def test_get_url_csl_item_zotero_github():
"""
This command creates two translation-server queries. The first query is
equivalent to:
```
curl --verbose \
--header "Content-Type: text/plain" \
--data 'https://github.com/pandas-dev/pandas/tree/d5e5bf761092c59eeb9b8750f05f2bc29fb45927' \
'https://translate.manubot.org/web'
```
Note: this test may have temporary failures, due to performance of
translation-server. It seems that sometimes translation-server
returns a different title for the same URL. A real mystery.
See also:
https://github.com/manubot/manubot/pull/139#discussion_r328703233
Proposed action:
Probably should inquire upstream or change the test.
"""
url = 'https://github.com/pandas-dev/pandas/tree/d5e5bf761092c59eeb9b8750f05f2bc29fb45927'
csl_item = get_url_csl_item_zotero(url)
# FIXME: arbitraryly, csl_item['abstract'], and not csl_item['title'] contains the title.
assert csl_item['title'].startswith('Flexible and powerful data analysis')
assert csl_item['source'] == 'GitHub'
def test_get_url_csl_item_zotero_no_url(monkeypatch):
"""
Ensure get_url_csl_item_zotero sets URL to the query URL,
when the Zotero translator does not return it.
https://github.com/manubot/manubot/issues/244
"""
query_url = "http://icbo2016.cgrb.oregonstate.edu/node/251"
def mock_web_query(url: str):
assert url == query_url
return [{
"key":
"J86G3MS7",
"version":
0,
"itemType":
"webpage",
"creators": [
{
"firstName": "Senay",
"lastName": "Kafkas",
"creatorType": "author",
},
{
"firstName": "Ian",
"lastName": "Dunham",
"creatorType": "author"
},
{
"firstName": "Helen",
"lastName": "Parkinson",
"creatorType": "author",
},
{
"firstName": "Johanna",
"lastName": "Mcentyre",
"creatorType": "author",
},
],
"tags": [],
"title":
"BIT106: Use of text mining for Experimental Factor Ontology coverage expansion in the scope of target validation",
"date":
"2016",
"shortTitle":
"BIT106",
}]
monkeypatch.setattr("manubot.cite.zotero.web_query", mock_web_query)
csl_item = get_url_csl_item_zotero(query_url)
assert "URL" in csl_item
assert csl_item["URL"] == query_url
def get_wikidata_csl_item(identifier):
"""
Get a CSL JSON item with the citation metadata for a Wikidata item.
identifier should be a Wikidata item ID corresponding to a citeable
work, such as Q50051684.
"""
url = f'https://www.wikidata.org/wiki/{identifier}'
from manubot.cite.url import get_url_csl_item_zotero
csl_item = get_url_csl_item_zotero(url)
if 'DOI' in csl_item:
csl_item['DOI'] = csl_item['DOI'].lower()
if not 'URL' in csl_item:
csl_item['URL'] = url
return csl_item
def test_get_url_csl_item_zotero_nyt():
"""
This command creates two translation-server queries. The first query is
equivalent to:
```
curl --verbose \
--header "Content-Type: text/plain" \
--data 'https://nyti.ms/1NuB0WJ' \
'https://translate.manubot.org/web'
```
"""
url = 'https://nyti.ms/1NuB0WJ'
csl_item = get_url_csl_item_zotero(url)
assert csl_item['title'] == 'Unraveling the Ties of Altitude, Oxygen and Lung Cancer'
assert csl_item['author'][0]['family'] == 'Johnson'
def get_wikidata_csl_item(identifier: str) -> Dict[str, Any]:
"""
Get a CSL JSON item with the citation metadata for a Wikidata item.
identifier should be a Wikidata item ID corresponding to a citeable
work, such as Q50051684.
"""
url = f"https://www.wikidata.org/wiki/{identifier}"
from manubot.cite.url import get_url_csl_item_zotero
csl_item = get_url_csl_item_zotero(url)
if "DOI" in csl_item:
csl_item["DOI"] = csl_item["DOI"].lower()
if "URL" not in csl_item:
csl_item["URL"] = url
return csl_item
def test_get_url_csl_item_zotero_manubot():
"""
This command creates two translation-server queries. The first query is
equivalent to:
```
curl --verbose \
--header "Content-Type: text/plain" \
--data 'https://greenelab.github.io/meta-review/v/0770300e1d5490a1ae8ff3a85ddca2cdc4ae0613/' \
'https://translate.manubot.org/web'
```
"""
url = 'https://greenelab.github.io/meta-review/v/0770300e1d5490a1ae8ff3a85ddca2cdc4ae0613/'
csl_item = get_url_csl_item_zotero(url)
assert csl_item['title'] == 'Open collaborative writing with Manubot'
assert csl_item['author'][1]['family'] == 'Slochower'
# Zotero CSL exporter returns mixed string/int date-parts
# https://github.com/zotero/zotero/issues/1603
assert [int(x) for x in csl_item['issued']
['date-parts'][0]] == [2018, 12, 18]