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Merged
lzehl merged 2 commits into from
Jun 5, 2025
Merged

Use openMINDS version 3, rather than "latest" #78

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54a4a11
use openMINDS version 3, rather than "latest"
apdavison Jun 4, 2025
748711d
Update report.py
Peyman-N Jun 5, 2025
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4 changes: 2 additions & 2 deletions bids2openminds/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,8 +6,8 @@
import pandas as pd
from nameparser import HumanName

import openminds.latest.core as omcore
import openminds.latest.controlled_terms as controlled_terms
import openminds.v3.core as omcore
import openminds.v3.controlled_terms as controlled_terms
from openminds import IRI

from .utility import table_filter, pd_table_value, file_hash, file_storage_size, detect_nifti_version
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8 changes: 4 additions & 4 deletions bids2openminds/report.py
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Expand Up @@ -9,20 +9,20 @@ def create_report(dataset, dataset_version, collection, dataset_description, inp
behavioral_protocols_numbers = 0

for item in collection:
if item.type_ == "https://openminds.ebrains.eu/core/Subject":
if item.type_.endswith("Subject"):

subject_number += 1
subject_state_numbers.append(len(item.studied_states))

if item.type_ == "https://openminds.ebrains.eu/core/File":
if item.type_.endswith("File"):

files_number += 1

if item.type_ == "https://openminds.ebrains.eu/core/FileBundle":
if item.type_.endswith("FileBundle"):

file_bundle_number += 1

if item.type_ == "https://openminds.ebrains.eu/core/BehavioralProtocol":
if item.type_.endswith("BehavioralProtocol"):

behavioral_protocols_numbers += 1

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6 changes: 3 additions & 3 deletions bids2openminds/utility.py
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Expand Up @@ -7,9 +7,9 @@

import pandas as pd

import openminds.latest.controlled_terms as controlled_terms
from openminds.latest.core import Hash, QuantitativeValue, ContentType
from openminds.latest.controlled_terms import UnitOfMeasurement
import openminds.v3.controlled_terms as controlled_terms
from openminds.v3.core import Hash, QuantitativeValue, ContentType
from openminds.v3.controlled_terms import UnitOfMeasurement


def read_json(file_path: str) -> dict:
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2 changes: 1 addition & 1 deletion pyproject.toml
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@@ -1,6 +1,6 @@
[project]
name = "bids2openminds"
version = "0.1.0"
version = "0.1.1.dev.0"
dependencies = [
"bids",
"openminds >= 0.2.3",
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2 changes: 1 addition & 1 deletion test/test_person.py
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@@ -1,7 +1,7 @@
# test for create_openminds_person function in the main
import pytest
from bids2openminds.main import create_openminds_person
import openminds.latest.core as omcore
import openminds.v3.core as omcore

# Test data: (full_name, given_name, family_name)
example_names = [("John Ronald Reuel Tolkien", "John Ronald Reuel", "Tolkien"),
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