinished.connect(self._activeStaticOpt)
+
+        # set up
+        self._oneLevelCB.setChecked(True)
+
+    def _activeStaticOpt(self, *args, **kwargs):
+        self._staticOpt.setChecked(True)
+
+    def _selectFolder(self):
+        dialog = qt.QFileDialog(self)
+        dialog.setWindowTitle("Select destination folder for symbolic link")
+        dialog.setModal(1)
+        dialog.setFileMode(qt.QFileDialog.DirectoryOnly)
+
+        if not dialog.exec_():
+            dialog.close()
+            return None
+
+        dest_folder = dialog.selectedFiles()[0]
+        self._qleFolder.setText(dest_folder)
+
+    def getOutputType(self) -> OutputType:
+        if self._oneLevelCB.isChecked():
+            return OutputType.ONE_LEVEL_UPPER
+        elif self._staticOpt.isChecked():
+            return OutputType.STATIC
+        else:
+            raise TypeError("Not managed")
+
+    def getOutputFolder(self):
+        return self._qleFolder.text()