From c9136883989728b5e8f2d2aa959f1401d5e45f8f Mon Sep 17 00:00:00 2001
From: Eric Tvedte <eric.tvedte@nih.gov>
Date: Tue, 11 Jun 2024 16:00:22 -0400
Subject: [PATCH] Add files via upload

---
 dist/fcs.py            | 35 +++++++++++++++++++++++++++++++++--
 dist/run_fcsadaptor.sh | 15 +++++++++++----
 2 files changed, 44 insertions(+), 6 deletions(-)

diff --git a/dist/fcs.py b/dist/fcs.py
index 2e824cc..74c1d2f 100644
--- a/dist/fcs.py
+++ b/dist/fcs.py
@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+# pylint: disable=C0301,C0114,C0103,C0116,R0913,R0914,W0511,R1732,R0916
 """
                           PUBLIC DOMAIN NOTICE
              National Center for Biotechnology Information
@@ -35,7 +37,7 @@
 
 CONTAINER = "run_gx"
 DEFAULT_CONTAINER_DB = "/app/db/gxdb/"
-DEFAULT_VERSION = "0.5.0"
+DEFAULT_VERSION = "0.5.4"
 DEFAULT_DOCKER_IMAGE = f"ncbi/fcs-gx:{DEFAULT_VERSION}"
 GX_BIN_DIR = Path("/app/bin")
 
@@ -425,7 +427,36 @@ def main() -> int:
         parser.print_usage()
         sys.exit()
 
-    GlobalStat.opt_in = (not args.no_report_analytics) and ("--help" not in extra_args) and (not args.dry_run)
+    GlobalStat.opt_in = (
+        not args.no_report_analytics
+        and "--help" not in extra_args
+        and not args.dry_run
+        and os.getenv("DO_NOT_TRACK", "0") == "0"               # GP-37725
+        and os.getenv("NCBI_FCS_REPORT_ANALYTICS", "1") == "1"  # GP-37725
+    )
+
+    if (  # If none of the banner-switches are set, display the banner. GP-37725
+        not args.no_report_analytics
+        and os.getenv("DO_NOT_TRACK") is None
+        and os.getenv("NCBI_FCS_REPORT_ANALYTICS") is None
+    ):
+        print("""
+--------------------------------------------------------------------------------------------
+
+NCBI collects limited usage data for each run of FCS by default. To disable usage reporting:
+
+python3 fcs.py --no-report-analytics ...
+
+or export NCBI_FCS_REPORT_ANALYTICS=1 to enable,
+or export NCBI_FCS_REPORT_ANALYTICS=0 to disable the reporting.
+
+Usage data collected by NCBI is documented in the FCS privacy notice
+at https://github.com/ncbi/fcs/blob/main/PRIVACY.md
+
+--------------------------------------------------------------------------------------------""",
+            file=sys.stderr)
+
+
     if hasattr(args, "cmd"):
         GlobalStat.ncbi_op = args.cmd
     retcode = 0
diff --git a/dist/run_fcsadaptor.sh b/dist/run_fcsadaptor.sh
index 865ab8d..7b347f3 100644
--- a/dist/run_fcsadaptor.sh
+++ b/dist/run_fcsadaptor.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 SCRIPT_NAME=$0
-DEFAULT_VERSION="0.5.0"
+DEFAULT_VERSION="0.5.4"
 DOCKER_IMAGE=ncbi/fcs-adaptor:${DEFAULT_VERSION}
 SINGULARITY_IMAGE=""
 CONTAINER_ENGINE="docker"
@@ -19,6 +19,7 @@ Options:
     --output-dir <directory>      output path (required)
     --image <file>                dockerhub address or sif file (required for singularity only)
     --container-engine <string>   default docker
+    --debug                       debug
 
     Taxonomy (exactly one required):
     --prok                        prokaryotes
@@ -29,6 +30,7 @@ EOF
 }
 
 DOCKER=docker
+DEBUG=""
 
 while [[ $# -gt 0 ]]
 do
@@ -60,6 +62,11 @@ do
         CONTAINER_ENGINE=$2
         shift
         ;;
+    --debug)
+        DEBUG="--debug"
+        shift
+        ;;
+
     -*)
       echo "invalid option : '$1'"
       usage 10
@@ -108,9 +115,9 @@ then
   }
   trap finish EXIT
 
-  $DOCKER run --init --name $CONTAINER --user "$(id -u):$(id -g)" -v $FASTA_DIRNAME:/sample-volume/ \
+  $DOCKER run --rm --init --name $CONTAINER --user "$(id -u):$(id -g)" -v $FASTA_DIRNAME:/sample-volume/ \
       -v $EXPANDED_OUTPUT:/output-volume/ $DOCKER_IMAGE \
-      /app/fcs/bin/av_screen_x -o /output-volume/ $TAX /sample-volume/$FASTA_FILENAME
+      /app/fcs/bin/av_screen_x -o /output-volume/ $TAX /sample-volume/$FASTA_FILENAME $DEBUG
 
 elif [[ ${CONTAINER_ENGINE} == "singularity" ]]
 then
@@ -118,7 +125,7 @@ then
   then
     singularity run $CONTAINER --bind $FASTA_DIRNAME:/sample-volume/ \
         --bind $EXPANDED_OUTPUT:/output-volume/ $SINGULARITY_IMAGE \
-        /app/fcs/bin/av_screen_x -o /output-volume/ $TAX /sample-volume/$FASTA_FILENAME
+        /app/fcs/bin/av_screen_x -o /output-volume/ $TAX /sample-volume/$FASTA_FILENAME $DEBUG
   else
     echo "--image is required when specifying --container-engine singularity"
   fi