scicat-widget 26.2.0__tar.gz

scicat_widget-26.2.0/.gitignore

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+# PythonBuild artifacts
+build
+dist
+node_modules
+*.egg-info
+.DS_Store
+src/*/_static
+
+# Documentation
+html
+docs/generated
+
+# Caches
+*.ipynb_checkpoints
+__pycache__/
+.virtual_documents
+.hypothesis
+.pytest_cache
+.ruff_cache
+.mypy_cache
+
+# Editor config / caches
+.idea/
+.vscode/
+.vs/
+
+# Environments
+Pipfile
+venv
+.venv
+
+# Ontologies
+*.jsonld
+
+# Data files
+*.data
+*.dat
+*.csv
+*.xye
+*.h5
+*.hdf5
+*.hdf
+*.nxs
+*.raw
+*.cif
+*.rcif
+*.ort
+*.zip
+*.sqw
+*.nxspe
+*.mtz

scicat_widget-26.2.0/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2026, SciCat Project
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

scicat_widget-26.2.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: scicat_widget
+Version: 26.2.0
+Summary: SciCat dataset widget
+Project-URL: Bug Tracker, https://github.com/jl-wynen/scicat_widget/issues
+Project-URL: Source, https://github.com/jl-wynen/scicat_widget
+License-File: LICENSE
+Classifier: Framework :: Jupyter
+Classifier: Framework :: Jupyter :: JupyterLab
+Classifier: Framework :: Jupyter :: JupyterLab :: 4
+Classifier: Framework :: Jupyter :: JupyterLab :: Extensions
+Classifier: Framework :: Jupyter :: JupyterLab :: Extensions :: Prebuilt
+Classifier: Intended Audience :: Science/Research
+Classifier: Natural Language :: English
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering
+Classifier: Typing :: Typed
+Requires-Python: >=3.11
+Requires-Dist: anywidget>=0.9.21
+Requires-Dist: ipykernel>=6.30.1
+Requires-Dist: jupyter-host-file-picker>=26.2.1
+Requires-Dist: pydantic>=2.12
+Requires-Dist: scitacean>=26.2.0
+Description-Content-Type: text/markdown
+
+# widget
+
+## Installation
+
+```sh
+pip install widget
+```
+
+or with [uv](https://github.com/astral-sh/uv):
+
+```sh
+uv add widget
+```
+
+## Development
+
+We recommend using [uv](https://github.com/astral-sh/uv) for development.
+It will automatically manage virtual environments and dependencies for you.
+
+```sh
+uv run jupyter lab example.ipynb
+```
+
+Alternatively, create and manage your own virtual environment:
+
+```sh
+python -m venv .venv
+source .venv/bin/activate
+pip install -e ".[dev]"
+jupyter lab example.ipynb
+```
+
+The widget front-end code bundles it's JavaScript dependencies. After setting up Python,
+make sure to install these dependencies locally:
+
+```sh
+npm install
+```
+
+While developing, you can run the following in a separate terminal to automatically
+rebuild JavaScript as you make changes:
+
+```sh
+npm run dev
+```
+
+Open `example.ipynb` in JupyterLab, VS Code, or your favorite editor
+to start developing. Changes made in `js/` will be reflected
+in the notebook.

scicat_widget-26.2.0/README.md

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+# widget
+
+## Installation
+
+```sh
+pip install widget
+```
+
+or with [uv](https://github.com/astral-sh/uv):
+
+```sh
+uv add widget
+```
+
+## Development
+
+We recommend using [uv](https://github.com/astral-sh/uv) for development.
+It will automatically manage virtual environments and dependencies for you.
+
+```sh
+uv run jupyter lab example.ipynb
+```
+
+Alternatively, create and manage your own virtual environment:
+
+```sh
+python -m venv .venv
+source .venv/bin/activate
+pip install -e ".[dev]"
+jupyter lab example.ipynb
+```
+
+The widget front-end code bundles it's JavaScript dependencies. After setting up Python,
+make sure to install these dependencies locally:
+
+```sh
+npm install
+```
+
+While developing, you can run the following in a separate terminal to automatically
+rebuild JavaScript as you make changes:
+
+```sh
+npm run dev
+```
+
+Open `example.ipynb` in JupyterLab, VS Code, or your favorite editor
+to start developing. Changes made in `js/` will be reflected
+in the notebook.

scicat_widget-26.2.0/pyproject.toml

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+[build-system]
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
+
+[project]
+name = "scicat_widget"
+dynamic = ["version"]
+readme = "README.md"
+description = "SciCat dataset widget"
+classifiers = [
+    "Framework :: Jupyter",
+    "Framework :: Jupyter :: JupyterLab",
+    "Framework :: Jupyter :: JupyterLab :: 4",
+    "Framework :: Jupyter :: JupyterLab :: Extensions",
+    "Framework :: Jupyter :: JupyterLab :: Extensions :: Prebuilt",
+    "Intended Audience :: Science/Research",
+    "Natural Language :: English",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering",
+    "Typing :: Typed",
+]
+requires-python = ">=3.11"
+dependencies = [
+    "anywidget>=0.9.21",
+    "ipykernel>=6.30.1",
+    "jupyter-host-file-picker>=26.2.1",
+    "pydantic>=2.12",
+    "scitacean>=26.2.0",
+]
+
+[dependency-groups]
+dev = [
+    { include-group = "test" },
+    "anywidget[dev]>=0.9.21",
+    "ipykernel>=6.30.1",
+    "jupyterlab>=4.5.0",
+    "mypy>=1.17",
+    "ruff>=0.14",
+    "watchfiles>=1.1"
+]
+test = [
+    "pytest>=9",
+]
+
+[project.urls]
+# "Documentation" = "https://scicatproject.github.io/scitacean"
+"Bug Tracker" = "https://github.com/jl-wynen/scicat_widget/issues"
+"Source" = "https://github.com/jl-wynen/scicat_widget"
+
+[tool.hatch.build]
+only-packages = true
+artifacts = ["src/scicat_widget/_static/*"]
+
+[tool.hatch.build.hooks.jupyter-builder]
+build-function = "hatch_jupyter_builder.npm_builder"
+ensured-targets = ["src/scicat_widget/_static/datasetUploadWidget.js"]
+skip-if-exists = ["src/scicat_widget/_static/datasetUploadWidget.js"]
+dependencies = ["hatch-jupyter-builder>=0.5.0"]
+
+[tool.hatch.build.hooks.jupyter-builder.build-kwargs]
+npm = "npm"
+build_cmd = "build"
+
+[tool.hatch.version]
+source = "vcs"
+
+[tool.pytest.ini_options]
+minversion = "7.0"
+testpaths = "tests"
+addopts = """
+--strict-config
+--strict-markers
+-ra
+-v
+"""
+filterwarnings = [
+    "error",
+]
+
+[tool.mypy]
+plugins = "pydantic.mypy"
+mypy_path = "src"
+exclude = ["docs/conf.py", "venv", ".venv"]
+ignore_missing_imports = true
+enable_error_code = [
+    "ignore-without-code",
+    "redundant-expr",
+    "truthy-bool",
+]
+strict = true
+show_error_codes = true
+warn_unreachable = true
+
+[tool.pydantic-mypy]
+init_forbid_extra = true
+init_typed = true
+warn_required_dynamic_aliases = true
+
+[tool.ruff]
+line-length = 88
+extend-include = ["*.ipynb"]
+extend-exclude = [".*", "__pycache__", "build", "dist", "venv"]
+
+[tool.ruff.lint]
+select = ["B", "C4", "D", "DTZ", "E", "F", "G", "I", "FBT003", "FURB", "PERF", "PGH", "PT", "PYI", "RUF", "S", "T20", "UP", "W"]
+ignore = [
+    "D105", # most magic methods don't need docstrings as their purpose is always the same
+    "E741", "E742", "E743", # do not use names ‘l’, ‘O’, or ‘I’; they are not a problem with a proper font
+    # Conflict with ruff format, see
+    # https://docs.astral.sh/ruff/formatter/#conflicting-lint-rules
+    "COM812", "COM819", "D206", "D300", "E111", "E114", "E117", "ISC001", "ISC002", "Q000", "Q001", "Q002", "Q003", "W191",
+]
+fixable = ["B010", "I001", "PT001", "RUF022"]
+isort.known-first-party = ["scicat_widget"]
+pydocstyle.convention = "numpy"
+
+[tool.ruff.lint.per-file-ignores]
+"tests/*" = [
+    "S101", # asserts are fine in tests
+    "D10", # no docstrings required in tests
+]
+"docs/*" = [
+    "D", "E402", "F811", "F841", "RUF015", "S101", "T201",
+]
+"*.ipynb" = ["I"]
+"docs/conf.py" = ["D10"]

scicat_widget-26.2.0/src/scicat_widget/__init__.py

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+"""Jupyter widget for uploading datasets to SciCat."""
+
+import importlib.metadata
+
+from ._widgets import DatasetUploadWidget, dataset_upload_widget
+
+try:
+    __version__ = importlib.metadata.version("scicat_widget")
+except importlib.metadata.PackageNotFoundError:
+    __version__ = "0.0.0"
+
+__all__ = ["DatasetUploadWidget", "dataset_upload_widget"]

scicat_widget-26.2.0/src/scicat_widget/_logging.py

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+# SPDX-License-Identifier: BSD-3-Clause
+# Copyright (c) 2026 SciCat Project (https://github.com/SciCatProject/scitacean)
+
+import logging
+
+
+# TODO does not show up in Jupyter (need to configure handler)
+def get_logger() -> logging.Logger:
+    return logging.getLogger("scicat-widget")

scicat_widget-26.2.0/src/scicat_widget/_model.py

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+# SPDX-License-Identifier: BSD-3-Clause
+# Copyright (c) 2026 SciCat Project (https://github.com/SciCatProject/scitacean)
+
+from pydantic import BaseModel, EmailStr
+from scitacean.model import Instrument
+
+
+class ProposalOverview(BaseModel):
+    id_: str
+    title: str
+    instrument_ids: list[str]
+
+
+class UserInfo(BaseModel):
+    user_id: str
+    display_name: str | None
+    email: EmailStr | None
+    access_groups: list[str]
+    orcid_id: str | None
+    # The proposals we know the user is a member of, they may have access to more:
+    proposals: list[ProposalOverview]
+
+
+__all__ = ["Instrument", "ProposalOverview", "UserInfo"]

scicat_widget-26.2.0/src/scicat_widget/_scicat_api.py

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+# SPDX-License-Identifier: BSD-3-Clause
+# Copyright (c) 2026 SciCat Project (https://github.com/SciCatProject/scitacean)
+
+from scitacean import Client
+
+# Not great but there is no need to reimplement this here,
+# and handling of ORCID iDs is not part of the core functionality of Scitacean.
+from scitacean._internal.orcid import parse_orcid_id
+
+from ._model import Instrument, ProposalOverview, UserInfo
+
+
+def get_user_and_scicat_info(client: Client) -> tuple[UserInfo, list[Instrument]]:
+    user_info = get_user_info(client)
+    instruments = get_instruments(client)
+    return user_info, instruments
+
+
+def get_user_info(client: Client) -> UserInfo:
+    identity = client.scicat.call_endpoint(
+        cmd="GET", url="users/my/identity", operation="get_user_info"
+    )
+    profile = identity["profile"]
+
+    access_groups = sorted(profile.get("accessGroups", []))
+    proposals = get_proposals(client, access_groups) if access_groups else []
+
+    return UserInfo(
+        user_id=identity["userId"],
+        display_name=profile.get("displayName", None),
+        email=profile.get("email", None),
+        access_groups=access_groups,
+        orcid_id=_maybe_parse_orcid_id(
+            profile.get("oidcClaims", {}).get("orcid", None)
+        ),
+        proposals=proposals,
+    )
+
+
+def get_proposals(client: Client, access_groups: list[str]) -> list[ProposalOverview]:
+    proposals = client.scicat.call_endpoint(
+        cmd="GET", url="proposals", operation="get_proposals"
+    )
+    # the API call returns all proposals, select only the ones the user has access to:
+    # assuming the access groups match proposals (the case at ESS)
+    return [
+        ProposalOverview(
+            id_=p["proposalId"], title=p["title"], instrument_ids=p["instrumentIds"]
+        )
+        for p in proposals
+        if p["proposalId"] in access_groups
+    ]
+
+
+def get_instruments(client: Client) -> list[Instrument]:
+    return [
+        Instrument.from_download_model(instrument)
+        for instrument in client.scicat.get_all_instrument_models()
+    ]
+
+
+def _maybe_parse_orcid_id(orcid_id: str | None) -> str | None:
+    if orcid_id is None:
+        return None
+    try:
+        return parse_orcid_id(orcid_id)
+    except ValueError:
+        return None

scicat_widget-26.2.0/src/scicat_widget/_static/assets.js

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+var e={accessGroups:{label:"Access groups",description:"Groups with access to the dataset."},checksumAlgorithm:{label:"Checksum algorithm",description:"Algorithm for computing checksums of files. The default is a good choice for most cases."},creationLocation:{label:"Creation location",description:"Identifier for the place where data was taken, usually of the form 'site:facility:instrument'."},datasetName:{label:"Name",description:"The name of the dataset."},description:{label:"Description",description:"Free text explanation of the contents of the dataset."},endTime:{label:"End",description:"End time of data acquisition for the dataset."},instrumentId:{label:"Instrument",description:"The instrument where the data was taken."},isPublished:{label:"Published",description:"Check to make the dataset publicly available immediately."},keywords:{label:"Keywords",description:"Tags associated with the dataset for search and categorization. Values should ideally come from defined vocabularies, taxonomies, ontologies or knowledge graphs."},license:{label:"License",description:"Name of the license under which the data can be used."},owners:{label:"Owners",description:"People who own the dataset and its data. The owners typically have full access to the data and decide who can use it and how."},ownerGroup:{label:"Owner group",description:"The group that owns the dataset in SciCat and the data on disk. As uploader, you need to be a member of this group."},principalInvestigator:{label:"PI",description:"Principal investigator and contact person for the dataset."},proposalId:{label:"Proposal",description:"The proposal, if any, under which this data was recorded or computed."},relationships:{label:"Relationships",description:"Relationships with other datasets. In particular the 'input' relationship indicates datasets that were processed to obtain the dataset you are uploading."},runNumber:{label:"Run number",description:"Facility or instrument run number that this data belongs to."},sampleId:{label:"Sample ID",description:"SciCat identifier for the sample that was used to record the data."},scientificMetadata:{label:"Scientific metadata",description:"Arbitrary metadata describing the dataset. Choose what to include based on how you want to search for and identify the dataset later. The unit can be omitted if it does not apply."},sourceFolder:{label:"Source folder",description:"Absolute file path on the file server for a folder where the data files will be uploaded."},startTime:{label:"Start",description:"Start time of data acquisition for the dataset."},techniques:{label:"Techniques",description:"Techniques (experimental, analysis) used to produce the dataset."},type:{label:"Type",description:"Characterize the type of the dataset."},usedSoftware:{label:"Used software",description:"Software used to produce the dataset."}};function n(t){return e[t]??null}export{n as fieldInfo};

scicat_widget-26.2.0/src/scicat_widget/_static/comm.js

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+var o=class{constructor(e){this.callbacks=new Map;this.model=e,this.model.on("msg:custom",t=>{if(t.hasOwnProperty("type")){let s=t.key,r=this.callbacks.get(t.type)?.get(s);r&&r(t.payload);return}console.warn(`Unknown message type: ${t}`)})}sendReqInspectFile(e,t){this.model.send({type:"req:inspect-file",key:e,payload:t})}onResInspectFile(e,t){this.getForMethod("res:inspect-file").set(e,t)}offResInspectFile(e){this.getForMethod("res:inspect-file").delete(e)}sendReqBrowseFiles(e,t){this.model.send({type:"req:browse-files",key:e,payload:t})}onResBrowseFiles(e,t){this.getForMethod("res:browse-files").set(e,t)}offResBrowseFiles(e){this.getForMethod("res:browse-files").delete(e)}sendReqUploadDataset(e,t){this.model.send({type:"req:upload-dataset",key:e,payload:t})}onResUploadDataset(e,t){this.getForMethod("res:upload-dataset").set(e,t)}getForMethod(e){let t=this.callbacks.get(e);if(t!==void 0)return t;let s=new Map;return this.callbacks.set(e,s),s}};export{o as BackendComm};

scicat_widget-26.2.0/src/scicat_widget/_static/datasetUploadWidget.css

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