schrodinger.application.matsci.wfmanagement module¶

Module for saving, deleting and managing template workflow information

schrodinger.application.matsci.wfmanagement.case_insensitive_file_exists(directory, filename)¶

Check if filename exists in directory in case-insensitive manner

Parameters

directory (str) – Directory to check the file existence
filename (str) – Name of the file to be checked in case-insensitive manner

Returns

True if file exists else False

Return type

bool

schrodinger.application.matsci.wfmanagement.read_workflow_metadata(metadata_file)¶

Read the workflow metadata contents from metadata_file

Parameters: metadata_file (str) – Path to the metadata json file
Returns: A json dictionary of workflow name to metadata
Return type: dict[dict]
Raises: IOError, JSONDecodeError

schrodinger.application.matsci.wfmanagement.update_workflow_metadata(metadata_file, workflow_metadata, orig_name=None)¶

Update the metadata.json file for the given workflow_metadata. If an existing entry needs to be renamed and updated, then pass its name in orig_name.

Parameters

metadata_file (str) – Path to the metadata.json file
workflow_metadata (WorkflowMetadata) – An instance of WorkflowMetadata
orig_name (str) – Name of the key in metadata.json file

Raises

PermissionError, IOError, JSONDecodeError

schrodinger.application.matsci.wfmanagement.delete_workflow_metadata(metadata_file, workflow_name)¶

Delete the workflow metadata from metadata_file for the given workflow_name

Parameters

metadata_file (str) – Path to the metadata.json file
workflow_name (str) – Name of the key in metadata.json file

Raises

PermissionError, IOError, JSONDecodeError

schrodinger.application.matsci.wfmanagement.validate_workflow_name(name, reserved_names=None)¶

Validate the given workflow name. The name is checked in reserved_names list in case-insensitive manner because this will be used as filename for the workflow and on Windows filenames are case-insensitive

Parameters: reserved_names (list(str)) – List of names not to accept
Returns: Error string if name is invalid else empty string
Return type: str

class schrodinger.application.matsci.wfmanagement.WorkflowMetadata(name='', description='', tags='', suite='', creator='')¶

Bases: object

Class to hold the workflow metadata

__init__(name='', description='', tags='', suite='', creator='')¶

Parameters

name (str) – Workflow name
description (str) – Description of the workflow
tags (str) – Comma separated keywords that describes the workflow
suite (str) – Schrodinger suite version with which the workflow has been created
creator (str) – Workflow creator

as_dict()¶

Return the WorkflowMetadata as a dict

Returns: The instance as a dict
Return type: dict

classmethod from_dict(data)¶

Return an instance of WorkflowMetadata from a dict

Parameters: data (dict) – Workflow metadata as a dictionary

empty()¶

Check if the WorkflowMetadata is empty. A WorkflowMetadata is considered empty if all of its values are empty

Returns: True if empty else False
Return type: bool

equals(data)¶

Check if the data is same as this instance

Parameters: data (WorkflowMetadata) – Workflow metadata instance to compare

tostring()¶

Return the string represenation of the WorkflowMetadata object where all the data members are concatenated by space

Returns: String represenatation of this instance
Rtye: str

class schrodinger.application.matsci.wfmanagement.WorkflowMetadataFrame(layout=None, wkf_metadata=None, mode='view', user_update_function=None)¶

Bases: schrodinger.ui.qt.widgetmixins.basicmixins.MessageBoxMixin, schrodinger.ui.qt.swidgets.SFrame

GUI for the workflow metadata. This class can be created in 3 different modes, MODE_VIEW (read_only), MODE_CREATE (‘write_only’) and MODE_UPDATE (‘read/write’)

NAME = 'Name:'¶

DESCRIPTION = 'Description:'¶

TAGS = 'Tags:'¶

SUITE = 'Suite:'¶

CREATOR = 'Creator:'¶

MODE_VIEW = 'view'¶

MODE_CREATE = 'create'¶

MODE_UPDATE = 'update'¶

__init__(layout=None, wkf_metadata=None, mode='view', user_update_function=None)¶

Create an instance of WorkflowMetadataFrame based on the mode. If wkf_metadata is passed, then the frame is initialized with this data.

Parameters

wkf_metadata (WorkflowMetadata) – Instance of WorkflowMetadata
layout (QLayout) – The layout to place this WorkflowMetadataFrame
mode (MODE_VIEW, MODE_CREATE, MODE_UPDATE) – Mode in which to create the workflow metadata frame
user_update_function (func(WorkflowMetadata)) – A callback function to be called when a workflow is saved after editing (used in MODE_UPDATE)

createTopFrame()¶: Create top frame for Update mode that contains the edit, save and close buttons

createViewFrame()¶: Create the WorkflowMetadataFrame in view mode

createEditableFrame()¶: Create the WorkflowMetadataFrame in editable mode

setEditable(editable)¶

Set the Update mode’s view. This method is applicable only for Update mode.

Parameters: editable (bool) – Whether the Update mode is editable or not

setMetadata(wkf_metadata)¶

Update the metadata frame contents based on the wkf_metadata. If None is passed, then clear all the fields

Parameters: wkf_metadata (WorkflowMetadata) – Instance of WorkflowMetadata

getName()¶

Return the name of the current workflow metadata

Returns: Name of the current workflow metadata
Return type: str or None

getMetadata()¶

Return the current workflow metadata instance

Returns: Current workflow metadata instance
Return type: WorkflowMetadata

class schrodinger.application.matsci.wfmanagement.WorkflowNamerDialog(*args, reserved_names=None, **kwargs)¶

Bases: schrodinger.ui.qt.swidgets.SDialog

A dialog that allows the user to provide a name and metadata for a new workflow

__init__(*args, reserved_names=None, **kwargs)¶

Create a WorkflowNamerDialog instance

See parent class for documentation

Parameters: reserved_names (list) – List of reserved workflow names

layOut()¶: See parent class for documentation

accept()¶: See parent class for documentation

class schrodinger.application.matsci.wfmanagement.WorkflowFilterWidget(label=None, filterlabel='Filter:', filter='within', filterside='bottom', case=False, layout=None, **kwargs)¶

Bases: schrodinger.ui.qt.swidgets.SFilteredListWidget

List widget that filter workflows based on its metadata

filterList(filtervalue)¶

Filter the items in the list widget according to the contents of the LineEdit and our filter rules

Parameters: filtervalue (str) – The current value to filter the ListWidget by

class schrodinger.application.matsci.wfmanagement.WorkflowFinder(user_location='', std_location='', file_suffix='', reserved_names=None, **kwargs)¶

Bases: schrodinger.ui.qt.widgetmixins.basicmixins.MessageBoxMixin, schrodinger.ui.qt.swidgets.SFrame

Class that lists workflows under specified user_location and std_location. On selecting a workflow, it displays its metadata if available

NO_WORKFLOWS = 'No workflows found'¶

workflow_selection_changed¶: A pyqtSignal emitted by instances of the class.

__init__(user_location='', std_location='', file_suffix='', reserved_names=None, **kwargs)¶

Create a WorkflowFinder instance

Parameters

user_location (str) – Directory that contains user created workflows
std_location – Directory that contains std workflows
file_suffix (str) – Workflow file suffix
reserved_names (list(str)) – List of reserved workflow names

workflowMetadataMode()¶

Mode in which the WorkflowMetadataFrame will be created.

Returns: WorkflowMetadataFrame creation mode
Return type: str

filterWorkflows(text, filtertext, case_sensitive)¶

Custom filter function to filter the listwidget entries. Checks if the filtertext is available in whole workflow metadata apart from the workflow name

Parameters

text (str) – Text to be filtered
filtertext (str) – Text to be searched for
case_sensitive (bool) – Enable case sensitive search if True

Returns

True if filtertext is found else False

Return type

bool

selectedWorkflowName()¶

Get the user-facing name for the selected workflow

Return type: str or None
Returns: The name of the selected workflow, or None if there is no selection

selectedWorkflowPath()¶

Get the path to the selected workflow

Return type: str or None
Returns: The path to the selected workflow, or None if there is no selection

selectedWorkflowBasename()¶

Return the basename of selected workflow file path

Return type: str or None
Returns: Basename of selected workflow filepath, or None if there is no selection

userWorkflow(workflow_path)¶

Check if the workflow_path is an user created workflow. Any workflow under self.user_location is treated as a user workflow

Returns: True if user workflow else False
Return type: bool

loadNewWorkflow()¶: Callback function when a workflow is selected in the list. Update the WorkflowMetadataFrame for the selected workflow

getUserText(workflow_filepath)¶

Return the user friendly name for the workflow based on the workflow_filepath

Returns: User friendly name from workflow filepath
Return type: str

getWorkflowPaths()¶

Get the list of workflow paths to be displyed

Returns: List of workflow paths to be displayed
Return type: list(str)

reset()¶: Reset the widgets

validate()¶

Validate that a workflow is selected

Return type: bool or (bool, str)
Returns: The bool is True if everything is OK, False if not. str is given if a dialog should pop up to show the given message. If bool is True, str will post as Question dialog.

class schrodinger.application.matsci.wfmanagement.WorkflowManagerMixin(*args, **kwargs)¶

Bases: object

A mixin to be used with WorkflowFinder that allows managing the workflows, like renaming the workflow, deleting the workflow and editing its metadata

__init__(*args, **kwargs)¶: Create a WorkflowManagerMixin instance

workflowMetadataMode()¶

Mode in which the WorkflowMetadataFrame will be created.

Returns: WorkflowMetadataFrame creation mode
Return type: str

onWorkflowSelected()¶: Slot called when workflow_selection_changed signal is emitted

updateMetadata(metadata)¶

Callback function called on saving the metadata. Rename the workflow file (if the name is modified) and update the workflow metadata file

Parameters: metadata (WorkflowMetadata) – Instance of WorkflowMetadata
Returns: True if success else False
Return type: bool

deleteWorkflow()¶: Delete the selected workflow

class schrodinger.application.matsci.wfmanagement.WorkflowManager(*args, **kwargs)¶

Bases: schrodinger.application.matsci.wfmanagement.WorkflowManagerMixin, schrodinger.application.matsci.wfmanagement.WorkflowFinder

Class that lists workflows and allows renaming workflows, deleting workflows and editing its metadata

class schrodinger.application.matsci.wfmanagement.BaseWorkflowFinderDialog(*args, user_location='', std_location='', file_suffix='', reserved_names=None, **kwargs)¶

Bases: schrodinger.ui.qt.swidgets.SDialog

A Base dialog that lists existing workflows. Should not be used directly

All subclasses _must_ implement createWidget method that creates and returns an instance of WorkflowFinder. This widget will be set as the main widget for the dialog

__init__(*args, user_location='', std_location='', file_suffix='', reserved_names=None, **kwargs)¶

Parameters

user_location (str) – Directory that contains user created workflows
std_location – Directory that contains std workflows
file_suffix (str) – Workflow file suffix
reserved_names (list(str)) – List of reserved workflow names

resizeDialog()¶: Subclasses can resize the dialog accordingly

layOut()¶: See parent class for documentation

createWidget(user_location='', std_location='', file_suffix='', reserved_names=None)¶

Create and return an instance of WorkflowFinder widget to be added to the dialog. To be implemented by subclasses.

Parameters

user_location (str) – Directory that contains user created workflows
std_location – Directory that contains std workflows
file_suffix (str) – Workflow file suffix
reserved_names (list(str)) – List of reserved workflow names

Returns

WorkflowFinder instance to be added to the dialog

Return type

WorkflowFinder

accept()¶: See parent class for documentation

class schrodinger.application.matsci.wfmanagement.WorkflowFinderDialog(*args, user_location='', std_location='', file_suffix='', reserved_names=None, **kwargs)¶

Bases: schrodinger.application.matsci.wfmanagement.BaseWorkflowFinderDialog

A dialog that allows the user to pick an existing workflow

createWidget(user_location='', std_location='', file_suffix='', reserved_names=None)¶: See parent class for documentation

class schrodinger.application.matsci.wfmanagement.WorkflowManagerDialog(*args, **kwargs)¶

Bases: schrodinger.application.matsci.wfmanagement.BaseWorkflowFinderDialog

A dialog that allows the user to manage the workflows, like edit the workflow metadata, rename and delete the workflow.

__init__(*args, **kwargs)¶: Initialize dialog with only Close button

createWidget(user_location='', std_location='', file_suffix='', reserved_names=None)¶: See parent class for documentation