v1.3.2 upload log bug fix (#110)

CDCgov · Feb 14, 2025 · 4cf34e3 · 4cf34e3
1 parent 273939c
commit 4cf34e3
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Showing 6 changed files with 7 additions and 5 deletions.
diff --git a/README.Rmd b/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**: v1.3.1. 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**: v1.3.2. 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.
 

diff --git a/README.md b/README.md
@@ -9,7 +9,7 @@
 
 <!-- ![GitHub last commit](https://img.shields.io/github/last-commit/montilab/cadra) -->
 
-**Beta Version**: 1.3.1. This pipeline is currently in Beta testing, and
+**Beta Version**: 1.3.2. 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\!
 

diff --git a/docs/app.json b/docs/app.json
diff --git a/settings.py b/settings.py
@@ -12,7 +12,7 @@
 PROG_DIR: str = os.path.dirname(os.path.abspath(__file__))
 
 # SeqSender version
-VERSION: str = "1.3.1 (Beta)"
+VERSION: str = "1.3.2 (Beta)"
 
 # Organism options with unique submission options
 ORGANISM_CHOICES: List[str] = ["FLU", "COV", "POX", "ARBO", "RSV", "OTHER"]

diff --git a/shiny/app.py b/shiny/app.py
@@ -20,7 +20,7 @@
 header = (
     ui.card_header(
         ui.HTML(
-            """<p><strong>Beta Version</strong>: 1.3.1. 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>: 1.3.2. 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>"""
         )
     ),
 )

diff --git a/upload_log.py b/upload_log.py
@@ -160,6 +160,8 @@ def load_submission_log(submission_dir: str) -> pd.DataFrame:
 	df = df.drop(columns=["Submission_Position", "Table2asn", "GFF_File"], errors="ignore")
 	# Remove duplicates and keep latest update
 	df = df.drop_duplicates(subset = ["Submission_Name", "Organism", "Database", "Submission_Type", "Config_File"], keep = "last", ignore_index = True)
+	# Force uppercase on columns if they are required to be uppercase
+	df[["Organism", "Database", "Submission_Type", "Submission_Status", "Submission_ID"]] = df[["Organism", "Database", "Submission_Type", "Submission_Status", "Submission_ID"]].astype(str).apply(lambda col: col.str.upper())
 	try:
 		upload_schema.validate(df, lazy = True)
 	except pandera.errors.SchemaErrors as schema_error: