girder-sample-tracker 2.0.0__tar.gz

girder_sample_tracker-2.0.0/.github/workflows/release.yml

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+name: Publish Python 🐍 distribution 📦 to PyPI and TestPyPI
+
+on: push
+
+jobs:
+  build:
+    name: Build distribution 📦
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.x"
+    - name: Set up Node.js
+      uses: actions/setup-node@v4
+      with:
+        node-version: "18"
+    - name: Install pypa/build
+      run: >-
+        python3 -m
+        pip install
+        build
+        --user
+    - name: Build js component in package/web_client
+      run: >-
+        cd $(find . -maxdepth 2 -mindepth 2 -type d -name web_client)
+        && npm ci
+        && npm run build
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build
+    - name: install check-manifest
+      run: >-
+        python3 -m
+        pip install
+        check-manifest
+        --user
+    - name: Check the package manifest
+      run: check-manifest -vvv
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-pypi:
+    name: >-
+      Publish Python 🐍 distribution 📦 to PyPI
+    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/girder-sample-tracker
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    name: >-
+      Sign the Python 🐍 distribution 📦 with Sigstore
+      and upload them to GitHub Release
+    needs:
+    - publish-to-pypi
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write  # IMPORTANT: mandatory for making GitHub Releases
+      id-token: write  # IMPORTANT: mandatory for sigstore
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Sign the dists with Sigstore
+      uses: sigstore/gh-action-sigstore-python@v3.0.0
+      with:
+        inputs: >-
+          ./dist/*.tar.gz
+          ./dist/*.whl
+    - name: Upload artifact signatures to GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      # Upload to GitHub Release using the `gh` CLI.
+      # `dist/` contains the built packages, and the
+      # sigstore-produced signatures and certificates.
+      run: >-
+        gh release upload
+        '${{ github.ref_name }}' dist/**
+        --repo '${{ github.repository }}'

girder_sample_tracker-2.0.0/.gitignore

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+Testing
+.vscode
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+node_modules/

girder_sample_tracker-2.0.0/LICENSE

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+Copyright (c) 2024, Kacper Kowalik, University of Illinois at Urbana-Champaign
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* 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.
+
+* Neither the name of girder_wholetale 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.

girder_sample_tracker-2.0.0/PKG-INFO

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+Metadata-Version: 2.2
+Name: girder-sample-tracker
+Version: 2.0.0
+Summary: Girder Plugin adding a simple tracker for material samples
+License: BSD
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Web Environment
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: girder>=5.0.0a5.dev0
+Requires-Dist: qrcode[pil]
+Requires-Dist: cairosvg
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: license
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+### Girder Sample Tracker
+
+This plugin provides a simple tracker for material samples. It is intended to be used in conjunction with the [Girder](https://girder.readthedocs.io/en/latest/) data management platform.

girder_sample_tracker-2.0.0/README.md

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+### Girder Sample Tracker
+
+This plugin provides a simple tracker for material samples. It is intended to be used in conjunction with the [Girder](https://girder.readthedocs.io/en/latest/) data management platform.

girder_sample_tracker-2.0.0/girder_sample_tracker/__init__.py

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+import os
+from girder.plugin import GirderPlugin, registerPluginStaticContent
+from girder.utility.model_importer import ModelImporter
+from .rest.sample import Sample
+from .models.sample import Sample as SampleModel
+
+
+class SampleTrackerPlugin(GirderPlugin):
+    DISPLAY_NAME = "Sample Tracker"
+
+    def load(self, info):
+        ModelImporter.registerModel("sample", SampleModel, plugin="sample_tracker")
+        info["apiRoot"].sample = Sample()
+        registerPluginStaticContent(
+            plugin="sample_tracker",
+            css=["/style.css"],
+            js=["/girder-plugin-sample-tracker.umd.cjs"],
+            staticDir=os.path.join(os.path.dirname(__file__), "web_client", "dist"),
+            tree=info["serverRoot"],
+        )

girder_sample_tracker-2.0.0/girder_sample_tracker/models/sample.py

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+import datetime
+import io
+
+import cairosvg
+import qrcode
+from girder.constants import AccessType
+from girder.models.model_base import AccessControlledModel
+from qrcode.compat.etree import ET
+from qrcode.image.svg import SvgPathFillImage
+
+
+class Sample(AccessControlledModel):
+    def initialize(self):
+        self.name = "sample"
+        self.ensureIndices(["name"])
+
+        self.exposeFields(
+            level=AccessType.READ,
+            fields=(
+                "_id",
+                "created",
+                "creator",
+                "description",
+                "eventTypes",
+                "updated",
+                "name",
+                "events",
+            ),
+        )
+
+    def validate(self, doc):
+        return doc
+
+    def create(
+        self, name, creator, description=None, eventTypes=None, access=None, save=True
+    ):
+        now = datetime.datetime.utcnow()
+
+        sample = {
+            "name": name,
+            "creator": creator["_id"],
+            "created": now,
+            "description": description,
+            "eventTypes": eventTypes or [],
+            "updated": now,
+            "events": [],
+        }
+
+        if access is not None:
+            self.setAccessList(sample, access, save=False, user=creator)
+        else:
+            self.setUserAccess(sample, user=creator, level=AccessType.ADMIN, save=False)
+        if save:
+            sample = self.save(sample)
+
+        return sample
+
+    def add_event(self, sample, event, save=True):
+        sample["events"].insert(0, event)
+        sample["updated"] = event["created"]
+
+        if save:
+            sample = self.save(sample)
+
+        return sample
+
+    def qr_code(self, sample, url):
+        buf = io.BytesIO()
+        qr = qrcode.QRCode(
+            version=6,
+            error_correction=qrcode.constants.ERROR_CORRECT_H,
+            border=10,
+            image_factory=SvgPathFillImage,
+        )
+        qr.add_data(f"{url}/#sample/{sample['_id']}/add")
+        qr.make(fit=True)
+
+        img = qr.make_image(fill_color="black", back_color="white")
+        text = ET.SubElement(
+            img._img,
+            "text",
+            {
+                "x": "50%",
+                "y": "93%",
+                "dominant-baseline": "middle",
+                "text-anchor": "middle",
+                "font-size": "5",
+                "fill": "black",
+            },
+        )
+        text.text = sample["name"]
+        cairosvg.svg2png(
+            bytestring=img.to_string(encoding="unicode"), write_to=buf, dpi=300
+        )
+        buf.seek(0)
+        return buf