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Merge pull request #77 from dkratzert/76-better-control-over-import-o…
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…f-cif-data
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@dkratzert
dkratzert authored Oct 3, 2023
2 parents 3f7edc7 + fb99cfb commit ef9b3d8
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Showing 12 changed files with 530 additions and 69 deletions.
115 changes: 55 additions & 60 deletions finalcif/appwindow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,8 +42,9 @@
cif_file_open_dialog, \
bad_z_message, show_res_checksum_warning, show_hkl_checksum_warning, cif_file_save_dialog, show_yes_now_question
from finalcif.gui.finalcif_gui_ui import Ui_FinalCifWindow
from finalcif.gui.import_selector import ImportSelector
from finalcif.gui.loop_creator import LoopCreator
from finalcif.gui.loops import Loop
from finalcif.gui.loops import Loop, LoopTableModel, MyQTableView
from finalcif.gui.plaintextedit import MyQPlainTextEdit
from finalcif.gui.text_value_editor import MyTextTemplateEdit, TextEditItem
from finalcif.gui.vrf_classes import MyVRFContainer, VREF
Expand All @@ -53,8 +54,8 @@
from finalcif.template.templates import ReportTemplates
from finalcif.tools.download import MyDownloader
from finalcif.tools.dsrmath import my_isnumeric
from finalcif.tools.misc import next_path, do_not_import_keys, celltxt, to_float, do_not_import_from_stoe_cfx, \
cif_to_header_label, grouper, is_database_number, file_age_in_days, open_file, \
from finalcif.tools.misc import next_path, celltxt, to_float, cif_to_header_label, grouper, is_database_number, \
file_age_in_days, open_file, \
strip_finalcif_of_name
from finalcif.tools.options import Options
from finalcif.tools.platon import PlatonRunner
Expand Down Expand Up @@ -305,7 +306,7 @@ def connect_signals_and_slots(self) -> None:
self.ui.BackPushButton.clicked.connect(self.back_to_main)
self.ui.BackFromDepositPushButton.clicked.connect(self.back_to_main)
self.ui.ExploreDirButton.clicked.connect(self.explore_current_dir)
self.ui.LoopsPushButton.clicked.connect(self.ui.MainStackedWidget.go_to_loops_page)
self.ui.LoopsPushButton.clicked.connect(self._on_go_to_loops_page)
self.ui.LoopsPushButton.clicked.connect(
lambda x: self.ui.LoopsTabWidget.setCurrentIndex(1) if self.ui.LoopsTabWidget.count() > 0 else None)
self.ui.LoopsPushButton.clicked.connect(lambda x: self.ui.TemplatesStackedWidget.setCurrentIndex(1))
Expand All @@ -332,6 +333,7 @@ def connect_signals_and_slots(self) -> None:
self.ui.CODpushButton.clicked.connect(self.open_cod_page)
self.ui.CCDCpushButton.clicked.connect(self._ccdc_deposit)
self.ui.newLoopPushButton.clicked.connect(self._go_to_new_loop_page)
self.ui.deleteLoopButton.clicked.connect(self._on_delete_current_loop)
#
save_shortcut = QShortcut(QtGui.QKeySequence('Ctrl+S'), self)
save_shortcut.activated.connect(self.save_current_cif_file)
Expand Down Expand Up @@ -385,6 +387,10 @@ def connect_signals_and_slots(self) -> None:
def finalcif_changes_filename(self):
return self.cif.finalcif_file_prefixed(prefix='', suffix='-finalcif_changes.cif', force_strip=True)

def _on_go_to_loops_page(self):
self.make_loops_tables()
self.ui.MainStackedWidget.go_to_loops_page()

def export_all_templates(self, filename: Path = None):
import pickle
if not filename:
Expand Down Expand Up @@ -620,7 +626,7 @@ def resizeEvent(self, a0: QtGui.QResizeEvent) -> None:
self.ui.LeftFrame.setMinimumWidth(int(left_frame))
# Not necessary here, it is done in MyCifTable
# threading.Thread(target=self.ui.cif_main_table.resizeRowsToContents).start()
#QtCore.QTimer(self).singleShot(0, self.ui.cif_main_table.resizeRowsToContents)
# QtCore.QTimer(self).singleShot(0, self.ui.cif_main_table.resizeRowsToContents)

def moveEvent(self, a0: QtGui.QMoveEvent) -> None:
"""Is called when the main window moves."""
Expand Down Expand Up @@ -1358,67 +1364,43 @@ def import_additional_cif(self, filename: str):
except RuntimeError as e:
show_general_warning(self, 'Could not import {}:\n'.format(filename) + str(e))
return
except ValueError as e:
except GemmiError as e:
warning = 'Problems parsing file: {}:\n'.format(filename) + str(e)
if 'data_' in str(e):
warning = warning + "\n\nA CIF needs to start with 'data_[some_name]'."
show_general_warning(self, warning)
show_general_warning(self, warning)
return
unable_to_open_message(self, Path(self.cif.filename), e)
return
except IOError as e:
show_general_warning(self, 'Unable to open file {}:\n'.format(filename) + str(e))
return
self.check_cif_for_missing_values_before_really_open_it()
try:
self.import_key_value_pairs(imp_cif)
self.import_loops(imp_cif)
except Exception as e:
print(e)
unable_to_open_message(self, Path(self.cif.filename), e)
self.import_selector = ImportSelector(self, import_cif=imp_cif, target_cif=self.cif, settings=self.settings)
self.import_selector.show_import_window()
self.import_selector.import_clicked.connect(self._do_import_cif_after_selection)

def _do_import_cif_after_selection(self, keys: List[str], loops: List[List[str]]) -> None:
self._import_key_value_pairs(keys)
self._import_loops(loops)
self.add_audit_creation_method()
# I think I leave the user possibilities to change the imported values:
# self.save_current_cif_file()
# self.load_cif_file(str(self.cif.finalcif_file))
self.import_selector.deleteLater()
self.import_selector.close()

def _import_key_value_pairs(self, keys: List[str]) -> None:
for key in keys:
value = self.import_selector.import_cif[key]
if key in self.ui.cif_main_table.vheaderitems:
self.ui.cif_main_table.setText(key=key, column=Column.EDIT, txt=value, color=light_green)
else:
self.add_row(key, value, at_start=True)

def import_loops(self, imp_cif: 'CifContainer'):
"""
Import all loops from the CifContainer imp_cif to the current block.
"""
for loop in imp_cif.loops:
if self.ui.importOnlyNewDataCheckBox.isChecked() and self.cif.block.find(loop.tags):
# Import only new loops
continue
# TODO: Make this work:
#if loop.tags[0] in do_not_loop_import:
# continue
new_loop = self.cif.block.init_loop('', loop.tags)
for row in imp_cif.block.find(loop.tags):
def _import_loops(self, loops: List[List[str]]):
for loop in loops:
new_loop = self.cif.block.init_loop('', loop)
for row in self.import_selector.import_cif.block.find(loop):
new_loop.add_row(row)

def import_key_value_pairs(self, imp_cif: CifContainer) -> None:
for item in imp_cif.block:
if item.pair is not None:
key, value = item.pair
# leave out unit cell etc.:
if self.do_not_import_this_key(key, value, imp_cif):
continue
if self.ui.importOnlyNewDataCheckBox.isChecked() and self.cif[key]:
# Import only new key/values
continue
value = cif.as_string(value)
if key in self.ui.cif_main_table.vheaderitems:
self.ui.cif_main_table.setText(key=key, column=Column.EDIT, txt=value, color=light_green)
else:
self.add_row(key, value) # , column =Column.EDIT

def do_not_import_this_key(self, key: str, value: str, cif: 'CifContainer') -> bool:
if value == '?' or value.strip() == '':
return True
if key in do_not_import_keys:
return True
if key in do_not_import_from_stoe_cfx and cif.fileobj.suffix == '.cfx':
return True
return False

def load_cif_file(self, filepath: Path, block=0, load_changes: bool = True) -> None:
"""
Opens the cif file and fills information into the main table.
Expand Down Expand Up @@ -1520,7 +1502,6 @@ def _load_block(self, index: int, load_changes: bool = True) -> None:
unable_to_open_message(parent=self, filepath=self.finalcif_changes_filename, not_ok=e)
if self.running_inside_unit_test and changes_exist:
self.load_changes_cif()
self.make_loops_tables()
if self.cif:
self.set_shredcif_state()
# saving current cif dir as last working directory:
Expand Down Expand Up @@ -1609,8 +1590,8 @@ def check_cif_for_missing_values_before_really_open_it(self) -> None:
print(str(e))
errlist = str(e).split(':')
if len(errlist) > 1:
show_general_warning(self,
f"Attention in CIF line {errlist[1]}:\n'{errlist[2].split()[0]}' has no value.")
show_general_warning(self, f"Attention in CIF line {errlist[1]}:\n"
f"'{errlist[2].split()[0]}' has no value.")

def get_last_workdir(self):
try:
Expand Down Expand Up @@ -1702,7 +1683,7 @@ def show_residuals(self) -> None:
self.ui.shelx_TextEdit.setPlainText(cif.as_string(self.cif.res_file_data))
try:
QtCore.QTimer(self).singleShot(0, self.view_molecule)
#threading.Thread(target=self.view_molecule).start()
# threading.Thread(target=self.view_molecule).start()
except Exception:
print('Molecule view crashed!')

Expand Down Expand Up @@ -1878,12 +1859,12 @@ def add_loops_tables(self) -> None:
"""
Generates a list of tables containing the cif loops.
"""
#do_not_display = ('_diffrn_refln_index_h')
# do_not_display = ('_diffrn_refln_index_h')
for num, loop in enumerate(self.cif.loops):
tags = loop.tags
if not tags or len(tags) < 1:
continue
#if tags[0] in do_not_display:
# if tags[0] in do_not_display:
# continue
self.new_loop_tab(loop, num, tags)
if self.cif.res_file_data:
Expand Down Expand Up @@ -1920,6 +1901,20 @@ def _go_to_new_loop_page(self):
self.ui.newLoopPushButton.hide()
self.loopcreate.saveLoopPushButton.clicked.connect(self.save_new_loop_to_cif)

def _on_delete_current_loop(self):
current_tab_index = self.ui.LoopsTabWidget.currentIndex()
current_table_view: MyQTableView = self.ui.LoopsTabWidget.widget(current_tab_index)
try:
header_model: LoopTableModel = current_table_view.horizontalHeader().model()
except AttributeError:
# Not a QTableView
return
header_item = header_model._header[0]
loop: gemmi.cif.Loop = self.cif.block.find_loop(header_item).get_loop()
table: gemmi.cif.Table = self.cif.block.find(loop.tags)
table.erase()
self.ui.LoopsTabWidget.removeTab(current_tab_index)

def save_new_loop_to_cif(self):
if self.loopcreate:
loop = self.loopcreate.save_new_loop_to_cif()
Expand Down
6 changes: 5 additions & 1 deletion finalcif/gui/finalcif_gui_ui.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1248,6 +1248,9 @@ def setupUi(self, FinalCifWindow):
self.newLoopPushButton = QtWidgets.QPushButton(self.page_Loops)
self.newLoopPushButton.setObjectName("newLoopPushButton")
self.gridLayout_16.addWidget(self.newLoopPushButton, 0, 4, 1, 1)
self.deleteLoopButton = QtWidgets.QPushButton(self.page_Loops)
self.deleteLoopButton.setObjectName("deleteLoopButton")
self.gridLayout_16.addWidget(self.deleteLoopButton, 3, 4, 1, 1)
self.verticalLayout_9.addLayout(self.gridLayout_16)
self.MainStackedWidget.addWidget(self.page_Loops)
self.page_checkcif = QtWidgets.QWidget()
Expand Down Expand Up @@ -1794,7 +1797,7 @@ def setupUi(self, FinalCifWindow):
self.retranslateUi(FinalCifWindow)
self.TemplatesStackedWidget.setCurrentIndex(0)
self.EquipmentTemplatesStackedWidget.setCurrentIndex(0)
self.MainStackedWidget.setCurrentIndex(6)
self.MainStackedWidget.setCurrentIndex(5)
self.PropertiesTemplatesStackedWidget.setCurrentIndex(1)
self.LoopsTabWidget.setCurrentIndex(0)
self.authorEditTabWidget.setCurrentIndex(1)
Expand Down Expand Up @@ -2105,6 +2108,7 @@ def retranslateUi(self, FinalCifWindow):
self.revertLoopsPushButton.setText(_translate("FinalCifWindow", "Revert Changes"))
self.BackFromLoopsPushButton.setText(_translate("FinalCifWindow", "Back to CIF Table"))
self.newLoopPushButton.setText(_translate("FinalCifWindow", "Add New Loop"))
self.deleteLoopButton.setText(_translate("FinalCifWindow", "Delete Loop"))
self.CheckCIFResultsTabWidget.setTabText(self.CheckCIFResultsTabWidget.indexOf(self.platon_page), _translate("FinalCifWindow", "PLATON CheckCIF result"))
self.ResponsesTabWidget.setTabText(self.ResponsesTabWidget.indexOf(self.htmlTabwidgetPage), _translate("FinalCifWindow", "html report"))
self.label_6.setText(_translate("FinalCifWindow", "Every form you fill out will be written to the cif file."))
Expand Down
9 changes: 8 additions & 1 deletion finalcif/gui/finalcif_gui_ui.ui
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Original file line number Diff line number Diff line change
Expand Up @@ -841,7 +841,7 @@
<item row="2" column="0" colspan="13">
<widget class="MyMainStackedWidget" name="MainStackedWidget">
<property name="currentIndex">
<number>6</number>
<number>5</number>
</property>
<widget class="QWidget" name="page_MainTable">
<layout class="QVBoxLayout" name="verticalLayout">
Expand Down Expand Up @@ -2874,6 +2874,13 @@ Contact authors should always also appear as regular authors.</string>
</property>
</widget>
</item>
<item row="3" column="4">
<widget class="QPushButton" name="deleteLoopButton">
<property name="text">
<string>Delete Loop</string>
</property>
</widget>
</item>
</layout>
</item>
</layout>
Expand Down
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