From 821d314cb6436968166c25099e45ccb1dec21ab9 Mon Sep 17 00:00:00 2001
From: Florez Ospina Juan Felipe <juan.florez-ospina@psi.ch>
Date: Sat, 22 Feb 2025 17:10:53 +0100
Subject: [PATCH] Change import statements with try except to enable explicit
 import of submodules from import to avoid conflicts with parent project.

---
 instruments/instrument_registry.xlsx       | Bin 0 -> 12089 bytes
 instruments/readers/acsm_tofware_reader.py |   5 ++++-
 instruments/readers/filereader_registry.py |  10 +++++++---
 instruments/readers/flag_reader.py         |   5 ++++-
 pipelines/data_integration.py              |  12 +++++++++---
 pipelines/metadata_revision.py             |   7 ++++++-
 src/git_ops.py                             |   9 +++++++--
 src/hdf5_ops.py                            |  10 +++++++---
 src/hdf5_writer.py                         |  12 ++++++++----
 visualization/hdf5_vis.py                  |   5 ++++-
 10 files changed, 56 insertions(+), 19 deletions(-)
 create mode 100644 instruments/instrument_registry.xlsx

diff --git a/instruments/instrument_registry.xlsx b/instruments/instrument_registry.xlsx
new file mode 100644
index 0000000000000000000000000000000000000000..283283bbe21aaa4cb7a490118e9275dc3db07ffc
GIT binary patch
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HcmV?d00001

diff --git a/instruments/readers/acsm_tofware_reader.py b/instruments/readers/acsm_tofware_reader.py
index a519c18..c45039c 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 fc4010d..ca745a2 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 8534bb4..46cc249 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 cd453c0..5bb5bb7 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 0089dc6..199c886 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 b7395dc..1c55231 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 ba71f73..9b8575d 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 3006b7e..c8f1475 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 c1d8a22..1fc4948 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):