Checkpoint

.github/workflows/main.yaml

@@ -0,0 +1,69 @@
+name: Build
+
+on:
+  push:
+    branches: [ main ]
+
+jobs:
+  update-requirements:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+
+      - name: Update requirements file
+        run: |
+          python -m pip install --upgrade pip
+          pip install pipenv-to-requirements
+          pipenv_to_requirements
+
+      - name: Check in requirements.txt and requirements-dev.txt
+        run: |
+          git add requirements*.txt
+          if [[ ! -z $(git status -s requirements*.txt) ]]
+          then
+            git config --local user.email "[email protected]"
+            git config --local user.name "GitHub Action"
+            git commit -m 'Automatically generated requirements.txt and requirements-dev.txt' requirements*.txt
+            git push
+          fi
+
+  unittests-n-commits:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.7.1, 3.8, 3.9]
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pipenv
+        pipenv install --dev
+
+    - name: Test with unittest
+      run: |
+        pipenv run python -m unittest
+
+    - name: Check in test outputs
+      if: ${{ matrix.python-version == '3.9' }}
+      run: |
+        find tests -name output -exec git add --force {} \;
+        if [[ ! -z $(git status -s tests) ]]
+        then
+          git config --local user.email "[email protected]"
+          git config --local user.name "GitHub Action"
+          git commit -m 'Automated adding outputs from tests' tests
+          git push
+        fi

.github/workflows/pr-test.yaml

@@ -0,0 +1,27 @@
+name: Pull request unit tests
+
+on:
+  pull_request:
+    branches: [ main ]
+
+jobs:
+
+  build-pipenv:
+
+    runs-on: ubuntu-latest
+    strategy:
+      python-version: [3.7.1, 3.8, 3.9]
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install pipenv
+      uses: dschep/install-pipenv-action@v1
+    - name: Install dependencies and test
+      run: |
+        pipenv install --dev
+        pipenv run python -m unittest

.github/workflows/pypi-publish.yaml

@@ -0,0 +1,34 @@
+name: Publish Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install wheel
+
+    - name: build a binary wheel dist
+      run: |
+        rm -fr dist
+        python setup.py bdist_wheel sdist
+
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/[email protected]
+      with:
+        user: __token__
+        password: ${{ secrets.pypi_password }}

.gitignore

@@ -137,3 +137,6 @@ tests/test_config.ini
 
 # Don't lock
 Pipfile.lock
+
+# No Pycharm
+.idea/

AUTHORS

@@ -0,0 +1,2 @@
+Harold Solbrig <[email protected]>
+hsolbrig <[email protected]>

ChangeLog

@@ -0,0 +1,7 @@
+CHANGES
+=======
+
+* Remove YAMLRoot dependency on JsonObj
+* Checkpoint
+* checkpoint
+* Initial commit

Pipfile

@@ -0,0 +1,19 @@
+[[source]]
+url = "https://pypi.org/simple"
+verify_ssl = true
+name = "pypi"
+
+[packages]
+hbreader = "*"
+pyld = { git = "https://github.com/hsolbrig/pyld"}
+jsonasobj = { git = "https://github.com/hsolbrig/jsonasobj"}
+pyyaml = ">=5.1"
+rdflib = "*"
+rdflib-pyld-compat = "*"
+rdflib-jsonld = "*"
+click = "*"
+prefixcommons = "*"
+shexjsg = "*"
+
+[dev-packages]
+requests = "*"

checkout_outputs.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+# checkout (update) all of the outputs to revert to what is on github
+git checkout  `find tests -name output | xargs`

db.sh

@@ -0,0 +1 @@
+docker image build . -t context_server

dr.sh

@@ -0,0 +1 @@
+docker run -it --rm -d -p 8000:80 -p 8443:443 --name context_server -v `pwd`/:/usr/share/nginx/html context_server 

ds.sh

@@ -0,0 +1 @@
+docker stop context_server

hide_test_changes.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+# Make all of the test output files invisible to git
+git update-index --assume-unchanged `git status -s | grep tests | grep \/output\/ | sed 's/.* tests\//tests\//' | xargs`

linkml_runtime/dumpers/__init__.py

@@ -0,0 +1,7 @@
+from linkml_runtime.dumpers.json_dumper import JSONDumper
+from linkml_runtime.dumpers.rdf_dumper import RDFDumper
+from linkml_runtime.dumpers.yaml_dumper import YAMLDumper
+
+json_dumper = JSONDumper()
+rdf_dumper = RDFDumper()
+yaml_dumper = YAMLDumper()

linkml_runtime/dumpers/dumper_root.py

@@ -0,0 +1,27 @@
+from abc import ABC, abstractmethod
+
+from linkml_runtime.utils.yamlutils import YAMLRoot
+
+
+class Dumper(ABC):
+    """ Abstract base class for all dumpers """
+
+    def dump(self, element: YAMLRoot, to_file: str, **_) -> None:
+        """
+        Write element to to_file
+        :param element: LinkML object to be dumped
+        :param to_file: file to dump to
+        :@param _: method specific arguments
+        """
+        with open(to_file, 'w') as output_file:
+            output_file.write(self.dumps(element, **_))
+
+    @abstractmethod
+    def dumps(self, element: YAMLRoot, **_) -> str:
+        """
+        Convert element to a string
+        @param element: YAMLRoot object to be rendered
+        @param _: method specific arguments
+        @return: stringified representation of element
+        """
+        raise NotImplementedError()

linkml_runtime/dumpers/json_dumper.py

@@ -1,47 +1,51 @@
+import json
 from typing import Dict
 
+from linkml_runtime.dumpers.dumper_root import Dumper
 from linkml_runtime.utils.context_utils import CONTEXTS_PARAM_TYPE
 from linkml_runtime.utils.yamlutils import YAMLRoot, as_json_object
-from jsonasobj import as_json
 
 
-def remove_empty_items(obj: Dict) -> Dict:
-    """
-    Remove empty items from obj
-    :param obj:
-    :return: copy of dictionary with empty lists/dicts and Nones removed
-    """
-    return {k: v for k, v in obj.items() if not (v is None or v == [] or v == {})}
+class JSONDumper(Dumper):
 
+    def dump(self, element: YAMLRoot, to_file: str, contexts: CONTEXTS_PARAM_TYPE = None) -> None:
+        """
+        Write element as json to to_file
+        :param element: LinkML object to be serialized as YAML
+        :param to_file: file to write to
+        :param contexts: JSON-LD context(s) in the form of:
+            * file name
+            * URL
+            * JSON String
+            * dict
+            * JSON Object
+            * A list containing elements of any type named above
+        """
+        super().dump(element, to_file, contexts=contexts)
 
-def dump(element: YAMLRoot, to_file: str, contexts: CONTEXTS_PARAM_TYPE = None) -> None:
-    """
-    Write element as json to to_file
-    :param element: LinkML object to be serialized as YAML
-    :param to_file: file to write to
-    :param contexts: JSON-LD context(s) in the form of:
-        * file name
-        * URL
-        * JSON String
-        * dict
-        * JSON Object
-        * A list containing elements of any type named above
-    """
-    with open(to_file, 'w') as outf:
-        outf.write(dumps(element, contexts))
+    def dumps(self, element: YAMLRoot, contexts: CONTEXTS_PARAM_TYPE = None) -> str:
+        """
+        Return element as a JSON or a JSON-LD string
+        :param element: LinkML object to be emitted
+        :param contexts: JSON-LD context(s) in the form of:
+            * file name
+            * URL
+            * JSON String
+            * dict
+            * JSON Object
+            * A list containing elements of any type named above
+        :return: JSON Object representing the element
+        """
+        return json.dumps(as_json_object(element, contexts),
+                          default=lambda o: self.remove_empty_items(o) if isinstance(o, YAMLRoot) else json.JSONDecoder().decode(o),
+                          indent='  ')
 
 
-def dumps(element: YAMLRoot, contexts: CONTEXTS_PARAM_TYPE = None) -> str:
-    """
-    Return element as a JSON or a JSON-LD string
-    :param element: LinkML object to be emitted
-    :param contexts: JSON-LD context(s) in the form of:
-        * file name
-        * URL
-        * JSON String
-        * dict
-        * JSON Object
-        * A list containing elements of any type named above
-    :return: JSON Object representing the element
-    """
-    return as_json(as_json_object(element, contexts), filtr=remove_empty_items, indent='  ')
+    @staticmethod
+    def remove_empty_items(obj: Dict) -> Dict:
+        """
+        Remove empty items from obj
+        :param obj:
+        :return: copy of dictionary with empty lists/dicts and Nones removed
+        """
+        return {k: v for k, v in obj.__dict__.items() if not (v is None or v == [] or v == {})}