V1.3.8 (#130)

* v1.3.8

Author: dthoward96

README.Rmd

@@ -26,7 +26,7 @@ github_pages_url <- description$GITHUB_PAGES
 
 <p style="font-size: 16px;"><em>Public Database Submission Pipeline</em></p>
 
-**Beta Version**: v1.3.7. This pipeline is currently in Beta testing, and issues could appear during submission. Please use it at your own risk. Feedback and suggestions are welcome! 
+**Beta Version**: v1.3.8. This pipeline is currently in Beta testing, and issues could appear during submission. Please use it at your own risk. Feedback and suggestions are welcome! 
 
 **General Disclaimer**: This repository was created for use by CDC programs to collaborate on public health related projects in support of the [CDC mission](https://www.cdc.gov/about/organization/mission.htm).  GitHub is not hosted by the CDC, but is a third party website used by CDC and its partners to share information and collaborate on software. CDC use of GitHub does not imply an endorsement of any one particular service, product, or enterprise.
 

README.md

@@ -9,7 +9,7 @@
 
 <!-- ![GitHub last commit](https://img.shields.io/github/last-commit/montilab/cadra) -->
 
-**Beta Version**: 1.3.7. This pipeline is currently in Beta testing, and
+**Beta Version**: 1.3.8. This pipeline is currently in Beta testing, and
 issues could appear during submission. Please use it at your own risk.
 Feedback and suggestions are welcome\!
 

docs/app.json

@@ -141,7 +141,17 @@ def create_authorset(config_dict: Dict[str, Any], metadata: pd.DataFrame, submis
 		f.write("  cit {\n")
 		f.write("    authors {\n")
 		f.write("      names std {\n")
-		authors = [HumanName(x.strip()) for x in metadata["authors"].unique()[0].split(";") if x.strip() != ""]
+		# If semi-colon in authors string, that is default delim
+		if ";" in metadata["authors"].unique()[0]:
+			author_delim = ";"
+		# If no semi-colon in authors string, attempt comma
+		elif "," in metadata["authors"].unique()[0]:
+			author_delim = ","
+			print("Warning: Metadata 'authors' field is not using a semi-colon ';' to separate individual names. Comma was detected instead and is being used to separate individual names. If this causes issues, separate each name with a semi-colon instead.", file = sys.stderr)
+		# Default delim is semi-colon
+		else:
+			author_delim = ";"
+		authors = [HumanName(x.strip()) for x in metadata["authors"].unique()[0].split(author_delim) if x.strip() != ""]
 		total_names = len(authors)
 		for index, name in enumerate(authors, start = 1):
 			f.write("        {\n")
@@ -179,7 +189,7 @@ def create_authorset(config_dict: Dict[str, Any], metadata: pd.DataFrame, submis
 		f.write("      cit \"" + publication_status_string + "\",\n")
 		f.write("      authors {\n")
 		f.write("        names std {\n")
-		authors = [HumanName(x.strip()) for x in metadata["authors"].unique()[0].split(";") if x.strip() != ""]
+		authors = [HumanName(x.strip()) for x in metadata["authors"].unique()[0].split(author_delim) if x.strip() != ""]
 		for index, name in enumerate(authors, start = 1):
 			f.write("          {\n")
 			f.write("            name name {\n")

genbank_handler.py

@@ -12,7 +12,7 @@
 PROG_DIR: str = os.path.dirname(os.path.abspath(__file__))
 
 # SeqSender version
-VERSION: str = "1.3.7 (Beta)"
+VERSION: str = "1.3.8 (Beta)"
 
 # Organism options with unique submission options
 ORGANISM_CHOICES: List[str] = ["FLU", "COV", "POX", "ARBO", "RSV", "OTHER"]

metadata.csv

@@ -20,7 +20,7 @@
 header = (
     ui.card_header(
         ui.HTML(
-            """<p><strong>Beta Version</strong>: 1.3.7. This pipeline is currently in Beta testing, and issues could appear during submission. Please use it at your own risk. Feedback and suggestions are welcome!</p>"""
+            """<p><strong>Beta Version</strong>: 1.3.8. This pipeline is currently in Beta testing, and issues could appear during submission. Please use it at your own risk. Feedback and suggestions are welcome!</p>"""
         )
     ),
 )