Source code for tmtk.arborist.common

import os
import shutil
import time
from IPython.display import display, IFrame, clear_output
import tempfile
import json

from ..utils import Message, ClassError, ArboristException

from .jstreecontrol import create_concept_tree, ConceptTree
import tmtk

[docs]def call_boris(study=None, **kwargs): """ This function loads the Arborist if it has been properly installed in your environment. :param study: a <tmtk.Study> object. """ if not isinstance(study, tmtk.Study): Message.error("Have to provide a tmtk.Study object.") raise ClassError(type(study, 'tmtk.Study')) concept_tree = create_concept_tree(study) try: ontology_tree = study.Clinical.OntologyMapping.as_json() except AttributeError: ontology_tree = None if ontology_tree: ver2_data = {"version": "2", "concept_tree": concept_tree, "ontology_tree": ontology_tree} json_data = json.dumps(ver2_data) else: json_data = concept_tree json_data = launch_arborist_gui(json_data, **kwargs) # Returns modified json_data if json_data: Message.okay('Successfully closed The Arborist. The updated column' ' mapping file has been returned as a dataframe.') Message.warning("Don't forget to save this dataframe to disk if you want to store it.") else: raise ArboristException('No json file returned from Arborist.') update_study_from_json(study, json_data=json_data)
[docs]def launch_arborist_gui(json_data: str, height=650): """ :param json_data: json data to launch the Arborist with. :param height: IFrame height for output cell. """ new_temp_dir = tempfile.mkdtemp() tmp_json = os.path.join(new_temp_dir, 'tmp_json') with open(tmp_json, 'w') as f: f.write(json_data) # Signal created by Javascript to continue work here. done_signal = os.path.join(os.path.dirname(tmp_json), 'DONE') base_url = os.environ.get("ARBORIST_BASE_URL", "/") running_on = '{}transmart-arborist?treefile={}'.format(base_url, os.path.abspath(tmp_json)) display(IFrame(src=running_on, width='100%', height=height)) try: # Wait for the done signal file to be created before breaking the GIL. while not os.path.exists(done_signal): time.sleep(0.1) except KeyboardInterrupt: # This stops the interpreter without showing a stacktrace. pass else: updated_json = None # We've been having issues with a slow file system where the json response was empty # Now we make sure something is sent back. while not updated_json: time.sleep(0.1) with open(tmp_json, 'r') as f: updated_json = return updated_json finally: shutil.rmtree(new_temp_dir) # Clear output from Jupyter Notebook cell clear_output() print('Cleaning up before closing...')
[docs]def update_study_from_json(study, json_data): """ Update an existing tmtk.Study object with the JSON response from the Arborist. :param study: tmtk.Study object. :param json_data: json response from Arborist. """ concept_tree = ConceptTree(json_data) study.Clinical.ColumnMapping.df = concept_tree.column_mapping_file study.Clinical.WordMapping.df = concept_tree.word_mapping # Some checks for whether to create Tags in the study. ct_tags = concept_tree.tags_file if hasattr(study, 'Tags') or ct_tags.shape[0]: study.ensure_metadata() study.Tags.df = concept_tree.tags_file high_dim_paths = concept_tree.high_dim_paths if high_dim_paths: study.HighDim.update_high_dim_paths(high_dim_paths)