import os
import sys
import pandas as pd
import h5py as h5
import ckg_utils
import config.ckg_config as ckg_config
from report_manager import report as rp, knowledge
from analytics_core import analytics_factory
from analytics_core.analytics import analytics
from analytics_core.viz import viz
from graphdb_connector import connector
log_config = ckg_config.report_manager_log
logger = ckg_utils.setup_logging(log_config, key="dataset")
class Dataset:
def __init__(self,
identifier,
dataset_type,
configuration=None,
data={},
analysis_queries={},
report=None):
self._identifier = identifier
self._dataset_type = dataset_type
self._configuration = configuration
self._data = data
self._analysis_queries = analysis_queries
self._report = report
import pandas as pd
import numpy as np
import ast
from operator import itemgetter
import networkx as nx
import ckg_utils
import config.ckg_config as ckg_config
import dash_cytoscape as cyto
from graphdb_connector import connector
from report_manager import report as rp
from analytics_core import utils
from analytics_core.viz import viz, color_list
from networkx.readwrite import json_graph
log_config = ckg_config.report_manager_log
logger = ckg_utils.setup_logging(log_config, key="knowledge")
cyto.load_extra_layouts()
class Knowledge:
def __init__(self,
identifier,
data,
nodes={},
relationships={},
queries_file=None,
keep_nodes=[],
colors={},
graph=None,
report={}):
self._identifier = identifier
import h5py as h5
import json
from collections import defaultdict
from json import dumps
import pandas as pd
import ckg_utils
import config.ckg_config as ckg_config
from report_manager.dataset import Dataset, DNAseqDataset, ProteomicsDataset, InteractomicsDataset, PhosphoproteomicsDataset, ClinicalDataset, LongitudinalProteomicsDataset, MultiOmicsDataset
from analytics_core.viz import viz
from analytics_core import utils as acore_utils
from report_manager import report as rp, utils, knowledge
from graphdb_connector import query_utils
from graphdb_connector import connector
log_config = ckg_config.report_manager_log
logger = ckg_utils.setup_logging(log_config, key="project")
class Project:
"""
A project class that defines an experimental project.
A project can be of different types, contain several datasets and reports.
Example::
p = Project(identifier="P0000001", datasets=None, report=None)
p.show_report(environment="notebook")
"""
def __init__(self,
identifier,
configuration_files={},
