diff --git a/nomad/datamodel/metainfo/eln/openbis.py b/nomad/datamodel/metainfo/eln/openbis.py
index bb47176bb3a1a38bf36c41a9fc2303bac5c2a843..8f6380862478969eca16b7a838aec90fd83cdf01 100644
--- a/nomad/datamodel/metainfo/eln/openbis.py
+++ b/nomad/datamodel/metainfo/eln/openbis.py
@@ -138,76 +138,67 @@ class OpenbisEntry(EntryData):
else:
# Initializing pybis object
try:
- from pybis import Openbis
+ from nomad_openbis.openbis import OpenbisHandler
- openbis = Openbis(self.project_url, verify_certificates=False)
- except Exception:
- self._clear_login_info(archive)
- raise OpenbisImportError(
- 'Failed to connect to the openbis server. Check the project url to be correct.'
- )
-
- try:
- openbis.login(self.username, self.password, save_token=True)
- except Exception:
- self._clear_login_info(archive)
- raise OpenbisImportError(
- 'Failed to login to the openbis server. Check the username and password to be correct.'
- )
-
- # remove potential old content
- self.spaces.clear()
-
- try:
- spaces = openbis.get_spaces()
- except Exception:
- self._clear_login_info(archive)
- raise OpenbisImportError(
- 'Failed to fetch spaces. The pybis package might have been changed.'
- )
-
- # parsing the content in the spaces
- for space in spaces:
- space_element = OpenbisSpace()
- space_element.m_update_from_dict(space.attrs.all())
-
- try:
- projects = space.get_projects()
- except Exception:
- self._clear_login_info(archive)
- raise OpenbisImportError(
- 'Failed to fetch projects. The pybis package might have been changed.'
- )
- for project in projects:
- project_element = OpenbisProject()
- project_element.m_update_from_dict(project.attrs.all())
- space_element.projects.append(project_element)
+ with OpenbisHandler(
+ self.project_url, self.username, self.password, archive, logger
+ ) as handler:
+ # remove potential old content
+ self.spaces.clear()
try:
- experiments = project.get_experiments()
+ spaces = handler.openbis.get_spaces()
except Exception:
self._clear_login_info(archive)
raise OpenbisImportError(
- 'Failed to fetch experiments. The pybis package might have been changed.'
+ 'Failed to fetch spaces. The pybis package might have been changed.'
)
- for experiment in experiments:
- experiment_element = OpenbisExperiment()
- experiment_element.m_update_from_dict(experiment.attrs.all())
- try:
- experiment_element.download_files(
- experiment, archive, logger
- )
- except Exception as e:
- logger.error('Failed to download attachments.', exec_info=e)
-
- project_element.experiments.append(experiment_element)
- self.spaces.append(space_element)
+ # parsing the content in the spaces
+ for space in spaces:
+ space_element = OpenbisSpace()
+ space_element.m_update_from_dict(space.attrs.all())
- openbis.logout()
+ try:
+ projects = space.get_projects()
+ except Exception:
+ self._clear_login_info(archive)
+ raise OpenbisImportError(
+ 'Failed to fetch projects. The pybis package might have been changed.'
+ )
+ for project in projects:
+ project_element = OpenbisProject()
+ project_element.m_update_from_dict(project.attrs.all())
+ space_element.projects.append(project_element)
+
+ try:
+ experiments = project.get_experiments()
+ except Exception:
+ self._clear_login_info(archive)
+ raise OpenbisImportError(
+ 'Failed to fetch experiments. The pybis package might have been changed.'
+ )
+ for experiment in experiments:
+ experiment_element = OpenbisExperiment()
+ experiment_element.m_update_from_dict(
+ experiment.attrs.all()
+ )
+ try:
+ experiment_element.download_files(
+ experiment, archive, logger
+ )
+ except Exception as e:
+ logger.error(
+ 'Failed to download attachments.', exec_info=e
+ )
+
+ project_element.experiments.append(experiment_element)
+
+ self.spaces.append(space_element)
+ except Exception as e:
+ raise OpenbisImportError(e)
self._clear_login_info(archive)
-
logger.info('Transferring openbis data is finished.')
diff --git a/pyproject.toml b/pyproject.toml
index fa2eb4608da33fb5b41572a4f4896eec37156d59..3feaa2d5c768b7894593b4154dec5297ffce6575 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -65,7 +65,7 @@ parsing = [
'asr==0.4.1',
'h5py==3.11.0',
'netCDF4==1.6.5',
- 'pybis@git+https://github.com/FAIRmat-NFDI/fairmat-pybis.git@91039c2a1df364c88ab7e284b59c43ec42f18370',
+ 'nomad-openbis',
'pynxtools[convert]==0.3.1',
'quippy-ase==0.9.14',
'rdkit==2023.9.5',
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 71a25d4c4561c7f2700418af6ee639cbfe483a6f..8dd1e510d41f0616f4819b8f83941e169200fa66 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -54,7 +54,7 @@ contourpy==1.2.1 # via matplotlib, -r requirements.txt
coverage==7.5.3 # via pytest-cov
cryptography==42.0.8 # via jwcrypto, pyjwt, pyopenssl, rfc3161ng, secretstorage, -r requirements.txt
cycler==0.12.1 # via matplotlib, -r requirements.txt
-dask==2024.6.0 # via hyperspy, kikuchipy, orix, pyxem, rosettasciio, -r requirements.txt
+dask==2024.6.1 # via hyperspy, kikuchipy, orix, pyxem, rosettasciio, -r requirements.txt
debugpy==1.8.1 # via ipykernel, -r requirements.txt
decorator==5.1.1 # via ipyparallel, ipython, validators, -r requirements.txt
defusedxml==0.7.1 # via nbconvert, -r requirements.txt
@@ -207,6 +207,7 @@ nionswift==16.11.0 # via pynxtools-em, -r requirements.txt
nionswift-io==15.2.1 # via nionswift, -r requirements.txt
nionui==7.1.1 # via nionswift, -r requirements.txt
nionutils==4.11.0 # via niondata, nionswift, nionswift-io, nionui, -r requirements.txt
+nomad-openbis==1.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
notebook==7.1.3 # via jupyter, -r requirements.txt
notebook-shim==0.2.4 # via jupyterlab, notebook, -r requirements.txt
nptyping==1.4.4 # via -r requirements.txt, nomad-lab (pyproject.toml)
@@ -225,7 +226,7 @@ packaging==24.1 # via build, dask, deprecation, f90wrap, gunicorn, hyp
paginate==0.5.6 # via mkdocs-material
palettable==3.3.3 # via pymatgen, -r requirements.txt
pamela==1.1.0 # via jupyterhub, -r requirements.txt
-pandas==1.5.3 # via ifes-apt-tc-data-modeling, panedr, pybis, pymatgen, pynxtools, radioactivedecay, xarray, -r requirements.txt, nomad-lab (pyproject.toml)
+pandas==1.5.3 # via ifes-apt-tc-data-modeling, nomad-openbis, panedr, pymatgen, pynxtools, radioactivedecay, xarray, -r requirements.txt, nomad-lab (pyproject.toml)
pandocfilters==1.5.1 # via nbconvert, -r requirements.txt
panedr==0.8.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
parmed==4.2.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
@@ -251,7 +252,6 @@ pure-eval==0.2.2 # via stack-data, -r requirements.txt
py-cpuinfo==9.0.0 # via blosc2, tables, -r requirements.txt
pyasn1==0.6.0 # via pyasn1-modules, rfc3161ng, -r requirements.txt
pyasn1-modules==0.4.0 # via rfc3161ng, -r requirements.txt
-pybis @ git+https://github.com/FAIRmat-NFDI/fairmat-pybis.git@91039c2a1df364c88ab7e284b59c43ec42f18370 # via -r requirements.txt, nomad-lab (pyproject.toml)
pybtex==0.24.0 # via pymatgen, -r requirements.txt
pycifrw==4.4.6 # via diffpy-structure, -r requirements.txt
pycodestyle==2.12.0 # via nomad-lab (pyproject.toml)
@@ -283,7 +283,7 @@ pytest-split==0.8.2 # via nomad-lab (pyproject.toml)
pytest-timeout==2.3.1 # via nomad-lab (pyproject.toml)
pytest-xdist==3.6.1 # via nomad-lab (pyproject.toml)
python-box==6.1.0 # via rosettasciio, -r requirements.txt
-python-dateutil==2.9.0.post0 # via arrow, celery, elasticsearch-dsl, ghp-import, hyperspy, ipyparallel, jupyter-client, jupyterhub, matplotlib, mkdocs-macros-plugin, pandas, pybis, rfc3161ng, rosettasciio, -r requirements.txt
+python-dateutil==2.9.0.post0 # via arrow, celery, elasticsearch-dsl, ghp-import, hyperspy, ipyparallel, jupyter-client, jupyterhub, matplotlib, mkdocs-macros-plugin, nomad-openbis, pandas, rfc3161ng, rosettasciio, -r requirements.txt
python-dotenv==1.0.1 # via uvicorn, -r requirements.txt
python-gitlab==2.10.1 # via nomad-lab (pyproject.toml)
python-json-logger==2.0.2 # via jupyter-events, jupyter-telemetry, -r requirements.txt, nomad-lab (pyproject.toml)
@@ -306,7 +306,7 @@ rdkit==2023.9.5 # via -r requirements.txt, nomad-lab (pyproject.toml)
readme-renderer==43.0 # via twine
recommonmark==0.7.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
regex==2024.5.15 # via mkdocs-material
-requests==2.31.0 # via docker, hyperspy, jupyterhub, jupyterlab-server, mkdocs-material, oauthenticator, optimade, pooch, pybis, pymatgen, python-gitlab, python-keycloak, requests-toolbelt, rfc3161ng, sphinx, twine, -r requirements.txt, nomad-lab (pyproject.toml)
+requests==2.31.0 # via docker, hyperspy, jupyterhub, jupyterlab-server, mkdocs-material, nomad-openbis, oauthenticator, optimade, pooch, pymatgen, python-gitlab, python-keycloak, requests-toolbelt, rfc3161ng, sphinx, twine, -r requirements.txt, nomad-lab (pyproject.toml)
requests-toolbelt==1.0.0 # via python-gitlab, python-keycloak, twine, -r requirements.txt
rfc3161ng==2.1.3 # via -r requirements.txt, nomad-lab (pyproject.toml)
rfc3339-validator==0.1.4 # via jsonschema, -r requirements.txt
@@ -325,7 +325,7 @@ scipy==1.13.1 # via ase, diffsims, findiff, griddataformats, hypersp
secretstorage==3.3.3 # via keyring
send2trash==1.8.3 # via jupyter-server, -r requirements.txt
sentinels==1.0.0 # via mongomock, -r requirements.txt
-setuptools==70.0.0 # via radioactivedecay, -r requirements.txt
+setuptools==70.1.0 # via radioactivedecay, -r requirements.txt
silx==2.1.0 # via pyfai, -r requirements.txt
six==1.16.0 # via anytree, asttokens, basicauth, bleach, diffpy-structure, elasticsearch-dsl, html5lib, isodate, pybtex, python-dateutil, rdflib, rfc3339-validator, validators, -r requirements.txt
smmap==5.0.1 # via gitdb, -r requirements.txt
@@ -347,11 +347,11 @@ starlette==0.27.0 # via fastapi, -r requirements.txt
structlog==24.2.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
sympy==1.12.1 # via findiff, hyperspy, pymatgen, radioactivedecay, -r requirements.txt
tables==3.9.2 # via ifes-apt-tc-data-modeling, -r requirements.txt
-tabulate==0.8.9 # via pybis, pymatgen, -r requirements.txt, nomad-lab (pyproject.toml)
+tabulate==0.8.9 # via nomad-openbis, pymatgen, -r requirements.txt, nomad-lab (pyproject.toml)
tenacity==8.4.1 # via plotly, -r requirements.txt
termcolor==2.4.0 # via mkdocs-macros-plugin
terminado==0.18.1 # via jupyter-server, jupyter-server-terminals, -r requirements.txt
-texttable==1.7.0 # via pybis, -r requirements.txt
+texttable==1.7.0 # via nomad-openbis, -r requirements.txt
threadpoolctl==3.5.0 # via mdanalysis, scikit-learn, -r requirements.txt
tifffile==2024.6.18 # via h5grove, hyperspy, scikit-image, -r requirements.txt
tinycss2==1.3.0 # via nbconvert, -r requirements.txt
@@ -373,8 +373,8 @@ tzlocal==5.2 # via nionswift, pynxtools-em, -r requirements.txt
uncertainties==3.2.1 # via lmfit, pymatgen, -r requirements.txt
unidecode==1.3.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
uri-template==1.3.0 # via jsonschema, -r requirements.txt
-urllib3==1.26.19 # via docker, elasticsearch, pybis, requests, -r requirements.txt
-uv==0.2.13 # via nomad-lab (pyproject.toml)
+urllib3==1.26.19 # via docker, elasticsearch, nomad-openbis, requests, -r requirements.txt
+uv==0.2.18 # via nomad-lab (pyproject.toml)
uvicorn==0.30.1 # via h5grove, -r requirements.txt, nomad-lab (pyproject.toml)
uvloop==0.19.0 # via uvicorn, -r requirements.txt
validators==0.18.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
diff --git a/requirements.txt b/requirements.txt
index 4322291cec7eb257315e8f485bb2d10f086e1901..03f266c39d1061ba36214bdf58a0c005c5ea1708 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -47,7 +47,7 @@ commonmark==0.9.1 # via recommonmark
contourpy==1.2.1 # via matplotlib
cryptography==42.0.8 # via jwcrypto, pyjwt, pyopenssl, rfc3161ng
cycler==0.12.1 # via matplotlib
-dask==2024.6.0 # via hyperspy, kikuchipy, orix, pyxem, rosettasciio
+dask==2024.6.1 # via hyperspy, kikuchipy, orix, pyxem, rosettasciio
debugpy==1.8.1 # via ipykernel
decorator==5.1.1 # via ipyparallel, ipython, validators
defusedxml==0.7.1 # via nbconvert
@@ -175,6 +175,7 @@ nionswift==16.11.0 # via pynxtools-em
nionswift-io==15.2.1 # via nionswift
nionui==7.1.1 # via nionswift
nionutils==4.11.0 # via niondata, nionswift, nionswift-io, nionui
+nomad-openbis==1.0.0 # via nomad-lab (pyproject.toml)
notebook==7.1.3 # via jupyter
notebook-shim==0.2.4 # via jupyterlab, notebook
nptyping==1.4.4 # via nomad-lab (pyproject.toml)
@@ -192,7 +193,7 @@ orjson==3.10.5 # via h5grove, nomad-lab (pyproject.toml)
packaging==24.1 # via dask, deprecation, f90wrap, gunicorn, hyperspy, ipykernel, jupyter-server, jupyterhub, jupyterlab, jupyterlab-server, matplotlib, mdanalysis, mongomock, nbconvert, pint, plotly, pooch, qtconsole, qtpy, scikit-image, silx, sphinx, tables, xarray, xraydb
palettable==3.3.3 # via pymatgen
pamela==1.1.0 # via jupyterhub
-pandas==1.5.3 # via ifes-apt-tc-data-modeling, panedr, pybis, pymatgen, pynxtools, radioactivedecay, xarray, eelsdbconverter (dependencies/parsers/eelsdb/pyproject.toml), nomad-lab (pyproject.toml)
+pandas==1.5.3 # via ifes-apt-tc-data-modeling, nomad-openbis, panedr, pymatgen, pynxtools, radioactivedecay, xarray, eelsdbconverter (dependencies/parsers/eelsdb/pyproject.toml), nomad-lab (pyproject.toml)
pandocfilters==1.5.1 # via nbconvert
panedr==0.8.0 # via nomad-lab (pyproject.toml)
parmed==4.2.2 # via nomad-lab (pyproject.toml)
@@ -215,7 +216,6 @@ pure-eval==0.2.2 # via stack-data
py-cpuinfo==9.0.0 # via blosc2, tables
pyasn1==0.6.0 # via pyasn1-modules, rfc3161ng
pyasn1-modules==0.4.0 # via rfc3161ng
-pybis @ git+https://github.com/FAIRmat-NFDI/fairmat-pybis.git@91039c2a1df364c88ab7e284b59c43ec42f18370 # via nomad-lab (pyproject.toml)
pybtex==0.24.0 # via pymatgen
pycifrw==4.4.6 # via diffpy-structure
pycparser==2.22 # via cffi
@@ -238,7 +238,7 @@ pyopenssl==24.1.0 # via certipy
pyparsing==3.1.2 # via matplotlib, rdflib
pyrsistent==0.20.0 # via jsonschema
python-box==6.1.0 # via rosettasciio
-python-dateutil==2.9.0.post0 # via arrow, celery, elasticsearch-dsl, hyperspy, ipyparallel, jupyter-client, jupyterhub, matplotlib, pandas, pybis, rfc3161ng, rosettasciio
+python-dateutil==2.9.0.post0 # via arrow, celery, elasticsearch-dsl, hyperspy, ipyparallel, jupyter-client, jupyterhub, matplotlib, nomad-openbis, pandas, rfc3161ng, rosettasciio
python-dotenv==1.0.1 # via uvicorn
python-json-logger==2.0.2 # via jupyter-events, jupyter-telemetry, nomad-lab (pyproject.toml)
python-keycloak==4.1.0 # via nomad-lab (pyproject.toml)
@@ -257,7 +257,7 @@ radioactivedecay==0.5.1 # via ifes-apt-tc-data-modeling
rdflib==5.0.0 # via nomad-lab (pyproject.toml)
rdkit==2023.9.5 # via nomad-lab (pyproject.toml)
recommonmark==0.7.1 # via nomad-lab (pyproject.toml)
-requests==2.31.0 # via docker, hyperspy, jupyterhub, jupyterlab-server, oauthenticator, optimade, pooch, pybis, pymatgen, python-keycloak, requests-toolbelt, rfc3161ng, sphinx, eelsdbconverter (dependencies/parsers/eelsdb/pyproject.toml), nomad-lab (pyproject.toml)
+requests==2.31.0 # via docker, hyperspy, jupyterhub, jupyterlab-server, nomad-openbis, oauthenticator, optimade, pooch, pymatgen, python-keycloak, requests-toolbelt, rfc3161ng, sphinx, eelsdbconverter (dependencies/parsers/eelsdb/pyproject.toml), nomad-lab (pyproject.toml)
requests-toolbelt==1.0.0 # via python-keycloak
rfc3161ng==2.1.3 # via nomad-lab (pyproject.toml)
rfc3339-validator==0.1.4 # via jsonschema
@@ -272,7 +272,7 @@ scikit-learn==1.5.0 # via kikuchipy, matid, pyxem, nomad-lab (pyproject.to
scipy==1.13.1 # via ase, diffsims, findiff, griddataformats, hyperspy, kikuchipy, lmfit, matid, mdanalysis, niondata, nionswift, orix, pyfai, pymatgen, pyxem, radioactivedecay, scikit-image, scikit-learn, sparse, xraydb, nomad-lab (pyproject.toml)
send2trash==1.8.3 # via jupyter-server
sentinels==1.0.0 # via mongomock
-setuptools==70.0.0 # via radioactivedecay
+setuptools==70.1.0 # via radioactivedecay
silx==2.1.0 # via pyfai
six==1.16.0 # via anytree, asttokens, basicauth, bleach, diffpy-structure, elasticsearch-dsl, html5lib, isodate, pybtex, python-dateutil, rdflib, rfc3339-validator, validators
smmap==5.0.1 # via gitdb
@@ -294,10 +294,10 @@ starlette==0.27.0 # via fastapi
structlog==24.2.0 # via nomad-lab (pyproject.toml)
sympy==1.12.1 # via findiff, hyperspy, pymatgen, radioactivedecay
tables==3.9.2 # via ifes-apt-tc-data-modeling
-tabulate==0.8.9 # via pybis, pymatgen, nomad-lab (pyproject.toml)
+tabulate==0.8.9 # via nomad-openbis, pymatgen, nomad-lab (pyproject.toml)
tenacity==8.4.1 # via plotly
terminado==0.18.1 # via jupyter-server, jupyter-server-terminals
-texttable==1.7.0 # via pybis
+texttable==1.7.0 # via nomad-openbis
threadpoolctl==3.5.0 # via mdanalysis, scikit-learn
tifffile==2024.6.18 # via h5grove, hyperspy, scikit-image
tinycss2==1.3.0 # via nbconvert
@@ -317,7 +317,7 @@ tzlocal==5.2 # via nionswift, pynxtools-em
uncertainties==3.2.1 # via lmfit, pymatgen
unidecode==1.3.2 # via nomad-lab (pyproject.toml)
uri-template==1.3.0 # via jsonschema
-urllib3==1.26.19 # via docker, elasticsearch, pybis, requests
+urllib3==1.26.19 # via docker, elasticsearch, nomad-openbis, requests
uvicorn==0.30.1 # via h5grove, nomad-lab (pyproject.toml)
uvloop==0.19.0 # via uvicorn
validators==0.18.2 # via nomad-lab (pyproject.toml)
diff --git a/tests/datamodel/metainfo/eln/test_openbis.py b/tests/datamodel/metainfo/eln/test_openbis.py
index cfc4f14fae408e5b094accfe1e6d736fa0cc1e6f..ae9f3712d6451143a9be229d8aeea40f8812df10 100644
--- a/tests/datamodel/metainfo/eln/test_openbis.py
+++ b/tests/datamodel/metainfo/eln/test_openbis.py
@@ -20,7 +20,7 @@ from urllib.parse import urlparse
import pytest
import json
-import pybis
+from nomad_openbis import openbis
from nomad.datamodel import ServerContext
from nomad.datamodel.metainfo.eln.openbis import OpenbisEntry, OpenbisImportError
@@ -151,7 +151,7 @@ def test_openbis(
return mock_response
# patching openbis attrs
- monkeypatch.setattr(pybis, 'Openbis', mock_openbis_response)
+ monkeypatch.setattr(openbis, 'Openbis', mock_openbis_response)
data = ExampleData(main_author=user1)
data.create_upload(upload_id='test_upload_id', published=False)