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update online omx validator
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@bstabler
bstabler committed May 17, 2020
1 parent d303b20 commit f912166
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82 changes: 23 additions & 59 deletions omx_validate.ipynb
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Expand Up @@ -22,10 +22,7 @@
"source": [
"# OMX Validator\n",
"\n",
"The OMX validator is a [Jupyter notebook](https://jupyter.org/) hosted in Google Colaboratory. It is an interactive Python environment that validates OMX matrices using the [openmatrix](https://github.com/osPlanning/omx-python) library. The validator has been tested with the [example](https://github.com/osPlanning/omx/blob/master/example.omx?raw=true) omx file. OMX files can also be inspected with the [OMX Viewer](https://github.com/osPlanning/omx/wiki/OMX-Viewer).\n",
"\n",
"This notebook is setup to run in the cloud, but it can also be run locally. To run it locally, download the ipynb file, run it with Jupyter, and skip the upload file step by instead referencing a local file. \n",
"\n"
"The OMX validator is a [Jupyter notebook](https://jupyter.org/) hosted in Google Colaboratory. It is an interactive Python environment that validates OMX matrices using the [openmatrix](https://github.com/osPlanning/omx-python) library. The validator has been tested with the [example](https://github.com/osPlanning/omx/blob/master/example.omx?raw=true) omx file. OMX files can also be inspected with the [OMX Viewer](https://github.com/osPlanning/omx/wiki/OMX-Viewer).\n"
]
},
{
Expand All @@ -35,70 +32,35 @@
"colab_type": "text"
},
"source": [
"# Upload File\n",
"# Upload Files\n",
"\n",
"Select local files for upload via the Table of Contents + Files + Upload. Run the code cell below to list the OMX files uploaded by clicking on the [ ] play button. While testing, you may need to reset the UI control, which you can do via Runtime + Restart runtime. The Files control can be accessed by clicking the File button.\n",
"\n",
"![upload](https://github.com/osPlanning/omx/raw/master/upload.png)\n",
"\n",
"This step creates a file selector UI control to select a local file for upload. Google Colab uploads the file and stores it with the Colab notebook Files. Run the code cell by clicking on the [ ] play button. The uploaded filename is referenced in the next section. While testing, you may need to reset the UI control, which you can do via Runtime + Restart runtime. Also, you can review the Files uploaded via View + Table of Contents + Files. "
"\n"
]
},
{
"cell_type": "code",
"metadata": {
"id": "Jx_VaZZdGYon",
"colab_type": "code",
"outputId": "9216908c-6fe8-4617-9f22-61219860de95",
"outputId": "d6f3696f-7b5f-4631-b1b7-b50b2e4ab4a8",
"colab": {
"resources": {
"http://localhost:8080/nbextensions/google.colab/files.js": {
"data": 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"ok": true,
"headers": [
[
"content-type",
"application/javascript"
]
],
"status": 200,
"status_text": ""
}
},
"base_uri": "https://localhost:8080/",
"height": 91
"height": 34
}
},
"source": [
"from google.colab import files\n",
"import io\n",
"uploaded = files.upload()\n",
"filename = list(uploaded.keys())[0]\n",
"print(\"File uploaded:\", filename)"
"!ls -d *omx"
],
"execution_count": 2,
"execution_count": 31,
"outputs": [
{
"output_type": "display_data",
"data": {
"text/html": [
"\n",
" <input type=\"file\" id=\"files-b6d3598e-9b28-4c9a-b321-5dfe626b9b35\" name=\"files[]\" multiple disabled />\n",
" <output id=\"result-b6d3598e-9b28-4c9a-b321-5dfe626b9b35\">\n",
" Upload widget is only available when the cell has been executed in the\n",
" current browser session. Please rerun this cell to enable.\n",
" </output>\n",
" <script src=\"/nbextensions/google.colab/files.js\"></script> "
],
"text/plain": [
"<IPython.core.display.HTML object>"
]
},
"metadata": {
"tags": []
}
},
{
"output_type": "stream",
"text": [
"Saving example.omx to example.omx\n",
"File uploaded: example.omx\n"
"example.omx\n"
],
"name": "stdout"
}
Expand All @@ -113,15 +75,15 @@
"source": [
"# Validator Functions\n",
"\n",
"This step installs the openmatrix package from [pypi.org](https://pypi.org/project/OpenMatrix/), which includes the OMX validation functions and command line tool."
"This step installs the openmatrix package from [pypi.org](https://pypi.org/project/OpenMatrix/), which includes the OMX validation functions and command line tool. Run the code cell to install the package."
]
},
{
"cell_type": "code",
"metadata": {
"id": "7rvtFHB8EVPz",
"colab_type": "code",
"outputId": "6c8f3f92-3408-464a-f79f-cf12183b79c3",
"outputId": "606854d5-4750-4de7-aa33-da7a7ece1528",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 173
Expand All @@ -130,17 +92,17 @@
"source": [
"!pip install openmatrix"
],
"execution_count": 3,
"execution_count": 25,
"outputs": [
{
"output_type": "stream",
"text": [
"Collecting openmatrix\n",
" Downloading https://files.pythonhosted.org/packages/05/e8/6a8227e97127a2a1db98f5a22ca565bfe942e89de0644837627920101213/OpenMatrix-0.3.5.0-py3-none-any.whl\n",
"Requirement already satisfied: numpy>=1.5.0 in /usr/local/lib/python3.6/dist-packages (from openmatrix) (1.17.4)\n",
"Requirement already satisfied: tables>=3.1.0 in /usr/local/lib/python3.6/dist-packages (from openmatrix) (3.4.4)\n",
"Requirement already satisfied: numpy>=1.5.0 in /usr/local/lib/python3.6/dist-packages (from openmatrix) (1.18.4)\n",
"Requirement already satisfied: six>=1.9.0 in /usr/local/lib/python3.6/dist-packages (from tables>=3.1.0->openmatrix) (1.12.0)\n",
"Requirement already satisfied: numexpr>=2.5.2 in /usr/local/lib/python3.6/dist-packages (from tables>=3.1.0->openmatrix) (2.7.0)\n",
"Requirement already satisfied: numexpr>=2.5.2 in /usr/local/lib/python3.6/dist-packages (from tables>=3.1.0->openmatrix) (2.7.1)\n",
"Installing collected packages: openmatrix\n",
"Successfully installed openmatrix-0.3.5.0\n"
],
Expand All @@ -157,7 +119,9 @@
"source": [
"# Validate\n",
"\n",
"This section validates the OMX file against the [Specification](https://github.com/osPlanning/omx/wiki/Specification). The following checks are run and an overall Pass or Fail is returned at the end.\n",
"This section validates the OMX file against the [Specification](https://github.com/osPlanning/omx/wiki/Specification) by using the omx-validate command line tool. Specify the file to validate in the command line call below and then run the code cell.\n",
"\n",
"The following checks are run and an overall Pass or Fail is returned at the end.\n",
"1. Has OMX_VERSION attribute set to 0.2\n",
"2. Has SHAPE array attribute set to two item integer array\n",
"1. Has data group for matrices\n",
Expand All @@ -177,7 +141,7 @@
"metadata": {
"id": "a8VncE6qKKLC",
"colab_type": "code",
"outputId": "588d7c8b-1f1d-47c8-8c9c-babed3d1f8c9",
"outputId": "305b785c-679c-4b0a-addc-f4e54c6b107c",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 1000
Expand All @@ -186,14 +150,14 @@
"source": [
"!omx-validate example.omx"
],
"execution_count": 4,
"execution_count": 33,
"outputs": [
{
"output_type": "stream",
"text": [
"File contents: example.omx\n",
"example.omx (File) ''\n",
"Last modif.: 'Sat Dec 21 17:55:01 2019'\n",
"Last modif.: 'Sun May 17 14:24:38 2020'\n",
"Object Tree: \n",
"/ (RootGroup) ''\n",
"/data (Group) ''\n",
Expand Down

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