Cookbook

These quickstart examples gloss over a lot of details in the API. The canonical API documentation (generated from the OpenAPI specification) is available at https://api.fatcat.wiki/redoc.

The first two simple cookbook examples here include full headers. Later examples only show python client library code snippets.

Lookup Fulltext URLs by DOI

Often you have a DOI or other paper identifier and want to find open copies of the paper to read. In fatcat terms, you want to lookup a release by external identifier, then sort through any associated file entities to find the best files and URLs to download. Note that the Unpaywall API is custom designed for this task and you should look in to using that instead.

This is read-only task and requires no authentication. The simple summary is to:

GET the release lookup endpoint with the external identifier as a query parameter. Also set the hide parameter to elide unused fields, and the expand parameter to files to include related files in a single request.
If you get a hit (HTTP 200), sort through the files field (an array) and for each file the urls field (also an array) to select the best URL(s).

The URL to use would look like https://api.fatcat.wiki/v0/release/lookup?doi=10.1088/0264-9381/19/7/380&expand=files&hide=abstracts,refs in a browser. The query parameters should be URL encoded (eg, the DOI / characters replaced with with %20), but almost all HTTP tools and libraries will do this automatically.

The raw HTTP request would look like:

GET /v0/release/lookup?doi=10.1088%2F0264-9381%2F19%2F7%2F380&expand=files&hide=abstracts%2Crefs HTTP/1.1
Accept: */*
Accept-Encoding: gzip, deflate
Connection: keep-alive
Host: api.fatcat.wiki
User-Agent: HTTPie/0.9.8

And the response (with some headers removed and JSON body paraphrased):

HTTP/1.1 200 OK
Connection: keep-alive
Content-Length: 1996
Content-Type: application/json
Date: Tue, 17 Sep 2019 22:47:54 GMT
X-Frame-Options: SAMEORIGIN
X-Span-ID: caa70cff-967d-4429-96c6-71909738ab4c

{
    "ident": "3j36alui7fcwncbc4xdaklywb4", 
    "title": "LIGO sensing system performance", 
    "publisher": "IOP Publishing", 
    "release_date": "2002-03-19", 
    "release_stage": "published", 
    "release_type": "article-journal", 
    "release_year": 2002, 
    "revision": "2e36dfbe-9a4b-4917-95bb-f02b04f6b5d0", 
    "state": "active", 
    "work_id": "ejllv7xq4rgrrffpsf3prqurwq"
    "container_id": "j5iizqxt2rainmxg6nfmpg2ds4", 
    "contribs": [],
    "ext_ids": {
        "doi": "10.1088/0264-9381/19/7/380"
    }, 
    "files": [
        {
            "ident": "vmfyqb77r5gs3pkoekzfcjgsb4", 
            "mimetype": "application/pdf", 
            "release_ids": [
                "3j36alui7fcwncbc4xdaklywb4"
            ], 
            "revision": "66639928-d9e2-45e2-a883-36616d5b0a67", 
            "sha1": "54244fe8d35bff2db2a3ff946e60c194f68821ae", 
            "state": "active", 
            "urls": [
                {
                    "rel": "web", 
                    "url": "http://www.gravity.uwa.edu.au/amaldi/papers/Landry.pdf"
                }, 
                {
                    "rel": "webarchive", 
                    "url": "https://web.archive.org/web/20081011163648/http://www.gravity.uwa.edu.au/amaldi/papers/Landry.pdf"
                }
            ]
        }, 
        {
            "ident": "3ta26geysncdxlgswjoaiqlbyu", 
            "mimetype": "application/pdf", 
            "release_ids": [
                "3j36alui7fcwncbc4xdaklywb4"
            ], 
            "revision": "5c7a8cb0-4710-415a-93d5-d7cb6c42dfd1", 
            "sha1": "954c0fb370af7f72a0cb47505b8793e8e5e23136", 
            "state": "active", 
            "urls": [
                {
                    "rel": "webarchive", 
                    "url": "https://web.archive.org/web/20050624182645/http://www.gravity.uwa.edu.au/amaldi/papers/Landry.pdf"
                }, 
                {
                    "rel": "webarchive", 
                    "url": "https://web.archive.org/web/20091024040004/http://www.gravity.uwa.edu.au/amaldi/papers/Landry.pdf"
                }, 
                {
                    "rel": "web", 
                    "url": "http://www.gravity.uwa.edu.au/amaldi/papers/Landry.pdf"
                }
            ]
        }
    ], 
}

An httpie and jq one-liner to grap the first URL would be:

http https://api.fatcat.wiki/v0/release/lookup doi==10.1088/0264-9381/19/7/380 expand==files hide==abstracts,refs | jq '.files[0].urls[0].url' -r

Using the python client library (fatcat-openapi-client), you might do something like:

import fatcat_openapi_client
from fatcat_openapi_client.rest import ApiException

conf = fatcat_openapi_client.Configuration()
conf.host = "https://api.fatcat.wiki/v0"
api = fatcat_openapi_client.DefaultApi(fatcat_openapi_client.ApiClient(conf))
doi = "10.1088/0264-9381/19/7/380"

try:
    r = api.lookup_release(doi=doi, expand="files", hide="abstracts,refs")
except ApiException as ae:
    if ae.status == 404:
        print("DOI not found!")
        return
    else:
        raise ae

print("Fatcat release found: https://fatcat.wiki/release/{}".format(r.ident))

for f in r.files:
    if f.mimetype != 'application/pdf':
        continue
    for u in r.urls:
        if u.rel == 'webarchive' and '//web.archive.org/' in u.url:
            print("Wayback PDF URL: {}".format(u.url)
            return

print("No Wayback PDF URL found")

A more advanced lookup tool would check for sibling releases under the same work and provide both alternative links ("no version of record available, but here is the pre-print") and notify the end user about any updates or retractions to the work as a whole.

Creating an Entity

Let's use a container (journal) entity as a simple example of mutation of the catalog. This assumes you already have an editor account and API token, both obtained through the web interface.

In summary:

Create (POST) an editgroup
Create (POST) the container entity as part of editgroup
Submit the editgroup for review
(privileged) Accept the editgroup

See the API docs for full details of authentication.

To create an editgroup, the raw HTTP request (to https://api.fatcat.wiki/v0/editgroup) and response would look like:

POST /v0/editgroup HTTP/1.1
Accept: application/json, */*
Accept-Encoding: gzip, deflate
Authorization: Bearer AgEPZGV2LmZhdGNhdC53aWtpAhYyMDE5MDEwMS1kZXYtZHVtbXkta2V5AAImZWRpdG9yX2lkID0gYWFhYWFhYWFhYWFhYmt2a2FhYWFhYWFhYWkAAht0aW1lID4gMjAxOS0wMS0wOVQwMDo1Nzo1MloAAAYgnroNha1hSftChtxHGTnLEmM/pY8MeQS/jBSV0UNvXug=
Connection: keep-alive
Content-Length: 2
Content-Type: application/json
Host: api.fatcat.wiki
User-Agent: HTTPie/0.9.8

{}

HTTP/1.1 201 Created
Connection: keep-alive
Content-Length: 126
Content-Type: application/json
Date: Tue, 17 Sep 2019 23:25:55 GMT
X-Span-ID: cc016e0e-77ae-4ca0-b1da-b0a38e48a130

{
    "created": "2019-09-17T23:25:55.273836Z", 
    "editgroup_id": "aqhyo2ulmzfbrewn3rv7dhl65u", 
    "editor_id": "4vmpwdwxxneitkonvgm2pk6kya"
}

It is important to parse the response to get the editgroup_id. Next POST to https://fatcat.wiki/v0/editgroup/EDITGROUP_ID/container (with the editgroup_id substituted) and the JSON container entity as the body:

POST /v0/editgroup/aqhyo2ulmzfbrewn3rv7dhl65u/container HTTP/1.1
Accept: application/json, */*
Accept-Encoding: gzip, deflate
Authorization: Bearer AgEPZGV2LmZhdGNhdC53aWtpAhYyMDE5MDEwMS1kZXYtZHVtbXkta2V5AAImZWRpdG9yX2lkID0gYWFhYWFhYWFhYWFhYmt2a2FhYWFhYWFhYWkAAht0aW1lID4gMjAxOS0wMS0wOVQwMDo1Nzo1MloAAAYgnroNha1hSftChtxHGTnLEmM/pY8MeQS/jBSV0UNvXug=
Connection: keep-alive
Content-Length: 54
Content-Type: application/json
Host: api.fatcat.wiki
User-Agent: HTTPie/0.9.8

{
    "issnl": "1234-5678", 
    "name": "Journal of Something"
}

HTTP/1.1 201 Created
Connection: keep-alive
Content-Length: 181
Content-Type: application/json
Date: Tue, 17 Sep 2019 23:30:32 GMT
X-Span-ID: eb2f4243-ed43-4a21-bbf0-d653590fcfe2

{
    "edit_id": "ea203496-ecb9-45c7-ac50-3cb24cdbb58f", 
    "editgroup_id": "aqhyo2ulmzfbrewn3rv7dhl65u", 
    "ident": "g3kyxylxjbej7drf6apqpfkl6i", 
    "revision": "796429d2-44a4-4ece-a9b2-e80edcd4277a"
}

To submit an editgroup, use the update endpoint with the submit query parameter set to true. The body should be the editgroup object (as JSON), but is mostly ignored:

PUT /v0/editgroup/aqhyo2ulmzfbrewn3rv7dhl65u?submit=true HTTP/1.1
Accept: application/json, */*
Accept-Encoding: gzip, deflate
Authorization: Bearer AgEPZGV2LmZhdGNhdC53aWtpAhYyMDE5MDEwMS1kZXYtZHVtbXkta2V5AAImZWRpdG9yX2lkID0gYWFhYWFhYWFhYWFhYmt2a2FhYWFhYWFhYWkAAht0aW1lID4gMjAxOS0wMS0wOVQwMDo1Nzo1MloAAAYgnroNha1hSftChtxHGTnLEmM/pY8MeQS/jBSV0UNvXug=
Connection: keep-alive
Content-Length: 131
Content-Type: application/json
Host: api.fatcat.wiki
User-Agent: HTTPie/0.9.8

{
    "created": "2019-09-17T23:25:55.273836Z", 
    "editgroup_id": "aqhyo2ulmzfbrewn3rv7dhl65u", 
    "editor_id": "4vmpwdwxxneitkonvgm2pk6kya"
}

HTTP/1.1 200 OK
Connection: keep-alive
Content-Length: 168
Content-Type: application/json
Date: Tue, 17 Sep 2019 23:37:06 GMT
X-Span-ID: c0ac0406-83ce-4e07-a892-3f83c02ec207

{
    "created": "2019-09-17T23:25:55.273836Z", 
    "editgroup_id": "aqhyo2ulmzfbrewn3rv7dhl65u", 
    "editor_id": "4vmpwdwxxneitkonvgm2pk6kya", 
    "submitted": "2019-09-17T23:37:06.288434Z"
}

Lastly, if your editor account as the admin role, you can "accept" the editgroup using the accept endpoint:

POST /v0/editgroup/aqhyo2ulmzfbrewn3rv7dhl65u/accept HTTP/1.1
Accept: */*
Accept-Encoding: gzip, deflate
Authorization: Bearer AgEPZGV2LmZhdGNhdC53aWtpAhYyMDE5MDEwMS1kZXYtZHVtbXkta2V5AAImZWRpdG9yX2lkID0gYWFhYWFhYWFhYWFhYmt2a2FhYWFhYWFhYWkAAht0aW1lID4gMjAxOS0wMS0wOVQwMDo1Nzo1MloAAAYgnroNha1hSftChtxHGTnLEmM/pY8MeQS/jBSV0UNvXug=
Connection: keep-alive
Content-Length: 0
Host: api.fatcat.wiki
User-Agent: HTTPie/0.9.8



HTTP/1.1 200 OK
Connection: keep-alive
Content-Length: 36
Content-Type: application/json
Date: Tue, 17 Sep 2019 23:40:21 GMT
X-Span-ID: cb4d66f0-9e67-4908-8dff-97489cc87ca2

{
    "message": "horray!", 
    "success": true
}

This whole exchange is, of course, must faster with the python library:

import fatcat_openapi_client
from fatcat_openapi_client.rest import ApiException

conf = fatcat_openapi_client.Configuration()
conf.host = "https://api.fatcat.wiki/v0"
conf.api_key_prefix["Authorization"] = "Bearer"
conf.api_key["Authorization"] = "AgEPZGV2LmZhdGNhdC53aWtpAhYyMDE5MDEwMS1kZXYtZHVtbXkta2V5AAImZWRpdG9yX2lkID0gYWFhYWFhYWFhYWFhYmt2a2FhYWFhYWFhYWkAAht0aW1lID4gMjAxOS0wMS0wOVQwMDo1Nzo1MloAAAYgnroNha1hSftChtxHGTnLEmM/pY8MeQS/jBSV0UNvXug="
api = fatcat_openapi_client.DefaultApi(fatcat_openapi_client.ApiClient(conf))

c = fatcat_openapi_client.ContainerEntity(
    name="Test Journal",
    issnl="1234-5678",
)
editgroup = api.create_editgroup(description="my test editgroup")
c_edit = api.create_container(editgroup.editgroup_id, c)
api.update_editgroup(editgroup.editgroup_id, submit=True)

# only if you have permissions
api.accept_editgroup(editgroup.editgroup_id)

Updating an Existing Entity

It is important to ensure that edits/updates are idempotent, in this case meaning that if you ran the same script twice in quick succession, no mutation or update would occur the second time. This is usually achieved by always fetching entities just before an edit and checking that updates are actually necessary.

The basic process is to:

Fetch (GET) or Lookup (GET) the existing entity. Check that edit is actually necessary!
Create (POST) a new editgroup
Update (PUT) the entity
Submit (PUT) the editgroup for review

Python example code:

import fatcat_openapi_client
from fatcat_openapi_client.rest import ApiException

conf = fatcat_openapi_client.Configuration()
conf.host = "https://api.fatcat.wiki/v0"
conf.api_key_prefix["Authorization"] = "Bearer"
conf.api_key["Authorization"] = "AgEPZGV2LmZhdGNhdC53aWtpAhYyMDE5MDEwMS1kZXYtZHVtbXkta2V5AAImZWRpdG9yX2lkID0gYWFhYWFhYWFhYWFhYmt2a2FhYWFhYWFhYWkAAht0aW1lID4gMjAxOS0wMS0wOVQwMDo1Nzo1MloAAAYgnroNha1hSftChtxHGTnLEmM/pY8MeQS/jBSV0UNvXug="
api = fatcat_openapi_client.DefaultApi(fatcat_openapi_client.ApiClient(conf))

new_name = "Classical and Quantum Gravity"
c = api.get_container('j5iizqxt2rainmxg6nfmpg2ds4')
if c.name == new_name:
    print("Already updated!")
    return

c.name = new_name

editgroup = api.create_editgroup(description="my test container editgroup")
c_edit = api.update_container(editgroup.editgroup_id, c.ident, c)
api.update_editgroup(editgroup.editgroup_id, submit=True)

Merging Duplicate Entities

Like other mutations, be careful that any merge oprations do not clobber the catalog if run multiple times.

Summary:

Fetch (GET) both entities. Ensure that merging is still required.
Decide which will be the "primary" entity (the other will redirect to it)
Create (POST) a new editgroup
Update (PUT) the "primary" entity with any updated metadata merged from the other entity (optional), and the editgroup id set
Update (PUT) the "other" entity with the redirect flag set to the primary's identifier.
Submit (PUT) the editgroup for review
Somebody (human or bot) with admin privileges will Accept (POST) the editgroup.

Python example code:

import fatcat_openapi_client
from fatcat_openapi_client.rest import ApiException

conf = fatcat_openapi_client.Configuration()
conf.host = "https://api.fatcat.wiki/v0"
conf.api_key_prefix["Authorization"] = "Bearer"
conf.api_key["Authorization"] = "AgEPZGV2LmZhdGNhdC53aWtpAhYyMDE5MDEwMS1kZXYtZHVtbXkta2V5AAImZWRpdG9yX2lkID0gYWFhYWFhYWFhYWFhYmt2a2FhYWFhYWFhYWkAAht0aW1lID4gMjAxOS0wMS0wOVQwMDo1Nzo1MloAAAYgnroNha1hSftChtxHGTnLEmM/pY8MeQS/jBSV0UNvXug="
api = fatcat_openapi_client.DefaultApi(fatcat_openapi_client.ApiClient(conf))

left = api.get_creator('iimvc523xbhqlav6j3sbthuehu')
right = api.get_creator('lav6j3sbthuehuiimvc523xbhq')

# check that merge/redirect hasn't happened yet
assert left.state == 'active' and right.state == 'active'
assert left.redirect = None and right.redirect_id = None
assert left.revision != right.revision

# decide to merge "right" into "left"
if not left.orcid:
    left.orcid = right.orcid
if not left.surname:
    left.surname = right.surname

editgroup = api.create_editgroup(description="my test creator merge editgroup")
left_edit = api.update_creator(editgroup.editgroup_id, left.ident, left)
right_edit = api.update_creator(eidtgroup.editgroup_id, right.ident,
    fatcat_openapi_client.CreatorEntity(redirect=left.ident))
api.update_editgroup(editgroup.editgroup_id, submit=True)

Batch Create Entities

When importing large numbers (thousands) of entities, it can be faster to use the batch create operations instead of individual editgroup and entity creation. Using the batch endpoints requires care because the potential to pollute the catalog with bad entities (and the effort required to clean up) can be much larger.

These methods always require the admin role, because they are the equivalent of creation and editgroup accept.

It is not currently possible to do batch updates or deletes in a single request.

The basic process is:

Confirm that input entities should be created (eg, using identifier lookups), and bundle into groups of 50-100 entities.
Batch create (POST) a set of entities, with editgroup metadata included along with list of entities (all of a single type). Entire batch is inserted in a single request.

import fatcat_openapi_client
from fatcat_openapi_client.rest import ApiException

conf = fatcat_openapi_client.Configuration()
conf.host = "https://api.fatcat.wiki/v0"
conf.api_key_prefix["Authorization"] = "Bearer"
conf.api_key["Authorization"] = "AgEPZGV2LmZhdGNhdC53aWtpAhYyMDE5MDEwMS1kZXYtZHVtbXkta2V5AAImZWRpdG9yX2lkID0gYWFhYWFhYWFhYWFhYmt2a2FhYWFhYWFhYWkAAht0aW1lID4gMjAxOS0wMS0wOVQwMDo1Nzo1MloAAAYgnroNha1hSftChtxHGTnLEmM/pY8MeQS/jBSV0UNvXug="
api = fatcat_openapi_client.DefaultApi(fatcat_openapi_client.ApiClient(conf))

releases = [
    ReleaseEntity(
      ext_ids=ReleaseExtIds(doi="10.123/456"),
      title="Dummy Release",
    ),
    ReleaseEntity(
      ext_ids=ReleaseExtIds(doi="10.123/789"),
      title="Another Dummy Release",
    ),
    # ... more releases here ...
]

# check that releases don't exist already; this could be a filter
for r in releases:
    existing = None
    try:
        existing = api.lookup_release(doi=r.ext_ids.doi)
    except ApiException as ae
        assert ae.status == 404
    assert existing is None

# ensure our batch size isn't too large
assert len(releases) <= 100

editgroup = api.create_release_auto_batch(
    fatcat_openapi_client.ReleaseAutoBatch(
        editgroup=fatcat_openapi_client.Editgroup(
            description="my test batch",
        ),
        entity_list=releases,
    )
)

Import New Files Linked to Releases

Let's say you knew of many open access PDFs, including their SHA-1, size, and a URL:

10.123/456  7043946a7afe0ee32c9d4c22a9b3fc2ba6d34b42    7238    https://archive.org/download/open_access_files/456.pdf
10.123/789  350a8d5c6fac151ec2c81d4df5d58d14aeefc72f    1277    https://archive.org/download/open_access_files/789.pdf
10.123/900  9d9a9868a661b13c32fd38021addadb7b4a31122     166    https://archive.org/download/open_access_files/900.pdf
[...]

The process for adding these could be something like:

For each row, check if file with SHA-1 exists; if so, skip
For each row, lookup the release by DOI; if it doesn't exist, skip
Transform into File entities
Group entities into batches
Submit batches to API

There are multiple ways to structure code to do this. You may want to look at the importer class under python/fatcat_tools/importers/common.py, and other existing import scripts in that directory for a framework to structure this type of import.

Here is a simpler example using only the python library:


# TODO: actually test this code

import sys
import fatcat_openapi_client
from fatcat_openapi_client import *
from fatcat_openapi_client.rest import ApiException

conf = fatcat_openapi_client.Configuration()
conf.host = "https://api.fatcat.wiki/v0"
conf.api_key_prefix["Authorization"] = "Bearer"
conf.api_key["Authorization"] = "AgEPZGV2LmZhdGNhdC53aWtpAhYyMDE5MDEwMS1kZXYtZHVtbXkta2V5AAImZWRpdG9yX2lkID0gYWFhYWFhYWFhYWFhYmt2a2FhYWFhYWFhYWkAAht0aW1lID4gMjAxOS0wMS0wOVQwMDo1Nzo1MloAAAYgnroNha1hSftChtxHGTnLEmM/pY8MeQS/jBSV0UNvXug="
api = fatcat_openapi_client.DefaultApi(fatcat_openapi_client.ApiClient(conf))

HAVE_ADMIN = False

def try_row(fields):
    # remove any extra whitespace
    fields = [f.strip() for f in fields]
    doi = fields[0]
    sha1 = fields[1]
    size = int(fields[2])
    url = fields[3]

    # check for existing file
    try:
        existing = api.lookup_file(sha1=sha1)
        print("File with SHA-1 exists: {}".format(sha1))
        return None
    except ApiException as ae:
        if ae.status != 404:
            raise ae

    # lookup release by DOI
    try:
        release = api.lookup_release(doi=doi)
    except ApiException as ae:
        if ae.status == 404:
            print("No existing release for DOI: {}".format(doi))
            return None
        else:
            raise ae

    fe = FileEntity(
        release_ids=[release.ident],
        sha1=sha1,
        size=size,
        urls=[FileUrl(rel="archive", url=url)],
    )
    return fe

def run(input_file):
    file_entities = []
    for line in input_file:
        fe = try_row(line.split('\t'))
        if fe:
            file_entities.append(fe)
    if not file_entities:
        print("Tried all lines, nothing to do!")

    # TODO: iterate over fixed-size batches
    first_batch = file_entities[:100]

    # easy way: create as a batch if you have permission
    if HAVE_ADMIN:
        editgroup = api.create_release_auto_batch(
            fatcat_openapi_client.ReleaseAutoBatch(
                editgroup=fatcat_openapi_client.Editgroup(
                    description="my test batch",
                ),
                entity_list=releases,
            )
        )
        return

    # longer way: create one-at-a-time
    editgroup = api.create_editgroup(Editgroup(
        description="batch import of files-by-DOI. Data from XYZ",
        extra={
            # put the name of your script/project here
            'agent': 'tutorial_example_script',
        },
    ))

    for fe in first_batch:
        edit = api.create_file(editgroup.editgroup_id, fe)

    # submit for review
    api.update_editgroup(editgroup.editgroup_id, editgroup, submit=True)
    print("Submitted editgroup: https://fatcat.wiki/editgroup/{}".format(editgroup.editgroup_id))

    print("Done!")

if __name__=='__main__':
    if len(sys.argv) != 2:
        print("Pass input TSV file as argument")
        sys.exit(-1)
    with open(sys.argv[1], 'r') as input_file:
        run(input_file)

# ensure our batch size isn't too large
assert len(releases) <= 100

editgroup = api.create_release_auto_batch(
    fatcat_openapi_client.ReleaseAutoBatch(
        editgroup=fatcat_openapi_client.Editgroup(
            description="my test batch",
        ),
        entity_list=releases,
    )
)

The Fatcat Guide