Add additional automation to Methods manuscript

.gitignore

@@ -41,6 +41,7 @@ Thumbs.db
 
 ## Text Editors
 .vscode
+.idea
 
 ## Spellcheck script
 spellcheck.lua

build/assets/acm-pandoc-conf.tex

@@ -1,3 +1,6 @@
+% Adaptation of the template by Wouter Groeneveld
+% https://brainbaking.com/post/2021/02/writing-academic-papers-in-markdown/
+
 \documentclass[sigconf]{acmart}
 
 \usepackage{balance}	% balancing bibstyles as per request in accepted submission
@@ -44,6 +47,25 @@
 			$endif$
 		}
 	$endfor$
+	$for(author.additionalaffiliations)$
+		\additionalaffiliation{
+			$if(author.additionalaffiliations.institution)$
+				\institution{$author.additionalaffiliations.institution$}
+			$endif$
+			$if(author.additionalaffiliations.department)$
+				\department{$author.additionalaffiliations.department$}
+			$endif$
+			$if(author.additionalaffiliations.city)$
+				\city{$author.additionalaffiliations.city$}
+			$endif$
+			$if(author.additionalaffiliations.state)$
+				\state{$author.additionalaffiliations.state$}
+			$endif$
+			$if(author.additionalaffiliations.country)$
+				\country{$author.additionalaffiliations.country$}
+			$endif$
+		}
+	$endfor$
 	$if(author.email)$
 		\email{$author.email$}
 	$endif$
@@ -90,6 +112,10 @@
 
 $body$
 
+% Add funding statement as a comment so it can be manually reviewed and condensed
+$if(funding)$
+	%{$funding$}
+$endif$
 
 $if(bibfile)$
 	\balance
@@ -98,5 +124,3 @@
 
 \end{document}
 \endinput
-%%
-%% End of file `sample-authordraft.tex'.

build/update-latex-metadata.py

@@ -8,7 +8,7 @@
 import yaml
 from manubot.util import read_serialized_data
 
-MISSING_AFFILIATIONS = [{"institution": "None"}]
+MISSING_AFFILIATIONS = [{"institution": " "}]
 MISSING_COI = "None"
 ACM_BCB_2021 = {"acm": [{"copyrightyear": "2021",
                          "copyright": "acmcopyright",
@@ -77,15 +77,21 @@ def update_latex(keyword, manubot_file, pandoc_file):
     keep_fields = {"name", "email", "orcid"}  # do not keep the old affiliations
     latex_authors = []
     conflicts = []
+    funding = []
     for author in individual_authors:
         latex_author = {field: author[field] for field in keep_fields if field in author}
 
         # A list of the author's affiliations formatted for the template
+        # The first affiliation is stored in the "affiliations" field
+        # Any additional affiliations are stored in the "additionalaffiliations" field
         affiliations = author["manuscripts"][keyword].get("affiliations", MISSING_AFFILIATIONS)
         if affiliations == MISSING_AFFILIATIONS:
             sys.stderr.write(f"Missing {keyword} affiliations for {author['name']}\n")
 
-        latex_author["affiliations"] = affiliations
+        if len(affiliations) > 0:
+            latex_author["affiliations"] = affiliations[0]
+        if len(affiliations) > 1:
+            latex_author["additionalaffiliations"] = affiliations[1:]
         latex_authors.append(latex_author)
 
         # Check whether the author has declared conflicts of interest
@@ -94,6 +100,17 @@ def update_latex(keyword, manubot_file, pandoc_file):
             if conflict != "None":
                 conflicts.append(f"{author['name']}: {conflict}.")
 
+        # Check whether the author has funding
+        # This text will not be used directly but will help write a funding statement manually
+        if "funders" in author:
+            # Less robust handling of funders field than Manubot
+            # https://github.com/manubot/manubot/blob/3ff3000f76dcf82a30694d076a4da95326e3f6ae/manubot/process/util.py#L78
+            funders = author["funders"]
+            if isinstance(funders, list):
+                funders = "; ".join(funders)
+            # Assumes initials are always provided
+            funding.append(f"{author['initials']}: {funders}.")
+
     sys.stderr.write(f"Found {len(latex_authors)} authors for {keyword} manuscript\n")
 
     # Do not retain the other metadata fields and add the .bib file references
@@ -102,6 +119,9 @@ def update_latex(keyword, manubot_file, pandoc_file):
     # Add conflicts if any exist
     if len(conflicts) > 0:
         metadata["conflicts"] = "Conflicts of interest. " + " ".join(conflicts)
+    # Add funding comment if funders were listed
+    if len(funding) > 0:
+        metadata["funding"] = "Author funding. " + " ".join(funding)
 
     dump_yaml(metadata, pandoc_file)
 

content/20.pharmaceuticals.md

@@ -117,7 +117,7 @@ Similarly, this medication was pursued for COVID-19, but a retrospective cohort
 Therefore, experience with prior severe threats from HCoV provided some ideas of how to approach the treatment of COVID-19, but it was not clear how effective these measures would be.
 
 However, one treatment adapted from prior HCoV outbreaks is currently the best-known treatment for severe cases of COVID-19.
-Corticosteroids are a well-known, widely available treatment for pneumonia [@doi:10.1002/14651858.CD007720.pub3; @doi:10.1002/14651858.CD007720.pub2; @doi: 10.1183/09031936.00154107; @doi:10.1007/s00408-007-9020-3; @doi:10.1371/journal.pone.0047926; @doi:10.1186/cc10103] that have also been debated as a possible treatment for ARDS [@doi:10/ggpxzc; @doi:10/gcv2; @doi:10.1378/chest.06-1743; @doi:10.1378/chest.07-0714; @doi:10.1056/NEJMoa051693; @doi:10.1136/bmj.39537.939039.BE].
+Corticosteroids are a well-known, widely available treatment for pneumonia [@doi:10.1002/14651858.CD007720.pub3; @doi:10.1002/14651858.CD007720.pub2; @doi:10.1183/09031936.00154107; @doi:10.1007/s00408-007-9020-3; @doi:10.1371/journal.pone.0047926; @doi:10.1186/cc10103] that have also been debated as a possible treatment for ARDS [@doi:10/ggpxzc; @doi:10/gcv2; @doi:10.1378/chest.06-1743; @doi:10.1378/chest.07-0714; @doi:10.1056/NEJMoa051693; @doi:10.1136/bmj.39537.939039.BE].
 Corticosteroids were also used and subsequently evaluated as possible supportive care for SARS and MERS.
 In general, studies and meta-analyses have not found strong support for efficacy of corticosteroids against mortality in these HCoV infections [@doi:10.1136/thx.2003.017665; @doi:10.1016/j.jinf.2006.01.005; @doi:10.1136/thx.2003.017665; @doi:10.1038/s41375-020-0848-3]; however, others did find that the treatments showed some potential and suggested that greater effects might be revealed by refining treatment protocols, such as dosage and timing [@doi:10.1007/s10156-003-0296-9].
 While much of the information available about the corticosteroid treatment of SARS focuses on methylprednisolone and hydrocortisone, availability issues for these drugs at the time led to dexamethasone also being used in North America [@doi:10.1056/NEJMp030072].