Python VistrailController.write_vistrail方法代碼示例

# 需要導入模塊: from vistrails.core.vistrail.controller import VistrailController [as 別名]
# 或者: from vistrails.core.vistrail.controller.VistrailController import write_vistrail [as 別名]
def run_and_get_results(w_list, parameters='', output_dir=None, 
                        update_vistrail=True, extra_info=None, 
                        reason='Console Mode Execution'):
    """run_and_get_results(w_list: list of (locator, version), parameters: str,
                           output_dir:str, update_vistrail: boolean,
                           extra_info:dict)
    Run all workflows in w_list, and returns an interpreter result object.
    version can be a tag name or a version id.
    
    """
    elements = parameters.split("$&$")
    aliases = {}
    params = []
    result = []
    for locator, workflow in w_list:
        (v, abstractions , thumbnails, mashups)  = load_vistrail(locator)
        controller = VistrailController(v, locator, abstractions, thumbnails,
                                        mashups, auto_save=update_vistrail)
        if isinstance(workflow, basestring):
            version = v.get_version_number(workflow)
        elif isinstance(workflow, (int, long)):
            version = workflow
        elif workflow is None:
            version = controller.get_latest_version_in_graph()
        else:
            msg = "Invalid version tag or number: %s" % workflow
            raise VistrailsInternalError(msg)
        controller.change_selected_version(version)
        
        for e in elements:
            pos = e.find("=")
            if pos != -1:
                key = e[:pos].strip()
                value = e[pos+1:].strip()
            
                if controller.current_pipeline.has_alias(key):
                    aliases[key] = value
                elif 'mashup_id' in extra_info:
                    # new-style mashups can have aliases not existing in pipeline
                    for mashuptrail in mashups:
                        if mashuptrail.vtVersion == version:
                            mashup = mashuptrail.getMashup(extra_info['mashup_id'])
                            c = mashup.getAliasByName(key).component
                            params.append((c.vttype, c.vtid, value))

        if output_dir is not None and controller.current_pipeline is not None:
            # FIXME DAK: why is this always done?!? there is a flag for it...
            if is_running_gui():
                controller.updatePipelineScene()
                base_fname = "%s_%s_pipeline.pdf" % (locator.short_filename, version)
                filename = os.path.join(output_dir, base_fname)
                controller.current_pipeline_scene.saveToPDF(filename)
            else:
                debug.critical("Cannot save pipeline figure when not "
                               "running in gui mode")
            base_fname = "%s_%s_pipeline.xml" % (locator.short_filename, version)
            filename = os.path.join(output_dir, base_fname)
            vistrails.core.db.io.save_workflow(controller.current_pipeline, filename)
        if not update_vistrail:
            conf = get_vistrails_configuration()
            if conf.has('thumbs'):
                conf.thumbs.autoSave = False
        
        jobMonitor = controller.jobMonitor
        current_workflow = jobMonitor.currentWorkflow()
        if not current_workflow:
            for job in jobMonitor.workflows.itervalues():
                try:
                    job_version = int(job.version)
                except ValueError:
                    job_version =  v.get_version_number(job.version)
                if version == job_version:
                    current_workflow = job
                    jobMonitor.startWorkflow(job)
            if not current_workflow:
                current_workflow = JobWorkflow(version)
                jobMonitor.startWorkflow(current_workflow)

        try:
            (results, _) = \
            controller.execute_current_workflow(custom_aliases=aliases,
                                                custom_params=params,
                                                extra_info=extra_info,
                                                reason=reason)
        finally:
            jobMonitor.finishWorkflow()
        new_version = controller.current_version
        if new_version != version:
            debug.log("Version '%s' (%s) was upgraded. The actual "
                      "version executed was %s" % (
                      workflow, version, new_version))
        run = results[0]
        run.workflow_info = (locator.name, new_version)
        run.pipeline = controller.current_pipeline

        if update_vistrail:
            controller.write_vistrail(locator)
        result.append(run)
        if current_workflow.jobs:
            if current_workflow.completed():
#.........這裏部分代碼省略.........

# 需要導入模塊: from vistrails.core.vistrail.controller import VistrailController [as 別名]
# 或者: from vistrails.core.vistrail.controller.VistrailController import write_vistrail [as 別名]
def run_and_get_results(w_list, parameters='', workflow_info=None, 
                        update_vistrail=True, extra_info=None, 
                        reason='Console Mode Execution'):
    """run_and_get_results(w_list: list of (locator, version), parameters: str,
                           workflow_info:str, update_vistrail: boolean,
                           extra_info:dict)
    Run all workflows in w_list, and returns an interpreter result object.
    version can be a tag name or a version id.
    
    """
    elements = parameters.split("$&$")
    aliases = {}
    result = []
    for locator, workflow in w_list:
        (v, abstractions , thumbnails, mashups)  = load_vistrail(locator)
        controller = VistrailController(v, locator, abstractions, thumbnails, 
                                        mashups, auto_save=update_vistrail)
        if isinstance(workflow, basestring):
            version = v.get_version_number(workflow)
        elif isinstance(workflow, (int, long)):
            version = workflow
        elif workflow is None:
            version = controller.get_latest_version_in_graph()
        else:
            msg = "Invalid version tag or number: %s" % workflow
            raise VistrailsInternalError(msg)
        controller.change_selected_version(version)
        
        for e in elements:
            pos = e.find("=")
            if pos != -1:
                key = e[:pos].strip()
                value = e[pos+1:].strip()
            
                if controller.current_pipeline.has_alias(key):
                    aliases[key] = value
                    
        if workflow_info is not None and controller.current_pipeline is not None:
            # FIXME DAK: why is this always done?!? there is a flag for it...
            if is_running_gui():
                controller.updatePipelineScene()
                base_fname = "%s_%s_pipeline.pdf" % (locator.short_filename, version)
                filename = os.path.join(workflow_info, base_fname)
                controller.current_pipeline_scene.saveToPDF(filename)
            else:
                debug.critical("Cannot save pipeline figure when not "
                               "running in gui mode")
            base_fname = "%s_%s_pipeline.xml" % (locator.short_filename, version)
            filename = os.path.join(workflow_info, base_fname)
            vistrails.core.db.io.save_workflow(controller.current_pipeline, filename)
        if not update_vistrail:
            conf = get_vistrails_configuration()
            if conf.has('thumbs'):
                conf.thumbs.autoSave = False
        
        (results, _) = \
            controller.execute_current_workflow(custom_aliases=aliases,
                                                extra_info=extra_info,
                                                reason=reason)
        new_version = controller.current_version
        if new_version != version:
            debug.warning("Version '%s' (%s) was upgraded. The actual "
                          "version executed was %s" % \
                              (workflow, version, new_version))
        run = results[0]
        run.workflow_info = (locator.name, new_version)
        run.pipeline = controller.current_pipeline

        if update_vistrail:
            controller.write_vistrail(locator)
        result.append(run)
    return result

# 需要導入模塊: from vistrails.core.vistrail.controller import VistrailController [as 別名]
# 或者: from vistrails.core.vistrail.controller.VistrailController import write_vistrail [as 別名]
 def exportMashup(filename, vtcontroller, mashuptrail, mashupversion, etype):
     """exportMashup(filename: str, vtcontroller: VistrailController, 
                     mashuptrail: Mashuptrail, type: int) -> bool 
         where etype is 
           0: include full tree 
           1: include only workflow and mashup identified by version
           2: as a link, it will point to a local file.
     """
     result = False
     if vtcontroller is not None and mashuptrail is not None:
         locator = vtcontroller.locator
         version = mashuptrail.vtVersion
         
         node = ElementTree.Element('vtlink')
     
         if isinstance(locator, DBLocator):
             node.set('host', str(locator.host))
             node.set('port', str(locator.port))
             node.set('database', str(locator.db))
             node.set('vtid', str(locator.obj_id))
         else:
             node.set('filename', str(locator.name))
             
         node.set('version', str(version))    
         node.set('execute', "True")
         node.set('forceDB', "False")
         node.set('showSpreadsheetOnly', "True")
         node.set('mashuptrail', str(mashuptrail.id))
         node.set('mashupVersion', str(mashupversion))
             
         if etype in [0,1]:
             if etype == 1: #minimal
                 pip = vtcontroller.vistrail.getPipeline(version)
                 vistrail = Vistrail()
                 id_remap = {}
                 action = vistrails.core.db.action.create_paste_action(pip, 
                                                     vistrail.idScope,
                                                     id_remap)
                 vistrail.add_action(action, 0L, 0)
                
                 tag = vtcontroller.vistrail.get_tag(version)
                 if tag is None:
                     tag = "Imported workflow"
                 vistrail.addTag(tag, action.id)
                 node.set('version', str(action.id))
                 id_scope = IdScope(1L)
                 newmashuptrail = Mashuptrail(
                                  MashupsManager.getNewMashuptrailId(), 
                                  action.id, 
                                  id_scope)
                 
                 maction = mashuptrail.actionMap[mashupversion]
                 mtag = mashuptrail.getTagForActionId(mashupversion)
                 newmashup = copy.copy(maction.mashup)
                 newmashup.remapPipelineObjects(id_remap)
                 currVersion = newmashuptrail.addVersion(
                                         newmashuptrail.getLatestVersion(),
                                         newmashup, maction.user, 
                                         maction.date)
                 newmashuptrail.currentVersion = currVersion
                 newmashuptrail.changeTag(currVersion, mtag, maction.user,
                                          maction.date)
                 newvtcontroller = BaseVistrailController(vistrail, None)
                 MashupsManager.addMashuptrailtoVistrailController(newvtcontroller,
                                                                   newmashuptrail)
                 node.set('mashuptrail', str(newmashuptrail.id))
                 node.set('mashupVersion', str(newmashuptrail.currentVersion))
             else:
                 vistrail = vtcontroller.vistrail
                 newvtcontroller = MashupsManager.copyBaseVistrailController(vtcontroller)
             
             #create temporary file
             (fd, name) = tempfile.mkstemp(prefix='vt_tmp',
                                       suffix='.vt')
             os.close(fd)
             try:
                 fileLocator = FileLocator(name)
                 newvtcontroller.write_vistrail(fileLocator)
                 contents = open(name).read()
                 vtcontent = base64.b64encode(contents)
             finally:
                 os.unlink(name)
             #if not vistrail.db_version:
             #    vistrail.db_version = currentVersion
             node.set('vtcontent',vtcontent)
             
         xmlstring = ElementTree.tostring(node)
         file_ = open(filename,'w')
         file_.write(xmlstring)
         file_.close()
         result = True
     return result

# 需要導入模塊: from vistrails.core.vistrail.controller import VistrailController [as 別名]
# 或者: from vistrails.core.vistrail.controller.VistrailController import write_vistrail [as 別名]
    def push_vistrail_to_repository(self, branching=False):
        """ uploads current VisTrail to web repository """

        self._repository_status['details'] = "Pushing to repository..."
        self._push_button.setEnabled(False)
        self._branch_button.setEnabled(False)
        self.update_push_information()
        try:
            # create temp file
            (fd, filename) = tempfile.mkstemp(suffix='.vt', prefix='vt_tmp')
            os.close(fd)

            # writing tmp vt and switching back to orginal vt
            locator = ZIPFileLocator(filename)
            controller = vistrails.api.get_current_controller()
            tmp_controller = VistrailController(controller.vistrail.do_copy(), 
                                                locator)
            tmp_controller.changed = True
            tmp_controller.write_vistrail(locator)

            # check if this vt is from the repository
            if controller.vistrail.get_annotation('repository_vt_id'):
                repository_vt_id = controller.vistrail.get_annotation('repository_vt_id').value
            else:
                repository_vt_id = -1

            # upload vistrail temp file to repository
            register_openers(cookiejar=self.dialog.cookiejar)
            project = self.serverCombo.itemData(self.serverCombo.currentIndex())[0]
            if project == "Default": project = ""

            params = {'vistrail_file': open(filename, 'rb'),
                      'action': 'upload',
                      'name': controller.locator.short_name,
                      'repository_vt_id': repository_vt_id if not branching else -1,
                      'is_runnable': not bool(len(self.unsupported_packages)+ \
                                              len(self.local_data_modules)),
                      'vt_id': 0,
                      'branched_from': "" if not branching else repository_vt_id,
                      'project': project,
                      'everyone_can_view': self.perm_view.checkState(),
                      'everyone_can_edit': self.perm_edit.checkState(),
                      'everyone_can_download': self.perm_download.checkState()
                     }

            upload_url = "%s/vistrails/remote_upload/" % \
                    self.config.webRepositoryURL

            datagen, headers = multipart_encode(params)
            request = urllib2.Request(upload_url, datagen, headers)
            result = urllib2.urlopen(request)
            updated_response = result.read()

            os.unlink(filename)

            if updated_response[:6] == "upload":
                # No update, just upload
                if result.code != 200:
                    self._repository_status['details'] = \
                            "Push to repository failed"
                    debug.critical("Push to repository failed (Please contact an administrator)")
                else:
                    repository_vt_id = int(updated_response[8:])
                    controller.vistrail.set_annotation('repository_vt_id',
                                                       repository_vt_id)
                    controller.vistrail.set_annotation('repository_creator',
                                                       self.dialog.loginUser)
                    # ensure that the annotations get saved
                    controller.set_changed(True)
                    self._repository_status['details'] = \
                            "Push to repository was successful"
            else:
                # update, load updated vistrail
                if result.code != 200:
                    self._repository_status['details'] = "Update Failed"
                    debug.critical("Update vistrail in web repository failed (Please contact an administrator)")
                else:
                    debug.log("getting version from web")
                    # request file to download
                    download_url = "%s/vistrails/download/%s/" % \
                            (self.config.webRepositoryURL, updated_response)

                    request = urllib2.Request(download_url)
                    result = urllib2.urlopen(request)
                    updated_file = result.read()

                    # create temp file of updated vistrail
                    (fd, updated_filename) = tempfile.mkstemp(suffix='.vtl',
                                                              prefix='vtl_tmp')
                    os.close(fd)
                    updated_vt = open(updated_filename, 'w')
                    updated_vt.write(updated_file)
                    updated_vt.close()

                    # switch vistrails to updated one
                    controller = vistrails.api.get_current_controller()

                    updated_locator = FileLocator(updated_filename)

                    (up_vistrail, abstractions, thumbnails, mashups) = \
#.........這裏部分代碼省略.........