diff --git a/build.sh b/build.sh index f0169bb..45242fb 100644 --- a/build.sh +++ b/build.sh @@ -1,7 +1,7 @@ #!/bin/bash python -m venv .venv -source venv/bin/activate +source .venv/bin/activate pip install --upgrade pip pip install -r requirements.txt pip install -e . \ No newline at end of file diff --git a/example_notebook.ipynb b/example_notebook.ipynb index d4926d3..d0137e9 100644 --- a/example_notebook.ipynb +++ b/example_notebook.ipynb @@ -11,9 +11,20 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 7, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "from gen3_metadata.logger import setup_logger\n", "from gen3_metadata.gen3_metadata_parser import Gen3MetadataParser\n", @@ -22,7 +33,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 8, "metadata": {}, "outputs": [], "source": [ @@ -33,9 +44,52 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 9, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "File not found: [Errno 2] No such file or directory: 'path/to/credentials.json'\n", + "An unexpected error occurred during authentication: [Errno 2] No such file or directory: 'path/to/credentials.json'\n", + "Unexpected exception formatting exception. Falling back to standard exception\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Traceback (most recent call last):\n", + " File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/IPython/core/interactiveshell.py\", line 3550, in run_code\n", + " File \"/var/folders/h1/smw4rryj4zs361v4bw9qqc0c0000gn/T/ipykernel_58301/122813687.py\", line 2, in \n", + " gen3metadata.authenticate()\n", + " File \"/Users/harrijh/projects/gen3-metadata/src/gen3metadata/gen3_metadata_parser.py\", line 110, in authenticate\n", + " key = self._load_api_key()\n", + " File \"/Users/harrijh/projects/gen3-metadata/src/gen3metadata/gen3_metadata_parser.py\", line 60, in _load_api_key\n", + " with open(self.key_file_path, \"r\") as f:\n", + "FileNotFoundError: [Errno 2] No such file or directory: 'path/to/credentials.json'\n", + "\n", + "During handling of the above exception, another exception occurred:\n", + "\n", + "Traceback (most recent call last):\n", + " File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/pygments/styles/__init__.py\", line 45, in get_style_by_name\n", + "ModuleNotFoundError: No module named 'pygments.styles.default'\n", + "\n", + "During handling of the above exception, another exception occurred:\n", + "\n", + "Traceback (most recent call last):\n", + " File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/IPython/core/interactiveshell.py\", line 2144, in showtraceback\n", + " File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/IPython/core/ultratb.py\", line 1435, in structured_traceback\n", + " File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/IPython/core/ultratb.py\", line 1326, in structured_traceback\n", + " File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/IPython/core/ultratb.py\", line 1173, in structured_traceback\n", + " File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/IPython/core/ultratb.py\", line 1063, in format_exception_as_a_whole\n", + " File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/IPython/core/ultratb.py\", line 1114, in get_records\n", + " File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/pygments/styles/__init__.py\", line 47, in get_style_by_name\n", + "pygments.util.ClassNotFound: Could not find style module 'pygments.styles.default', though it should be builtin.\n" + ] + } + ], "source": [ "# Authenticate\n", "gen3metadata.authenticate()" @@ -43,13 +97,58 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 10, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "File not found: [Errno 2] No such file or directory: 'path/to/credentials.json'\n", + "An error occurred: [Errno 2] No such file or directory: 'path/to/credentials.json'\n", + "Unexpected exception formatting exception. Falling back to standard exception\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Traceback (most recent call last):\n", + " File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/IPython/core/interactiveshell.py\", line 3550, in run_code\n", + " File \"/var/folders/h1/smw4rryj4zs361v4bw9qqc0c0000gn/T/ipykernel_58301/3932466949.py\", line 4, in \n", + " gen3metadata.fetch_data_pd(program_name, project_code, node_label= \"medical_history\")\n", + " File \"/Users/harrijh/projects/gen3-metadata/src/gen3metadata/gen3_metadata_parser.py\", line 256, in fetch_data_pd\n", + " data = self.fetch_data(program_name, project_code, node_label, api_version=api_version, return_data=True)\n", + " File \"/Users/harrijh/projects/gen3-metadata/src/gen3metadata/gen3_metadata_parser.py\", line 185, in fetch_data\n", + " creds = self._load_api_key()\n", + " File \"/Users/harrijh/projects/gen3-metadata/src/gen3metadata/gen3_metadata_parser.py\", line 60, in _load_api_key\n", + " with open(self.key_file_path, \"r\") as f:\n", + "FileNotFoundError: [Errno 2] No such file or directory: 'path/to/credentials.json'\n", + "\n", + "During handling of the above exception, another exception occurred:\n", + "\n", + "Traceback (most recent call last):\n", + " File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/pygments/styles/__init__.py\", line 45, in get_style_by_name\n", + "ModuleNotFoundError: No module named 'pygments.styles.default'\n", + "\n", + "During handling of the above exception, another exception occurred:\n", + "\n", + "Traceback (most recent call last):\n", + " File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/IPython/core/interactiveshell.py\", line 2144, in showtraceback\n", + " File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/IPython/core/ultratb.py\", line 1435, in structured_traceback\n", + " File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/IPython/core/ultratb.py\", line 1326, in structured_traceback\n", + " File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/IPython/core/ultratb.py\", line 1173, in structured_traceback\n", + " File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/IPython/core/ultratb.py\", line 1063, in format_exception_as_a_whole\n", + " File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/IPython/core/ultratb.py\", line 1114, in get_records\n", + " File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/pygments/styles/__init__.py\", line 47, in get_style_by_name\n", + "pygments.util.ClassNotFound: Could not find style module 'pygments.styles.default', though it should be builtin.\n" + ] + } + ], "source": [ "# fetching data and returning as dataframe\n", "program_name= \"program1\"\n", - "project_code= \"project1\"\n", + "project_code= \"AusDiab_Simulated\"\n", "gen3metadata.fetch_data_pd(program_name, project_code, node_label= \"medical_history\")" ] }, diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..fdafb7e --- /dev/null +++ b/poetry.lock @@ -0,0 +1,637 @@ +# This file is automatically @generated by Poetry 2.1.3 and should not be changed by hand. + +[[package]] +name = "certifi" +version = "2025.7.9" +description = "Python package for providing Mozilla's CA Bundle." +optional = false +python-versions = ">=3.7" +groups = ["main"] +files = [ + {file = "certifi-2025.7.9-py3-none-any.whl", hash = "sha256:d842783a14f8fdd646895ac26f719a061408834473cfc10203f6a575beb15d39"}, + {file = "certifi-2025.7.9.tar.gz", hash = "sha256:c1d2ec05395148ee10cf672ffc28cd37ea0ab0d99f9cc74c43e588cbd111b079"}, +] + +[[package]] +name = "charset-normalizer" +version = "3.4.2" +description = "The Real First Universal Charset Detector. 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