pyworkflow.project.project module

exception pyworkflow.project.project.MissingProjectDbException

Bases: exceptions.Exception

class pyworkflow.project.project.Project(path)

Bases: object

This class will handle all information related with a Project

checkPid(protocol)

Check if a running protocol is still alive or not. The check will only be done for protocols that have not been sent to a queue system.

closeMapper()

continueProtocol(protocol)

This function should be called to mark a protocol that have an interactive step waiting for approval that can continue

copyProtocol(protocol)

Make a copy of the protocol, Return a new instance with copied values.

create(runsView=1, readOnly=False, hostsConf=None, protocolsConf=None)

Prepare all required paths and files to create a new project. Params:

hosts: a list of configuration hosts associated to this projects

(class ExecutionHostConfig)

createMapper(sqliteFn)

Create a new SqliteMapper object and pass as classes dict all globals and update with data and protocols from em.

createSettings(runsView=1, readOnly=False)

deleteProtocol(*protocols)

deleteProtocolOutput(protocol, output)

Delete a given object from the project. Usually to clean up some outputs.

doesProtocolExists(protId)

exportProtocols(protocols, filename)

Create a text json file with the info to import the workflow into another project. This methods is very similar to copyProtocol Params:

protocols: a list of protocols to export. filename: the filename where to write the workflow.

fixLinks(searchDir)

getCreationTime()

Return the time when the project was created.

getCurrentProtocolView()

Select the view that is currently selected. Read from the settings the last selected view and get the information from the self._protocolViews dict.

getDbLastModificationDate()

Return the last modification date of the database

classmethod getDbName()

Return the name of the database file of projects.

getDbPath()

Return the path to the sqlite db.

getElapsedTime()

Returns the time elapsed from the creation to the last execution time.

getGraphFromRuns(runs)

This function will build a dependencies graph from a set

of given runs.

Parameters:runs – The input runs to build the graph Returns:The graph taking into account run dependencies

getHostConfig(hostName)

getHostNames()

Return the list of host name in the project.

getLeftTime()

getLogPath(*paths)

getName()

getObjId()

Return the unique id assigned to this project.

getObject(objId)

Retrieve an object from the db given its id.

getPath(*paths)

Return path from the project root

getProtocol(protId)

getProtocolViews()

getProtocolsByClass(className)

getProtocolsDict(protocols=None, namesOnly=False)

Create a dict with the information of the given protocols. Params:

protocols: list of protocols or None to include all. namesOnly: the output list will contain only the protocol names.

getProtocolsJson(protocols=None, namesOnly=False)

Wraps getProtocolsDict to get a json string Params:

protocols: list of protocols or None to include all. namesOnly: the output list will contain only the protocol names.

getRelatedObjects(relation, obj, direction=0, refresh=False)

Get all objects related to obj by a give relation. Params:

relation: the relation name to search for. obj: object from which the relation will be search,

actually not only this, but all other objects connected to this one by the RELATION_TRANSFORM.

direction: this say if search for childs or parents in the relation.

getRuns(iterate=False, refresh=True, checkPids=False)

Return the existing protocol runs in the project.

getRunsGraph(refresh=True, checkPids=False)

Build a graph taking into account the dependencies between different runs, ie. which outputs serves as inputs of other protocols.

getSettings()

getSettingsCreationTime()

getShortName()

getSourceChilds(obj)

Return all the objects have used obj as a source.

getSourceGraph(refresh=False)

Get the graph from the SOURCE relation.

getSourceParents(obj)

Return all the objects that are SOURCE of this object.

getTmpPath(*paths)

getTransformGraph(refresh=False)

Get the graph from the TRASNFORM relation.

isInReadOnlyFolder()

isLink()

Returns if the project path is a link to another folder.

isReadOnly()

iterSubclasses(classesName, objectFilter=None)

Retrieve all objects from the project that are instances

of any of the classes in classesName list.

Params:

classesName: String with commas separated values of classes name. objectFilter: a filter function to discard some of the retrieved objects.

launchProtocol(protocol, wait=False, scheduled=False, force=False)

In this function the action of launching a protocol will be initiated. Actions done here are: 1. Store the protocol and assign name and working dir 2. Create the working dir and also the protocol independent db 3. Call the launch method in protocol.job to handle submission:

mpi, thread, queue,

and also take care if the execution is remotely.

If the protocol has some prerequisited (other protocols that needs to be finished first), it will be scheduled.

launchWorkflow(initialProtocol, mode=2)

This function can launch a workflow from a selected protocol in two modes depending on the ‘mode’ value (RESTART, CONTINUE) Actions done here are: 1. Check if the workflow has active protocols. 2. Fix the workflow if is not properly configured 3. Restart or Continue a workflow starting from the protocol depending

of the ‘mode’ value

load(dbPath=None, hostsConf=None, protocolsConf=None, chdir=True, loadAllConfig=True)

Load project data, configuration and settings. Params:

dbPath: the path to the project database.

If None, use the project.sqlite in the project folder.

hosts: where to read the host configuration.

If None, check if exists in .config/hosts.conf or read from ~/.config/scipion/hosts.conf

settings: where to read the settings.

If None, use the settings.sqlite in project folder. If forProtocol is True, the settings and protocols.conf will not be loaded.

loadProtocols(filename=None, jsonStr=None)

Load protocols generated in the same format as self.exportProtocols. Params:

filename: the path of the file where to read the workflow. jsonStr: read the protocols from a string instead of file.

Note: either filename or jsonStr should be not None.

needRefresh()

True if any run is active and its timestamp is older than its corresponding runs.db NOTE: If an external script changes the DB this will fail. It uses only in memory objects.

newProtocol(protocolClass, **kwargs)

Create a new protocol from a given class.

openedAsReadOnly()

saveProtocol(protocol)

saveSettings()

scheduleProtocol(protocol, prerequisites=[])

Schedule a new protocol that will run when the input data is available and the prerequisited finished. Params:

protocol: the protocol that will be scheduled. prerequisites: a list with protocols ids that the scheduled

protocol will wait for.

setDbPath(dbPath)

Set the project db path. This function is used when running a protocol where a project is loaded but using the protocol own sqlite file.

setReadOnly(value)

stopProtocol(protocol)

Stop a running protocol

stopWorkFlow(initialProtocol)

This function can stop a workflow from a selected protocol :param initialProtocol: selected protocol