diff --git a/.gitignore b/.gitignore
index ce175e3fcf..c3511ff453 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,6 +5,8 @@ _site
vendor
debug.log
__pycache__
+.cache
+!cache.db
.DS_STORE
.env*
package.json
diff --git a/CHANGELOG.md b/CHANGELOG.md
index d7ab5a2c93..57e130452c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,12 @@
Reference: common-changelog.org
+## 1.1.4 - 2023-04-28
+
+### Changed
+
+- Fix ORCID plugin and other cite process bugs.
+
## 1.1.3 - 2023-04-20
### Changed
diff --git a/CITATION.cff b/CITATION.cff
index 6d40cbc530..4870fb24c2 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -1,8 +1,8 @@
# citation metadata for the template itself
title: "Lab Website Template"
-version: 1.1.3
-date-released: 2023-04-20
+version: 1.1.4
+date-released: 2023-04-28
url: "https://github.com/greenelab/lab-website-template"
authors:
- family-names: "Rubinetti"
diff --git a/_cite/.cache/cache.db b/_cite/.cache/cache.db
index 23703d7497..fb6f435a43 100644
Binary files a/_cite/.cache/cache.db and b/_cite/.cache/cache.db differ
diff --git a/_cite/cite.py b/_cite/cite.py
index 8828a9f69e..e0b7dcff37 100644
--- a/_cite/cite.py
+++ b/_cite/cite.py
@@ -89,11 +89,11 @@
# merge sources with matching (non-blank) ids
for a in range(0, len(sources)):
- _id = sources[a].get("id")
+ _id = sources[a].get("id", "")
if not _id:
continue
for b in range(a + 1, len(sources)):
- if sources[b].get("id") == _id:
+ if sources[b].get("id", "") == _id:
sources[a].update(sources[b])
sources[b] = {}
sources = [entry for entry in sources if entry]
@@ -109,6 +109,7 @@
# list of new citations
citations = []
+
# loop through compiled sources
for index, source in enumerate(sources):
log(f"Processing source {index + 1} of {len(sources)}, {label(source)}")
@@ -130,7 +131,7 @@
# if Manubot cannot cite source
except Exception as e:
# if regular source (id entered by user), throw error
- if source.get("plugin") == "sources.py":
+ if source.get("plugin", "") == "sources.py":
log(e, 3, "ERROR")
error = True
# otherwise, if from metasource (id retrieved from some third-party API), just warn
@@ -143,7 +144,8 @@
citation.update(source)
# ensure date in proper format for correct date sorting
- citation["date"] = format_date(citation.get("date"))
+ if citation.get("date", ""):
+ citation["date"] = format_date(citation.get("date", ""))
# add new citation to list
citations.append(citation)
@@ -153,6 +155,7 @@
log("Saving updated citations")
+
# save new citations
try:
save_data(output_file, citations)
diff --git a/_cite/plugins/google-scholar.py b/_cite/plugins/google-scholar.py
index 0a05a00568..f04dec811d 100644
--- a/_cite/plugins/google-scholar.py
+++ b/_cite/plugins/google-scholar.py
@@ -9,41 +9,41 @@ def main(entry):
returns list of sources to cite
"""
- # get id from entry
- id = entry.get("gsid")
- if not id:
- raise Exception('No "gsid" key')
-
# get api key
- api_key = os.environ.get("GOOGLE_SCHOLAR_API_KEY")
+ api_key = os.environ.get("GOOGLE_SCHOLAR_API_KEY", "")
if not api_key:
raise Exception('No "GOOGLE_SCHOLAR_API_KEY" env var')
# serp api
params = {
"engine": "google_scholar_author",
- "author_id": id,
"api_key": api_key,
- "num": 100,
+ "num": 100, # max allowed
}
+ # get id from entry
+ _id = entry.get("gsid", "")
+ if not _id:
+ raise Exception('No "gsid" key')
+
# query api
@log_cache
@cache.memoize(name=__file__, expire=1 * (60 * 60 * 24))
- def query():
+ def query(_id):
+ params["author_id"] = _id
return GoogleSearch(params).get_dict().get("articles", [])
- response = query()
+ response = query(_id)
# list of sources to return
sources = []
# go through response and format sources
for work in response:
-
# create source
source = {
"id": work.get("citation_id", ""),
+ # api does not provide Manubot-citeable id, so keep citation details
"title": work.get("title", ""),
"authors": list(map(str.strip, work.get("authors", "").split(","))),
"publisher": work.get("publication", ""),
diff --git a/_cite/plugins/orcid.py b/_cite/plugins/orcid.py
index 28817482e5..1d47e72b7e 100644
--- a/_cite/plugins/orcid.py
+++ b/_cite/plugins/orcid.py
@@ -10,42 +10,102 @@ def main(entry):
"""
# orcid api
- endpoint = "https://pub.orcid.org/v2.0/$ORCID/works"
+ endpoint = "https://pub.orcid.org/v3.0/$ORCID/works"
headers = {"Accept": "application/json"}
# get id from entry
- id = entry.get("orcid")
- if not id:
+ _id = entry.get("orcid", "")
+ if not _id:
raise Exception('No "orcid" key')
# query api
@log_cache
@cache.memoize(name=__file__, expire=1 * (60 * 60 * 24))
- def query():
- url = endpoint.replace("$ORCID", id)
+ def query(_id):
+ url = endpoint.replace("$ORCID", _id)
request = Request(url=url, headers=headers)
response = json.loads(urlopen(request).read())
- return response.get("group")
+ return response.get("group", [])
- response = query()
+ response = query(_id)
# list of sources to return
sources = []
# go through response structure and pull out ids e.g. doi:1234/56789
for work in response:
- for id in work["external-ids"]["external-id"]:
- # get id and id-type from response
- id_type = id["external-id-type"]
- id_value = id["external-id-value"]
+ # get list of ids
+ ids = work.get("external-ids", {}).get("external-id", [])
+ for summary in work.get("work-summary", []):
+ ids = ids + summary.get("external-ids", {}).get("external-id", [])
- # create source
- source = {"id": f"{id_type}:{id_value}"}
+ # prefer doi id type, or fallback to first id
+ _id = next(
+ (id for id in ids if id.get("external-id-type", "") == "doi"),
+ ids[0] if len(ids) > 0 else {},
+ )
- # copy fields from entry to source
- source.update(entry)
+ # get id and id-type from response
+ id_type = _id.get("external-id-type", "")
+ id_value = _id.get("external-id-value", "")
- # add source to list
- sources.append(source)
+ # create source
+ source = {"id": f"{id_type}:{id_value}"}
+
+ # if not a doi, Manubot likely can't cite, so keep citation details
+ if id_type != "doi":
+ # get summaries
+ summaries = work.get("work-summary", [])
+
+ # sort summary entries by most recent
+ summaries = sorted(
+ summaries,
+ key=lambda summary: (
+ summary.get("last-modified-date", {}).get("value", 0)
+ )
+ or summary.get("created-date", {}).get("value", 0)
+ or 0,
+ reverse=True,
+ )
+
+ # get first summary with defined sub-value
+ def first(get_func):
+ return next(value for value in map(get_func, summaries) if value)
+
+ # get title
+ title = first(
+ lambda s: s.get("title", {}).get("title", {}).get("value", "")
+ )
+
+ # get publisher
+ publisher = first(lambda s: s.get("journal-title", {}).get("value", ""))
+
+ # get date
+ date = (
+ work.get("last-modified-date", {}).get("value", 0)
+ or first(lambda s: s.get("last-modified-date", {}).get("value", 0))
+ or work.get("created-date", {}).get("value", 0)
+ or first(lambda s: s.get("created-date", {}).get("value", 0))
+ or 0
+ )
+
+ # get link
+ link = first(lambda s: s.get("url", {}).get("value", ""))
+
+ # keep available details
+ if title:
+ source["title"] = title
+ if publisher:
+ source["publisher"] = publisher
+ if date:
+ source["date"] = format_date(date)
+ if link:
+ source["link"] = link
+
+ # copy fields from entry to source
+ source.update(entry)
+
+ # add source to list
+ sources.append(source)
return sources
diff --git a/_cite/plugins/pubmed.py b/_cite/plugins/pubmed.py
index ac9fac7c66..63eefb7b84 100644
--- a/_cite/plugins/pubmed.py
+++ b/_cite/plugins/pubmed.py
@@ -14,28 +14,28 @@ def main(entry):
endpoint = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=$TERM&retmode=json&retmax=1000&usehistory=y"
# get id from entry
- id = entry.get("term")
- if not id:
+ _id = entry.get("term", "")
+ if not _id:
raise Exception('No "term" key')
# query api
@log_cache
@cache.memoize(name=__file__, expire=1 * (60 * 60 * 24))
- def query():
- url = endpoint.replace("$TERM", quote(id))
+ def query(_id):
+ url = endpoint.replace("$TERM", quote(_id))
request = Request(url=url)
response = json.loads(urlopen(request).read())
- return response.get("esearchresult", {}).get("idlist")
+ return response.get("esearchresult", {}).get("idlist", [])
- response = query()
+ response = query(_id)
# list of sources to return
sources = []
# go through response and format sources
- for id in response:
+ for _id in response:
# create source
- source = {"id": f"pubmed:{id}"}
+ source = {"id": f"pubmed:{_id}"}
# copy fields from entry to source
source.update(entry)
diff --git a/_cite/util.py b/_cite/util.py
index 87efe940a4..74638a6c57 100644
--- a/_cite/util.py
+++ b/_cite/util.py
@@ -49,7 +49,7 @@ def log(message="\n--------------------\n", indent=0, level="", newline=True):
"SUCCESS": "[black on #10B981]",
"INFO": "[grey70]",
}
- color = palette.get(level) or palette.get(indent) or "[white]"
+ color = palette.get(level, "") or palette.get(indent, "") or "[white]"
if newline:
print()
print(indent * " " + color + str(message) + "[/]", end="", flush=True)
@@ -76,6 +76,8 @@ def format_date(date):
format date as YYYY-MM-DD, or no date if malformed
"""
+ if isinstance(date, int):
+ return datetime.fromtimestamp(date // 1000.0).strftime("%Y-%m-%d")
try:
return datetime.strptime(date, "%Y-%m-%d").strftime("%Y-%m-%d")
except Exception:
@@ -178,7 +180,7 @@ def cite_with_manubot(_id):
# authors
citation["authors"] = []
- for author in manubot.get("author", []):
+ for author in manubot.get("author", {}):
given = author.get("given", "").strip()
family = author.get("family", "").strip()
if given or family:
@@ -193,8 +195,8 @@ def cite_with_manubot(_id):
# extract date part
def date_part(citation, index):
try:
- return citation.get("issued").get("date-parts")[0][index]
- except Exception:
+ return citation["issued"]["date-parts"][0][index]
+ except (KeyError, IndexError, TypeError):
return ""
# date
diff --git a/_layouts/member.html b/_layouts/member.html
index 23b665646e..034b5d080d 100644
--- a/_layouts/member.html
+++ b/_layouts/member.html
@@ -32,16 +32,20 @@
research/?search={% for alias in aliases %}"{{ alias }}" {% endfor %}
{%- endcapture %}
-
- Search for {{ page.name | default: page.title }}'s papers on the Research page
-
+
+
+ Search for {{ page.name | default: page.title }}'s papers on the Research page
+
+
{% capture search -%}
blog/?search={{ page.name }}
{%- endcapture %}
-
+