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auto-import from our Zenodo community #114

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b934d5e
auto-import from our Zenodo community
haesleinhuepf Jul 11, 2024
32cc997
Merge branch 'main' into import-zenodo-communities
haesleinhuepf Jul 11, 2024
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3 changes: 2 additions & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -21,4 +21,5 @@ docs/29_algorithm_validation/ideas.ipynb
docs/29_algorithm_validation/solution for exercise - metrics to investigate segmentation results.ipynb
docs/22_feature_extraction/blobs_analysis.csv

Untitled*
Untitled*
notebooks/generate_link_lists.py
337 changes: 337 additions & 0 deletions notebooks/import_from_zenodo_communities.ipynb
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@@ -0,0 +1,337 @@
{
"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",
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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})

# Raises an HTTPError for bad responses
response.raise_for_status()  
online_data = response.json()

except requests.exceptions.RequestException as e:
print(f"Error fetching data: {e}")

# Ensuring online_data is defined in case of an error
online_data = {}

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online_data = {}

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

" 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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