diff --git a/examples/notebooks/Harvest_zenodo.ipynb b/examples/notebooks/Harvest_zenodo.ipynb
index 06a835b530f6a8d2f770b1846a1c9a237f0eac99..40b8387ba6cfceae86171d59ac7a330d36dd6b30 100644
--- a/examples/notebooks/Harvest_zenodo.ipynb
+++ b/examples/notebooks/Harvest_zenodo.ipynb
@@ -5,7 +5,7 @@
"id": "b0fcf1bf",
"metadata": {},
"source": [
- "<h1><center> <font size=\"36\"> How to harvest metadata from Zenodo </font> </center></h1>\n",
+ "<h1><center> <font size=\"36\"> Example of protocols to harvest metadata from Zenodo </font> </center></h1>\n",
"\n",
"---------------------\n",
"#### Notebook outline \n",
@@ -13,7 +13,6 @@
" - Zenodo REST API\n",
" - Explore the REST API answer (payload) with the `request` library\n",
" - Using `eossr` library\n",
- " - Using `PyZenodo3` library\n",
" - Pros and cons of both methods\n",
" \n",
"---------------------"
@@ -191,16 +190,6 @@
"However, you would need to [create one](https://zenodo.org/account/settings/applications/) if you would like to write or publish through the API."
]
},
- {
- "cell_type": "code",
- "execution_count": 4,
- "id": "ddccf248",
- "metadata": {},
- "outputs": [],
- "source": [
- "token = ''"
- ]
- },
{
"cell_type": "markdown",
"id": "4cd8011b",
@@ -441,16 +430,16 @@
" 'title': 'EOSC Symposium 2021 Report'},\n",
" 'owners': [91736],\n",
" 'revision': 8,\n",
- " 'stats': {'downloads': 438.0,\n",
- " 'unique_downloads': 374.0,\n",
- " 'unique_views': 475.0,\n",
- " 'version_downloads': 438.0,\n",
- " 'version_unique_downloads': 374.0,\n",
- " 'version_unique_views': 475.0,\n",
- " 'version_views': 494.0,\n",
- " 'version_volume': 724854084.0,\n",
- " 'views': 494.0,\n",
- " 'volume': 724854084.0},\n",
+ " 'stats': {'downloads': 479.0,\n",
+ " 'unique_downloads': 411.0,\n",
+ " 'unique_views': 514.0,\n",
+ " 'version_downloads': 479.0,\n",
+ " 'version_unique_downloads': 411.0,\n",
+ " 'version_unique_views': 514.0,\n",
+ " 'version_views': 537.0,\n",
+ " 'version_volume': 792705722.0,\n",
+ " 'views': 537.0,\n",
+ " 'volume': 792705722.0},\n",
" 'updated': '2021-08-24T14:27:14.603504+00:00'}"
]
},
@@ -676,227 +665,14 @@
"source": [
"## eossr\n",
"\n",
- "All these methods are implemented in the [Zenodo client](https://gitlab.in2p3.fr/escape2020/wp3/eossr/-/blob/master/eossr/api/zenodo.py) (a REST API handler) of the [eossr library](https://gitlab.in2p3.fr/escape2020/wp3/eossr). \n",
- "\n",
- "The library is also in charge of automatise the project's uploads from GitLab to Zenodo (by the use of the GitLab-CI and the REST API handler)."
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 17,
- "id": "6cd7f714",
- "metadata": {},
- "outputs": [],
- "source": [
- "# pip install https://gitlab.in2p3.fr/escape2020/wp3/eossr/-/archive/master/eossr-master.zip"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 18,
- "id": "0dbbbd64",
- "metadata": {},
- "outputs": [],
- "source": [
- "from eossr.api.zenodo import ZenodoAPI\n",
- "z = ZenodoAPI(access_token=token, sandbox=False)"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 19,
- "id": "2037338d",
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "15"
- ]
- },
- "execution_count": 19,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "entries = z.fetch_community_entries(community_name='escape2020', \n",
- " results_per_query=100)\n",
- "entries.json()['hits']['total']"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 20,
- "id": "3985383f",
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "5176089 EOSC Symposium 2021 Report\n",
- "5153369 agnpy: Modelling Active Galactic Nuclei radiative processes with python.\n",
- "5093909 ESCAPE Data Science Summer School 2021\n",
- "4923992 ESCAPE template project\n",
- "4786641 ZenodoCI\n",
- "4601451 gLike: numerical maximization of heterogeneous joint likelihood functions of a common free parameter plus nuisance parameters\n",
- "4419866 IndexedConv/IndexedConv: v1.3\n",
- "4044010 EOSC - a tool for enabling Open Science in Europe\n",
- "3854976 FairRootGroup/DDS\n",
- "3743489 ESCAPE the maze\n",
- "3675081 ESFRI cluster projects - Position papers on expectations and planned contributions to the EOSC\n",
- "3659184 ctapipe_io_mchdf5\n",
- "3614662 FairRoot\n",
- "3362435 FairMQ\n",
- "3356656 A prototype for a real time pipeline for the detection of transient signals and their automatic classification\n"
- ]
- }
- ],
- "source": [
- "ids = z.fetch_community_entries_per_id(community_name='escape2020', \n",
- " results_per_query=100)\n",
- "\n",
- "titles = z.fetch_community_entries_per_title(community_name='escape2020', \n",
- " results_per_query=100)\n",
- "\n",
- "for id, title in zip(ids, titles):\n",
- " print(id, title)"
- ]
- },
- {
- "cell_type": "markdown",
- "id": "595ba083",
- "metadata": {},
- "source": [
- "## PyZenodo3\n",
- "\n",
- "Another equivalent example with the pyzenodo3 library"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 21,
- "id": "91985172",
- "metadata": {},
- "outputs": [],
- "source": [
- "# pip install pyzenodo3"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 22,
- "id": "7cd937b9",
- "metadata": {},
- "outputs": [],
- "source": [
- "import pyzenodo3\n",
- "\n",
- "zen = pyzenodo3.Zenodo()\n",
- "records = zen.search('agnpy')"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 23,
- "id": "815578d9",
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "{'conceptdoi': '10.5281/zenodo.5174757',\n",
- " 'conceptrecid': '5174757',\n",
- " 'created': '2021-08-10T07:43:16.545873+00:00',\n",
- " 'doi': '10.5281/zenodo.5174758',\n",
- " 'files': [{'bucket': '4a6752c9-f922-45f5-a6e5-82f9a016ba87',\n",
- " 'checksum': 'md5:516ae662f4d8a251a7d8b9fb41007e56',\n",
- " 'key': 'cosimoNigro/agnpy_paper-v0.1.0.zip',\n",
- " 'links': {'self': 'https://zenodo.org/api/files/4a6752c9-f922-45f5-a6e5-82f9a016ba87/cosimoNigro/agnpy_paper-v0.1.0.zip'},\n",
- " 'size': 45740,\n",
- " 'type': 'zip'}],\n",
- " 'id': 5174758,\n",
- " 'links': {'badge': 'https://zenodo.org/badge/doi/10.5281/zenodo.5174758.svg',\n",
- " 'bucket': 'https://zenodo.org/api/files/4a6752c9-f922-45f5-a6e5-82f9a016ba87',\n",
- " 'conceptbadge': 'https://zenodo.org/badge/doi/10.5281/zenodo.5174757.svg',\n",
- " 'conceptdoi': 'https://doi.org/10.5281/zenodo.5174757',\n",
- " 'doi': 'https://doi.org/10.5281/zenodo.5174758',\n",
- " 'html': 'https://zenodo.org/record/5174758',\n",
- " 'latest': 'https://zenodo.org/api/records/5174758',\n",
- " 'latest_html': 'https://zenodo.org/record/5174758',\n",
- " 'self': 'https://zenodo.org/api/records/5174758'},\n",
- " 'metadata': {'access_right': 'open',\n",
- " 'access_right_category': 'success',\n",
- " 'creators': [{'affiliation': \"Institut de FÃsica d'Altes Energies (IFAE), The Barcelona Institute of Science and Technology, Campus UAB, 08193 Bellaterra (Barcelona), Spain\",\n",
- " 'name': 'Cosimo Nigro',\n",
- " 'orcid': '0000-0001-8375-1907'},\n",
- " {'affiliation': 'University of Lodz, Faculty of Physics and Applied Informatics, Department of Astrophysics, 90-236 Lodz, Poland',\n",
- " 'name': 'Julian Sitarek',\n",
- " 'orcid': '0000-0002-1659-5374'},\n",
- " {'affiliation': 'University of Lodz, Faculty of Physics and Applied Informatics, Department of Astrophysics, 90-236 Lodz, Poland',\n",
- " 'name': 'Paweł Gliwny',\n",
- " 'orcid': '0000-0002-4183-391X'},\n",
- " {'affiliation': \"Laboratoire d'Annecy de Physique des Particules, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LAPP, 74000 Annecy, France\",\n",
- " 'name': 'David Sanchez'},\n",
- " {'affiliation': 'Minnesota State University Moorhead, Moorhead, Minnesota, US',\n",
- " 'name': 'Matthew Craig',\n",
- " 'orcid': '0000-0002-4183-391X'}],\n",
- " 'description': \"This repository contains the scripts to generate the figures included in the paper 'agnpy: an open-source python package modelling the radiative processes of jetted active galactic nuclei'.\",\n",
- " 'doi': '10.5281/zenodo.5174758',\n",
- " 'keywords': ['radiative processes',\n",
- " 'blazars',\n",
- " 'radio galaxies',\n",
- " 'AGN',\n",
- " 'jets',\n",
- " 'MWL',\n",
- " 'astropy',\n",
- " 'numpy',\n",
- " 'python'],\n",
- " 'license': {'id': 'other-open'},\n",
- " 'publication_date': '2021-08-10',\n",
- " 'related_identifiers': [{'identifier': 'https://github.com/cosimoNigro/agnpy_paper/tree/v0.1.0',\n",
- " 'relation': 'isSupplementTo',\n",
- " 'scheme': 'url'},\n",
- " {'identifier': '10.5281/zenodo.5174757',\n",
- " 'relation': 'isVersionOf',\n",
- " 'scheme': 'doi'}],\n",
- " 'relations': {'version': [{'count': 1,\n",
- " 'index': 0,\n",
- " 'is_last': True,\n",
- " 'last_child': {'pid_type': 'recid', 'pid_value': '5174758'},\n",
- " 'parent': {'pid_type': 'recid', 'pid_value': '5174757'}}]},\n",
- " 'resource_type': {'title': 'Software', 'type': 'software'},\n",
- " 'title': 'agnpy: an open-source python package modelling the radiative processes of jetted active galactic nuclei',\n",
- " 'version': '0.1.0'},\n",
- " 'owners': [99841],\n",
- " 'revision': 3,\n",
- " 'stats': {'downloads': 0.0,\n",
- " 'unique_downloads': 0.0,\n",
- " 'unique_views': 12.0,\n",
- " 'version_downloads': 0.0,\n",
- " 'version_unique_downloads': 0.0,\n",
- " 'version_unique_views': 12.0,\n",
- " 'version_views': 13.0,\n",
- " 'version_volume': 0.0,\n",
- " 'views': 13.0,\n",
- " 'volume': 0.0},\n",
- " 'updated': '2021-08-10T13:48:43.185119+00:00'}"
- ]
- },
- "execution_count": 23,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "records[0].data"
+ "The eossr library uses Zenodo REST API.\n",
+ "See the [OSSR API notebook](ossr_search.ipynb) for an example on how to use it.\n"
]
},
{
"cell_type": "code",
"execution_count": null,
- "id": "a304d374",
+ "id": "563902f1",
"metadata": {},
"outputs": [],
"source": []
@@ -918,7 +694,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.6.10"
+ "version": "3.9.2"
}
},
"nbformat": 4,
diff --git a/examples/notebooks/ossr_search.ipynb b/examples/notebooks/ossr_api.ipynb
similarity index 93%
rename from examples/notebooks/ossr_search.ipynb
rename to examples/notebooks/ossr_api.ipynb
index bd1793556f1b5653deb3842dc180d89cee75b7e1..c5d386f2624f11e52bdc703defc880589c3ba782 100644
--- a/examples/notebooks/ossr_search.ipynb
+++ b/examples/notebooks/ossr_api.ipynb
@@ -266,6 +266,37 @@
"metadata": {},
"outputs": [],
"source": []
+ },
+ {
+ "cell_type": "markdown",
+ "id": "d5e9bc28",
+ "metadata": {},
+ "source": [
+ "# Upload records on the OSSR"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "a4123841",
+ "metadata": {},
+ "source": [
+ "To upload records on the OSSR, you may use the [Zenodo client](https://gitlab.in2p3.fr/escape2020/wp3/eossr/-/blob/master/eossr/api/zenodo.py).\n",
+ "\n",
+ "This is also used by the continuous integration to automatise project's uploads from GitLab to Zenodo.\n",
+ "\n",
+ "To do so, you will need to use your Zenodo token ([create one](https://zenodo.org/account/settings/applications/tokens/new/))."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 13,
+ "id": "69c6f758",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "from eossr.api.zenodo import ZenodoAPI\n",
+ "z = ZenodoAPI(access_token=token, sandbox=False)"
+ ]
}
],
"metadata": {