From e7f1a56e8d314157bbc4183949de982fc5b135e1 Mon Sep 17 00:00:00 2001
From: Vincent Rubinetti <vince.rubinetti@gmail.com>
Date: Mon, 28 Jul 2025 22:02:01 -0400
Subject: [PATCH 1/2] test upstream LWT v1.3.6 change

---
 _cite/plugins/orcid.py | 80 +++++++++++++++++++++++++++++++-----------
 1 file changed, 59 insertions(+), 21 deletions(-)

diff --git a/_cite/plugins/orcid.py b/_cite/plugins/orcid.py
index 2f7d04de..7552d71d 100644
--- a/_cite/plugins/orcid.py
+++ b/_cite/plugins/orcid.py
@@ -1,7 +1,7 @@
 import json
 from urllib.request import Request, urlopen
 from util import *
-from manubot.cite.handlers import prefix_to_handler as manubot_prefixes
+from manubot.cite.handlers import prefix_to_handler as manubot_citable
 
 
 def main(entry):
@@ -33,36 +33,66 @@ def query(_id):
     # list of sources to return
     sources = []
 
-    # go through response structure and pull out ids e.g. doi:1234/56789
+    # filter id by some criteria. return true to accept, false to reject.
+    def filter_id(_id):
+        # is id of certain "relationship" type
+        relationships = ["self", "version-of", "part-of"]
+        if not get_safe(_id, "external-id-relationship", "") in relationships:
+            return False
+
+        id_type = get_safe(_id, "external-id-type", "")
+
+        # is id of certain type
+        # types = ["doi"]
+        # if id_type not in types:
+        #     return False
+
+        # is id citable by manubot
+        if id_type not in manubot_citable:
+            return False
+
+        return True
+
+    # prefer some ids over others by some criteria. return lower number to prefer more.
+    def sort_id(_id):
+        types = [
+            "doi",
+            # "arxiv",
+            # "url",
+        ]
+        return index_of(types, get_safe(_id, "external-id-type", ""))
+
+    # go through each source
     for work in response:
-        # get list of ids
+        # list of ids in work
         ids = []
+
+        # use "work-summary" field instead of top-level "external-ids" to reflect author-selected preferred sources
         for summary in get_safe(work, "work-summary", []):
             ids = ids + get_safe(summary, "external-ids.external-id", [])
 
-        # find first id of particular "relationship" type
-        _id = next(
-            (
-                id
-                for id in ids
-                if get_safe(id, "external-id-relationship", "")
-                in ["self", "version-of", "part-of"]
-            ),
-            ids[0] if len(ids) > 0 else None,
-        )
-
-        if _id == None:
-            continue
-
-        # get id and id-type from response
+        # filter ids by criteria
+        ids = list(filter(filter_id, ids))
+        # sort ids by criteria
+        ids.sort(key=sort_id)
+
+        # pick first id
+        _id = ids[0] if len(ids) > 0 else None
+
+        # id parts
         id_type = get_safe(_id, "external-id-type", "")
         id_value = get_safe(_id, "external-id-value", "")
 
         # create source
-        source = {"id": f"{id_type}:{id_value}"}
+        source = {}
 
-        # if not an id type that Manubot can cite, keep citation details
-        if id_type not in manubot_prefixes:
+        # if id citable by manubot
+        if id_type and id_value and id_type in manubot_citable:
+            # id to cite with manubot
+            source = {"id": f"{id_type}:{id_value}"}
+
+        # if not citable by manubot, keep citation details from orcid
+        else:
             # get summaries
             summaries = get_safe(work, "work-summary", [])
 
@@ -107,3 +137,11 @@ def first(get_func):
         sources.append(source)
 
     return sources
+
+
+# index of, with fallback
+def index_of(_list, value):
+    try:
+        return _list.index(value)
+    except ValueError:
+        return float("inf")

From e3af24e7b33941b7ff06d26080c5c4b48610760f Mon Sep 17 00:00:00 2001
From: vincerubinetti <8326331+vincerubinetti@users.noreply.github.com>
Date: Tue, 29 Jul 2025 02:06:19 +0000
Subject: [PATCH 2/2] Update citations

---
 .../f3/f2cd541712598cbdcf355b2e89e5.val}      | Bin
 _cite/.cache/cache.db                         | Bin 352256 -> 356352 bytes
 _data/citations.yaml                          | 122 ++++++++++++++++--
 3 files changed, 113 insertions(+), 9 deletions(-)
 rename _cite/.cache/{d4/d1/b46ff3878f5a1c5193b14f61b4c7.val => af/f3/f2cd541712598cbdcf355b2e89e5.val} (100%)

diff --git a/_cite/.cache/d4/d1/b46ff3878f5a1c5193b14f61b4c7.val b/_cite/.cache/af/f3/f2cd541712598cbdcf355b2e89e5.val
similarity index 100%
rename from _cite/.cache/d4/d1/b46ff3878f5a1c5193b14f61b4c7.val
rename to _cite/.cache/af/f3/f2cd541712598cbdcf355b2e89e5.val
diff --git a/_cite/.cache/cache.db b/_cite/.cache/cache.db
index c27baa379cbb66ec9e1b9d61e2564cae40563380..f4a42e873ace0376d594c58fd6f993d412771a92 100644
GIT binary patch
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diff --git a/_data/citations.yaml b/_data/citations.yaml
index a46d099e..b76a941e 100644
--- a/_data/citations.yaml
+++ b/_data/citations.yaml
@@ -1948,6 +1948,26 @@
   buttons:
   - type: preprint
     link: https://arxiv.org/abs/2104.11364
+- id: doi:10.48550/arxiv.2109.08633
+  title: An Open-Publishing Response to the COVID-19 Infodemic
+  authors:
+  - Halie M. Rando
+  - Simina M. Boca
+  - Lucy D'Agostino McGowan
+  - Daniel S. Himmelstein
+  - Michael P. Robson
+  - Vincent Rubinetti
+  - Ryan Velazquez
+  - COVID-19 Review Consortium
+  - Casey S. Greene
+  - Anthony Gitter
+  publisher: arXiv
+  date: '2021-01-01'
+  link: https://doi.org/gt6s6s
+  orcid: 0000-0001-8713-9213
+  member: casey-greene
+  plugin: orcid.py
+  file: orcid.yaml
 - id: doi:10.1016/j.cels.2021.07.007
   title: Analysis of scientific society honors reveals disparities
   authors:
@@ -4473,6 +4493,29 @@
   - open science
   - collaboration
   repo: greenelab/meta-review
+- id: issn:23356936 23356928
+  title: ''
+  authors: []
+  publisher: ''
+  date: ''
+  link: https://portal.issn.org/resource/ISSN/23356936 23356928
+  orcid: 0000-0001-8713-9213
+  member: casey-greene
+  plugin: orcid.py
+  file: orcid.yaml
+- id: doi:10.1101/385534
+  title: Parameter tuning is a key part of dimensionality reduction via deep variational
+    autoencoders for single cell RNA transcriptomics
+  authors:
+  - Qiwen Hu
+  - Casey S. Greene
+  publisher: Cold Spring Harbor Laboratory
+  date: '2018-08-05'
+  link: https://doi.org/gdxxjf
+  orcid: 0000-0001-8713-9213
+  member: casey-greene
+  plugin: orcid.py
+  file: orcid.yaml
 - id: doi:10.1101/573782
   title: Sequential compression of gene expression across dimensionalities and methods
     reveals no single best method or dimensionality
@@ -8215,6 +8258,16 @@
   member: casey-greene
   plugin: sources.py
   file: sources.yaml
+- id: wosuid:WOS:000386326200051
+  title: Web of Science
+  authors: []
+  publisher: ''
+  date: ''
+  link: https://www.webofscience.com/wos/woscc/full-record/WOS:WOS:000386326200051
+  orcid: 0000-0001-8713-9213
+  member: casey-greene
+  plugin: orcid.py
+  file: orcid.yaml
 - id: doi:10.7717/peerj.1621
   title: Cross-platform normalization of microarray and RNA-seq data for machine learning
     applications
@@ -8356,6 +8409,17 @@
   buttons:
   - type: source
     link: https://github.com/greenelab/adni-netwas
+- id: doi:10.1126/scitranslmed.aaf9196
+  title: Nothing but a hound dog
+  authors:
+  - Casey S. Greene
+  publisher: Science Translational Medicine
+  date: '2016-05-25'
+  link: https://doi.org/gg7qr2
+  orcid: 0000-0001-8713-9213
+  member: casey-greene
+  plugin: sources.py
+  file: sources.yaml
 - id: doi:10.1093/bib/bbv087
   title: Recent Advances and Emerging Applications in Text and Data Mining for Biomedical
     Discovery
@@ -9016,6 +9080,15 @@
     text: Raw networks
   - type: app
     link: http://giant.princeton.edu/
+- title: Unsupervised feature construction and knowledge extraction from genome-wide
+    assays of breast cancer with denoising autoencoders
+  publisher: 20th Pacific Symposium on Biocomputing, PSB 2015
+  date: '2024-08-07'
+  link: http://www.scopus.com/inward/record.url?eid=2-s2.0-84971231452&partnerID=MN8TOARS
+  orcid: 0000-0001-8713-9213
+  member: casey-greene
+  plugin: orcid.py
+  file: orcid.yaml
 - id: wosuid:MEDLINE:25592575
   title: Web of Science
   authors: []
@@ -9026,6 +9099,15 @@
   member: casey-greene
   plugin: orcid.py
   file: orcid.yaml
+- title: Applications of bioinformatics to non-coding RNAs in the era of next-generation
+    sequencing
+  publisher: 19th Pacific Symposium on Biocomputing, PSB 2014
+  date: '2024-08-07'
+  link: http://www.scopus.com/inward/record.url?eid=2-s2.0-84905885881&partnerID=MN8TOARS
+  orcid: 0000-0001-8713-9213
+  member: casey-greene
+  plugin: orcid.py
+  file: orcid.yaml
 - id: wosuid:MEDLINE:24297566
   title: Web of Science
   authors: []
@@ -9155,6 +9237,17 @@
   member: casey-greene
   plugin: orcid.py
   file: orcid.yaml
+- id: issn:23356936
+  title: ISSN 2335-6936 (Online) | Pacific symposium on biocomputing ... | The ISSN
+    Portal
+  authors: []
+  publisher: ''
+  date: ''
+  link: https://portal.issn.org/resource/ISSN/23356936
+  orcid: 0000-0001-8713-9213
+  member: casey-greene
+  plugin: orcid.py
+  file: orcid.yaml
 - id: doi:10.1007/978-3-642-37189-9_2
   title: Time-Point Specific Weighting Improves Coexpression Networks from Time-Course
     Experiments
@@ -9298,6 +9391,16 @@
   member: casey-greene
   plugin: orcid.py
   file: orcid.yaml
+- id: wosuid:WOS:000411479100034
+  title: Web of Science
+  authors: []
+  publisher: ''
+  date: ''
+  link: https://www.webofscience.com/wos/woscc/full-record/WOS:WOS:000411479100034
+  orcid: 0000-0001-8713-9213
+  member: casey-greene
+  plugin: orcid.py
+  file: orcid.yaml
 - id: wosuid:MEDLINE:19908385
   title: Web of Science
   authors: []
@@ -9574,6 +9677,16 @@
   member: casey-greene
   plugin: orcid.py
   file: orcid.yaml
+- title: Using expert knowledge in initialization for genome-wide analysis of epistasis
+    using genetic programming
+  publisher: 'GECCO''08: Proceedings of the 10th Annual Conference on Genetic and
+    Evolutionary Computation 2008'
+  date: '2024-08-07'
+  link: http://www.scopus.com/inward/record.url?eid=2-s2.0-57349142365&partnerID=MN8TOARS
+  orcid: 0000-0001-8713-9213
+  member: casey-greene
+  plugin: orcid.py
+  file: orcid.yaml
 - id: doi:10.1007/978-3-540-75286-8_4
   title: An Expert Knowledge-Guided Mutation Operator for Genome-Wide Genetic Analysis
     Using Genetic Programming
@@ -11382,15 +11495,6 @@
     link: http://dx.doi.org/10.1101/062695
   plugin: sources.py
   file: sources.yaml
-- id: doi:10.1126/scitranslmed.aaf9196
-  title: Nothing but a hound dog
-  authors:
-  - Casey S. Greene
-  publisher: Science Translational Medicine
-  date: '2016-05-25'
-  link: https://doi.org/gg7qr2
-  plugin: sources.py
-  file: sources.yaml
 - id: doi:10.1534/g3.116.033514
   title: Comprehensive Cross-Population Analysis of High-Grade Serous Ovarian Cancer
     Supports No More Than Three Subtypes