diff --git a/instruments/instrument_registry.xlsx b/instruments/instrument_registry.xlsx new file mode 100644 index 0000000000000000000000000000000000000000..283283bbe21aaa4cb7a490118e9275dc3db07ffc Binary files /dev/null and b/instruments/instrument_registry.xlsx differ diff --git a/instruments/readers/acsm_tofware_reader.py b/instruments/readers/acsm_tofware_reader.py index a519c18cbf586c1a7d19bd67e69a506213fd0e68..c45039cbe6ac024d557a69c1855146aeafb76f94 100644 --- a/instruments/readers/acsm_tofware_reader.py +++ b/instruments/readers/acsm_tofware_reader.py @@ -6,7 +6,10 @@ import yaml #root_dir = os.path.abspath(os.curdir) #sys.path.append(root_dir) -import utils.g5505_utils as utils +try: + from dima.utils import g5505_utils as utils +except ModuleNotFoundError: + import utils.g5505_utils as utils diff --git a/instruments/readers/filereader_registry.py b/instruments/readers/filereader_registry.py index fc4010dfe33a9fb0185b98b5bf5afafaf3093dd4..ca745a255198883e53d98612ed5341ba4ceccf3c 100644 --- a/instruments/readers/filereader_registry.py +++ b/instruments/readers/filereader_registry.py @@ -3,9 +3,13 @@ import sys #root_dir = os.path.abspath(os.curdir) #sys.path.append(root_dir) -from instruments.readers.xps_ibw_reader import read_xps_ibw_file_as_dict -from instruments.readers.g5505_text_reader import read_txt_files_as_dict - +try: + from dima.instruments.readers.xps_ibw_reader import read_xps_ibw_file_as_dict + from dima.instruments.readers.g5505_text_reader import read_txt_files_as_dict + +except ModuleNotFoundError: + from instruments.readers.xps_ibw_reader import read_xps_ibw_file_as_dict + from instruments.readers.g5505_text_reader import read_txt_files_as_dict file_extensions = ['.ibw','.txt','.dat','.h5','.TXT','.csv','.pkl','.json','.yaml'] diff --git a/instruments/readers/flag_reader.py b/instruments/readers/flag_reader.py index 8534bb4440902e81cbd6e0ab9882113f34fa641d..46cc249e40bd34c1166147b6025995a6e15ebe5a 100644 --- a/instruments/readers/flag_reader.py +++ b/instruments/readers/flag_reader.py @@ -8,7 +8,10 @@ import json #from instruments.readers import set_dima_path as configpath #configpath.set_dima_path() -from utils import g5505_utils +try: + from dima.utils import g5505_utils as utils +except ModuleNotFoundError: + import utils.g5505_utils as utils def read_jsonflag_as_dict(path_to_file): diff --git a/pipelines/data_integration.py b/pipelines/data_integration.py index cd453c0e6abd4099a8fe4f32ef99dd4107061a58..5bb5bb74f5fd0bca83b77139b9ebc2bccbaf68f0 100644 --- a/pipelines/data_integration.py +++ b/pipelines/data_integration.py @@ -22,9 +22,15 @@ from datetime import datetime from itertools import chain # Import DIMA modules -import src.hdf5_writer as hdf5_lib -import utils.g5505_utils as utils -from instruments.readers import filereader_registry +try: + from dima.src import hdf5_writer as hdf5_lib + from dima.utils import g5505_utils as utils + from dima.instruments.readers import filereader_registry +except ModuleNotFoundError: + print(':)') + import src.hdf5_writer as hdf5_lib + import utils.g5505_utils as utils + from instruments.readers import filereader_registry allowed_file_extensions = filereader_registry.file_extensions diff --git a/pipelines/metadata_revision.py b/pipelines/metadata_revision.py index 0089dc6abe4e44ae81527d3f7e698361e9600851..199c8869defa2b67858bcf6355c3beded5e80d8e 100644 --- a/pipelines/metadata_revision.py +++ b/pipelines/metadata_revision.py @@ -15,7 +15,12 @@ if dimaPath not in sys.path: # Avoid duplicate entries import h5py import yaml -import src.hdf5_ops as hdf5_ops + +try: + from dima.src import hdf5_ops as hdf5_ops +except ModuleNotFoundError: + import src.hdf5_ops as hdf5_ops + def load_yaml(review_yaml_file): diff --git a/src/git_ops.py b/src/git_ops.py index b7395dcb316e8517b2e6dc8f32525a9d7ef18964..1c55231c4e80d80160478c8360f83394f98a8bc5 100644 --- a/src/git_ops.py +++ b/src/git_ops.py @@ -1,7 +1,12 @@ import subprocess import os -import utils.g5505_utils as utils -from pipelines.metadata_revision import update_hdf5_file_with_review + +try: + from dima.utils import g5505_utils as utils + from dima.pipelines.metadata_revision import update_hdf5_file_with_review +except ModuleNotFoundError: + import utils.g5505_utils as utils + from pipelines.metadata_revision import update_hdf5_file_with_review def perform_git_operations(hdf5_upload): status_command = ['git', 'status'] diff --git a/src/hdf5_ops.py b/src/hdf5_ops.py index ba71f73c4ff3745b3248c73bb2febb28dff5d26a..9b8575d221b8420342232d2ff10ea5ee7bbce89f 100644 --- a/src/hdf5_ops.py +++ b/src/hdf5_ops.py @@ -17,9 +17,6 @@ if dimaPath not in sys.path: # Avoid duplicate entries import h5py import pandas as pd import numpy as np - -import utils.g5505_utils as utils -import src.hdf5_writer as hdf5_lib import logging import datetime @@ -29,6 +26,13 @@ import yaml import json import copy +try: + from dima.utils import g5505_utils as utils + from dima.src import hdf5_writer as hdf5_lib +except ModuleNotFoundError: + import utils.g5505_utils as utils + import src.hdf5_writer as hdf5_lib + class HDF5DataOpsManager(): """ diff --git a/src/hdf5_writer.py b/src/hdf5_writer.py index 3006b7e602872ed4fb876a670d8931edfd5ca61d..c8f14758428af737b4b94586f83099494a1be929 100644 --- a/src/hdf5_writer.py +++ b/src/hdf5_writer.py @@ -1,15 +1,19 @@ import sys import os -root_dir = os.path.abspath(os.curdir) -sys.path.append(root_dir) +#root_dir = os.path.abspath(os.curdir) +#sys.path.append(root_dir) import pandas as pd import numpy as np import h5py import logging -import utils.g5505_utils as utils -import instruments.readers.filereader_registry as filereader_registry +try: + from dima.utils import g5505_utils as utils + from dima.instruments.readers import filereader_registry as filereader_registry +except ModuleNotFoundError: + import utils.g5505_utils as utils + import instruments.readers.filereader_registry as filereader_registry diff --git a/visualization/hdf5_vis.py b/visualization/hdf5_vis.py index c1d8a225a8c95e97770cc50671b47a0e4496426a..1fc4948e8530ea6820ad53a0f1a50f5c52b5d86f 100644 --- a/visualization/hdf5_vis.py +++ b/visualization/hdf5_vis.py @@ -13,8 +13,11 @@ from plotly.subplots import make_subplots import plotly.graph_objects as go import plotly.express as px #import plotly.io as pio -from src.hdf5_ops import get_parent_child_relationships +try: + from dima.src.hdf5_ops import get_parent_child_relationships +except ModuleNotFoundError: + from src.hdf5_ops import get_parent_child_relationships def display_group_hierarchy_on_a_treemap(filename: str):