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added jupyter notebooks examples in documentation #1868

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merged 3 commits into from
Oct 23, 2024
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added jupyter notebooks examples in documentation #1868

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1a7777d
added jupyter notebooks examples in documentation
alinvetian Sep 30, 2024
76b9605
added documentation
alinvetian Sep 30, 2024
cce5520
removed outputs and file upload
alinvetian Oct 3, 2024
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3 changes: 3 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -221,3 +221,6 @@ yarn-debug.log*
.yarn-integrity

/config/credentials/development.key

# Jupyter notebooks checkpoints
documentation/apis/Jupyter-Notebooks/.ipynb_checkpoints/
274 changes: 274 additions & 0 deletions documentation/apis/Jupyter-Notebooks/create_dataset_notebook.ipynb
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@@ -0,0 +1,274 @@
{
"cells": [
{
"cell_type": "markdown",
"id": "cd03e984-7b12-4689-9d22-42a4b495a09e",
"metadata": {},
"source": [
"Import all needed libraries"
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "e02e99ee-1c49-4197-b452-15ea2478beb6",
"metadata": {},
"outputs": [],
"source": [
"import requests\n",
"import urllib.parse\n",
"import urllib.request\n",
"import json"
]
},
{
"cell_type": "markdown",
"id": "a4388476-7221-4591-b391-269fe2cd02f1",
"metadata": {},
"source": [
"Set host and API credentials\n",
"* __host__ - API host\n",
"* __API_CLIENT_ID__ - API client ID\n",
"* __API_CLIENT_SECRET__ - API client secret\n"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "c265b1b2-d713-4b0b-bcdc-def9ef474e2f",
"metadata": {},
"outputs": [],
"source": [
"host = 'https://sandbox.datadryad.org'\n",
"API_CLIENT_ID = \"[CLIENT_ID]\"\n",
"API_CLIENT_SECRET = \"[CLIENT_SECRET]\"\n",
"\n",
"headers = {\"Content-Type\": \"application/json\"}"
]
},
{
"cell_type": "markdown",
"id": "5a9e7dea-9d24-4128-91e0-0dac589da4ea",
"metadata": {},
"source": [
"Authorize API connection and retrieve access token"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "6f3bd89a-e475-4cec-8aa9-8254929a4842",
"metadata": {},
"outputs": [],
"source": [
"payload = {'client_id': API_CLIENT_ID, 'client_secret': API_CLIENT_SECRET, 'grant_type': 'client_credentials'}\n",
"payload = {\n",
" \"client_id\": API_CLIENT_ID,\n",
" \"client_secret\": API_CLIENT_SECRET, \n",
" \"grant_type\": \"client_credentials\"\n",
"}\n",
"url = f'{host}/oauth/token'\n",
"response = requests.post(url, data=json.dumps(payload), headers=headers)\n",
"\n",
"if response.status_code != 200:\n",
" raise SystemExit(response.json()['error_description'])\n",
"token = response.json()['access_token']\n",
"\n",
"if not token:\n",
" raise SystemExit('Unable to retrieve access token')\n",
"\n",
"headers['Authorization'] = f'{response.json()['token_type']} {token}'"
]
},
{
"cell_type": "markdown",
"id": "a9a42849-70f6-42e7-9a57-086be116325c",
"metadata": {},
"source": [
"Create dataset"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "9072c664-e89c-4286-9f4d-40387bff0e58",
"metadata": {},
"outputs": [],
"source": [
"payload = {\n",
" \"title\": \"Data from: Jupyter Notebook uploaded through API\",\n",
" \"abstract\" : \"This study develops the random phylogenies rate test (RAPRATE), a likelihood method that simulates morphological evolution along randomly generated phylogenies, and uses it to determine whether a considerable difference in morphological diversity between two sister clades of South American fishes should be taken as evidence of differing rates of morphological change or lineage turnover.\",\n",
" \"authors\" : [ \n",
" {\n",
" \"firstName\" : \"Test\",\n",
" \t \"lastName\" : \"Author\",\n",
" \t \"email\" : \"test@examples.com\",\n",
" \t \"orcid\" : \"0009-0000-4404-1689\",\n",
" \t \"affiliation\" : \"Oregon State University\",\n",
" \t \"affiliationROR\" : \"https://ror.org/00ysfqy60\"\n",
" \t}\n",
" ]\n",
"}\n",
"headers['Content-Type'] = 'application/json'\n",
"url = f'{host}/api/v2/datasets'\n",
"response = requests.post(url, data=json.dumps(payload), headers=headers)\n",
"dataset_id = response.json()['id']\n",
"dataset_url = f'{host}{response.json()['_links']['self']['href']}'\n",
"\n",
"if 'error' in response.json():\n",
" raise SystemExit(response.json()['error']); exit\n",
"else:\n",
" print('Resource successfully created')"
]
},
{
"cell_type": "markdown",
"id": "6c4e2b56-ca10-4c26-a2ec-38cca903928f",
"metadata": {},
"source": [
"Update dataset and set missing information"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "71a45f81-0063-4643-a78a-f39a6144afbf",
"metadata": {},
"outputs": [],
"source": [
"payload = {\n",
" \"title\": \"A Study of Red-Black Trees with Weight\",\n",
" \"authors\": [\n",
" {\n",
" \"firstName\": \"Matilda\",\n",
" \"lastName\": \"Swinton\",\n",
" \"email\": \"matilda.swinton@example.com\",\n",
" \"affiliation\": \"Example Organization\"\n",
" }\n",
" ],\n",
" \"abstract\": \"<p>Information theorists agree that \\\"fuzzy\\\" models are an interesting new topic in the field of machine learning.</p>\\r\\n\",\n",
" \"funders\": [\n",
" {\n",
" \"organization\": \"Stichting Sem Presser Archief\",\n",
" \"identifierType\": \"ror\",\n",
" \"identifier\": \"https://ror.org/02f5r3008\",\n",
" \"awardNumber\": \"12345\"\n",
" }\n",
" ],\n",
" \"keywords\": [\n",
" \"Cat\",\n",
" \"Host\",\n",
" \"Computer\",\n",
" \"Log\"\n",
" ],\n",
" \"methods\": \"<p><br>\\r\\nMany mathematicians would agree that, had it not been for systems, the emulation of active networks might never have occurred. We view algorithms as following a cycle of four phases: simulation, investigation, observation, and investigation. After years of robust research into Boolean logic, we confirm the evaluation of Smalltalk. to what extent can spreadsheets be evaluated to realize this intent?</p>\\r\\n\",\n",
" \"relatedWorks\": [\n",
" {\n",
" \"relationship\": \"article\",\n",
" \"identifierType\": \"URL\",\n",
" \"identifier\": \"http://example.org/cats\"\n",
" }\n",
" ],\n",
" \"userId\": 2,\n",
" \"email\": \"some_email@example.com\"\n",
"}\n",
"\n",
"headers['Content-Type'] = 'application/json'\n",
"response = requests.put(dataset_url, data=json.dumps(payload), headers=headers)\n",
"if response.status_code != 200:\n",
" raise SystemExit(response.json()['error_description'])"
]
},
{
"cell_type": "markdown",
"id": "f6fe81b0-1fe0-43cb-9a00-b9a5a6bdeea8",
"metadata": {},
"source": [
"Embed a file on the dataset using file "
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "eef23b0f-8dff-421e-8585-37ef6b8e3c43",
"metadata": {},
"outputs": [],
"source": [
"embed_url = f'{dataset_url}/urls'\n",
"payload = {\n",
" \"url\": \"https://github.com/datadryad/dryad-app/blob/e927b514efe97fc08c7fc30d99389a5ec6d8a493/documentation/apis/sample_dataset.json\",\n",
" \"digest\": \"aca3032d20c829a6060f1b90afda6d14\",\n",
" \"digestType\": \"md5\",\n",
" \"description\": \"This is the best file ever!\",\n",
" \"size\": 1234,\n",
" \"path\": \"api_submission.md\",\n",
" \"mimeType\": \"text/plain\",\n",
" \"skipValidation\": True\n",
"}\n",
"\n",
"headers['Content-Type'] = 'application/json'\n",
"response = requests.post(embed_url, data=json.dumps(payload), headers=headers)\n",
"if 'error' in response.json():\n",
" raise SystemExit(response.json()['error']); exit\n",
"else:\n",
" print('File successfuly embeded')\n",
" \n",
"response.json()"
]
},
{
"cell_type": "markdown",
"id": "8ce4c50a-5c38-4d0a-866b-95307b87dd13",
"metadata": {},
"source": [
"Submit dataset"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "c1e18f98-e8bd-489e-9d88-9aea1191be5e",
"metadata": {},
"outputs": [],
"source": [
"payload = {\n",
" \"op\": \"replace\",\n",
" \"path\": \"/versionStatus\",\n",
" \"value\": \"submitted\"\n",
"}\n",
"\n",
"headers['Content-Type'] = 'application/json-patch+json'\n",
"response = requests.patch(dataset_url, data=json.dumps(payload), headers=headers)\n",
"\n",
"errors = [obj['error'] for obj in response.json()]\n",
"\n",
"if len(errors) > 0:\n",
" print('Errors: ')\n",
" print(', '.join(errors))\n",
"else:\n",
" print('Status successfully updated')"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.6"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
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