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auto-import from our Zenodo community #114
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Original file line number | Diff line number | Diff line change |
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{ | ||
"cells": [ | ||
{ | ||
"cell_type": "markdown", | ||
"id": "4a41efb5-2f4a-41dd-98ba-eeecf01fdb68", | ||
"metadata": {}, | ||
"source": [ | ||
"# Importing new entries from Zenodo communities\n", | ||
"This notebook allows to import entries from Zenodo communities. It does not re-import entries that are already in our database." | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": 1, | ||
"id": "22ccdd0e-5d18-448d-a343-1ab634771d26", | ||
"metadata": {}, | ||
"outputs": [], | ||
"source": [ | ||
"import os\n", | ||
"import requests\n", | ||
"import bia_bob\n", | ||
"import shutil\n", | ||
"import pandas as pd" | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": 2, | ||
"id": "7065b8ba-f726-41f0-ab49-48c9767fcda1", | ||
"metadata": {}, | ||
"outputs": [ | ||
{ | ||
"data": { | ||
"text/plain": [ | ||
"'./generate_link_lists.py'" | ||
] | ||
}, | ||
"execution_count": 2, | ||
"metadata": {}, | ||
"output_type": "execute_result" | ||
} | ||
], | ||
"source": [ | ||
"# workaround: Until our utilities are a python library, we need to copy it here.\n", | ||
"shutil.copy('../scripts/generate_link_lists.py', './generate_link_lists.py')" | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": 3, | ||
"id": "a1863536-3d4e-4144-a86e-92eff0cca25a", | ||
"metadata": {}, | ||
"outputs": [], | ||
"source": [ | ||
"from generate_link_lists import load_dataframe\n", | ||
"from generate_link_lists import update_yaml_file" | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": 4, | ||
"id": "f6c69566-1d52-4ec0-8733-2cc11e002cac", | ||
"metadata": {}, | ||
"outputs": [], | ||
"source": [ | ||
"token = os.getenv('ZENODO_API_KEY')\n", | ||
"community = 'nfdi4bioimage'\n", | ||
"\n", | ||
"response = requests.get('https://zenodo.org/api/records',\n", | ||
" params={'communities': community,\n", | ||
" 'access_token': token})" | ||
] | ||
}, | ||
{ | ||
"cell_type": "markdown", | ||
"id": "ecd9050d-8dcd-4b69-9d1f-00fa1a37db80", | ||
"metadata": {}, | ||
"source": [ | ||
"## That's what's listed in the community" | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": 5, | ||
"id": "efa9ffa0-159c-4996-a6bd-c5e1f4197c2a", | ||
"metadata": {}, | ||
"outputs": [], | ||
"source": [ | ||
"online_data = response.json()\n", | ||
"hits = online_data[\"hits\"][\"hits\"]" | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": 6, | ||
"id": "1c59f531-ab9d-480a-81a2-7e5dbb9f8609", | ||
"metadata": {}, | ||
"outputs": [ | ||
{ | ||
"data": { | ||
"text/plain": [ | ||
"25" | ||
] | ||
}, | ||
"execution_count": 6, | ||
"metadata": {}, | ||
"output_type": "execute_result" | ||
} | ||
], | ||
"source": [ | ||
"len(hits)" | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": 7, | ||
"id": "28cbcc3a-a43c-47ee-b249-30032957411a", | ||
"metadata": {}, | ||
"outputs": [ | ||
{ | ||
"data": { | ||
"text/plain": [ | ||
"['https://zenodo.org/records/11548617',\n", | ||
" 'https://zenodo.org/records/11501662',\n", | ||
" 'https://zenodo.org/records/11350689',\n", | ||
" 'https://zenodo.org/records/11235513',\n", | ||
" 'https://zenodo.org/records/11109616',\n", | ||
" 'https://zenodo.org/records/11031747',\n", | ||
" 'https://zenodo.org/records/10939520',\n", | ||
" 'https://zenodo.org/records/10886750',\n", | ||
" 'https://zenodo.org/records/10808486',\n", | ||
" 'https://zenodo.org/records/10793700',\n", | ||
" 'https://zenodo.org/records/10730424',\n", | ||
" 'https://zenodo.org/records/10687659',\n", | ||
" 'https://zenodo.org/records/10389955',\n", | ||
" 'https://zenodo.org/records/10083555',\n", | ||
" 'https://zenodo.org/records/10008465',\n", | ||
" 'https://zenodo.org/records/8414319',\n", | ||
" 'https://zenodo.org/records/8349563',\n", | ||
" 'https://zenodo.org/records/8340248',\n", | ||
" 'https://zenodo.org/records/8329306',\n", | ||
" 'https://zenodo.org/records/8139354',\n", | ||
" 'https://zenodo.org/records/8070038',\n", | ||
" 'https://zenodo.org/records/8019760',\n", | ||
" 'https://zenodo.org/records/7928333',\n", | ||
" 'https://zenodo.org/records/7890311',\n", | ||
" 'https://zenodo.org/records/7394675']" | ||
] | ||
}, | ||
"execution_count": 7, | ||
"metadata": {}, | ||
"output_type": "execute_result" | ||
} | ||
], | ||
"source": [ | ||
"urls = [u[\"links\"][\"self_html\"] for u in hits]\n", | ||
"urls" | ||
] | ||
}, | ||
{ | ||
"cell_type": "markdown", | ||
"id": "658e8be1-37bd-4830-8e0d-4a6d6b79452d", | ||
"metadata": {}, | ||
"source": [ | ||
"## Checking what we already have" | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": 8, | ||
"id": "1bba931f-1766-4b4c-b700-9550efdc0fec", | ||
"metadata": {}, | ||
"outputs": [ | ||
{ | ||
"name": "stdout", | ||
"output_type": "stream", | ||
"text": [ | ||
"Adding blog_posts.yml\n", | ||
"Adding events.yml\n", | ||
"Adding imported.yml\n", | ||
"Adding materials.yml\n", | ||
"Adding nfdi4bioimage.yml\n", | ||
"Adding papers.yml\n", | ||
"Adding workflow-tools.yml\n", | ||
"Adding youtube_channels.yml\n" | ||
] | ||
} | ||
], | ||
"source": [ | ||
"df = load_dataframe(\"../resources/\")\n", | ||
"\n", | ||
"all_urls = str(df[\"url\"].tolist())\n", | ||
"#all_urls" | ||
] | ||
}, | ||
{ | ||
"cell_type": "markdown", | ||
"id": "5183ae2c-5144-4bff-a08f-d7a81f89ccef", | ||
"metadata": {}, | ||
"source": [ | ||
"## Identifying entries we are missing yet" | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": 9, | ||
"id": "4d91a514-be3f-4629-85fa-fda961ebe275", | ||
"metadata": {}, | ||
"outputs": [ | ||
{ | ||
"data": { | ||
"text/plain": [ | ||
"['https://zenodo.org/records/11501662',\n", | ||
" 'https://zenodo.org/records/11350689',\n", | ||
" 'https://zenodo.org/records/11235513',\n", | ||
" 'https://zenodo.org/records/11031747',\n", | ||
" 'https://zenodo.org/records/10939520',\n", | ||
" 'https://zenodo.org/records/10886750',\n", | ||
" 'https://zenodo.org/records/10808486',\n", | ||
" 'https://zenodo.org/records/10793700',\n", | ||
" 'https://zenodo.org/records/10730424',\n", | ||
" 'https://zenodo.org/records/10687659',\n", | ||
" 'https://zenodo.org/records/10389955',\n", | ||
" 'https://zenodo.org/records/8414319',\n", | ||
" 'https://zenodo.org/records/8349563',\n", | ||
" 'https://zenodo.org/records/8340248',\n", | ||
" 'https://zenodo.org/records/8139354',\n", | ||
" 'https://zenodo.org/records/8070038',\n", | ||
" 'https://zenodo.org/records/8019760',\n", | ||
" 'https://zenodo.org/records/7928333',\n", | ||
" 'https://zenodo.org/records/7890311',\n", | ||
" 'https://zenodo.org/records/7394675']" | ||
] | ||
}, | ||
"execution_count": 9, | ||
"metadata": {}, | ||
"output_type": "execute_result" | ||
} | ||
], | ||
"source": [ | ||
"new_urls = []\n", | ||
"for url in urls:\n", | ||
" if url not in all_urls:\n", | ||
" new_urls.append(url)\n", | ||
"\n", | ||
"new_urls" | ||
] | ||
}, | ||
{ | ||
"cell_type": "markdown", | ||
"id": "11fe5ad3-b68f-46cb-b9d6-3c9e6875cb64", | ||
"metadata": {}, | ||
"source": [ | ||
"## Saving new entries" | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": 10, | ||
"id": "4eee8bc1-9d9e-481c-b3ac-5867407eed96", | ||
"metadata": {}, | ||
"outputs": [], | ||
"source": [ | ||
"with open('../resources/imported.yml', 'a') as file:\n", | ||
" for url in new_urls:\n", | ||
" file.write(\"- url: \" + url + '\\n')" | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": 11, | ||
"id": "c3e92c51-0b07-4b6b-a095-91b79252f96c", | ||
"metadata": {}, | ||
"outputs": [ | ||
{ | ||
"name": "stdout", | ||
"output_type": "stream", | ||
"text": [ | ||
"https://zenodo.org/api/records/11548617\n", | ||
"https://zenodo.org/api/records/11501662\n", | ||
"https://zenodo.org/api/records/11350689\n", | ||
"https://zenodo.org/api/records/11235513\n", | ||
"https://zenodo.org/api/records/11031747\n", | ||
"https://zenodo.org/api/records/10939520\n", | ||
"https://zenodo.org/api/records/10886750\n", | ||
"https://zenodo.org/api/records/10808486\n", | ||
"https://zenodo.org/api/records/10793700\n", | ||
"https://zenodo.org/api/records/10730424\n", | ||
"https://zenodo.org/api/records/10687659\n", | ||
"https://zenodo.org/api/records/10389955\n", | ||
"https://zenodo.org/api/records/8414319\n", | ||
"https://zenodo.org/api/records/8349563\n", | ||
"https://zenodo.org/api/records/8340248\n", | ||
"https://zenodo.org/api/records/8139354\n", | ||
"https://zenodo.org/api/records/8070038\n", | ||
"https://zenodo.org/api/records/8019760\n", | ||
"https://zenodo.org/api/records/7928333\n", | ||
"https://zenodo.org/api/records/7890311\n", | ||
"https://zenodo.org/api/records/7394675\n" | ||
] | ||
} | ||
], | ||
"source": [ | ||
"update_yaml_file(\"../resources/imported.yml\")" | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": null, | ||
"id": "8fa55de8-b51a-45ce-934c-75c090166dab", | ||
"metadata": {}, | ||
"outputs": [], | ||
"source": [] | ||
} | ||
], | ||
"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": "3.11.9" | ||
} | ||
}, | ||
"nbformat": 4, | ||
"nbformat_minor": 5 | ||
} |
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There seems to be no theoretical error. What about add some error test like API rate limits, or other HTTP-related errors?
maybe like:
try:
response = requests.get('https://zenodo.org/api/records',
params={'communities': community,
'access_token': token})
except requests.exceptions.RequestException as e:
print(f"Error fetching data: {e}")
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If there is no online data, running the rest of the code is pointless.
But I agree some error handling would be nice
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Should I also mark this as viewed?
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I'm not sure. I never marked any files as viewed. Let me know what it does to the file :-)
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like this, viewed and approve