tests: Minor formatting update to coverage-test.sh

tests/coverage-test.sh

@@ -3,7 +3,6 @@
 # Removes objects from the bucket and indexd records, then runs monorepo tests (clean, normal, clone) twice.
 set -euo pipefail
 
-
 usage() {
   cat <<-EOF
 Usage: $0 [options]
@@ -40,7 +39,6 @@ EOF
   exit 0
 }
 
-
 # Accept named parameters (flags override environment variables)
 POD="${POD:-}"
 POSTGRES_PASSWORD="${POSTGRES_PASSWORD:-}"
@@ -70,7 +68,6 @@ while [ $# -gt 0 ]; do
   esac
 done
 
-
 # echo commands as they are executed
 if [ -z "${GIT_TRACE:-}" ]; then
   echo "For more verbose git output, consider setting the following environment variables before re-running the script:" >&2
@@ -94,7 +91,6 @@ gofmt -s -w .
 # build to ensure no compile errors
 go build
 
-
 # Derive PROJECT_ID from RESOURCE (e.g. /programs/<prog>/projects/<proj> -> <prog>-<proj>)
 _resource_clean="${RESOURCE#/}"        # drop leading slash if present
 _resource_clean="${_resource_clean%/}" # drop trailing slash if present
@@ -147,18 +143,13 @@ if [ ! -d "$UTIL_DIR" ]; then
   exit 1
 fi
 
-# before running tests, build the executables with coverage instrumentation
-
-
 # build git-drs with coverage instrumentation
 go build -cover -covermode=atomic -coverpkg=./... -o "${BUILD_DIR}/git-drs" .
 
 export PATH="${BUILD_DIR}:${PATH}"
 
 # get rid of old binary if exists
 rm git-drs || true
-#go build
-# unit tests
 which git-drs
 rm -rf coverage/unit
 mkdir -p coverage/unit
@@ -231,14 +222,10 @@ if ! $UTIL_DIR/list-indexd-sha256.sh "$POD" "$POSTGRES_PASSWORD" "$RESOURCE" | $
   exit 1
 fi
 
-
 echo "coverage-test.sh: all steps completed successfully." >&2
 go tool covdata textfmt -i="${INTEGRATION_COV_DIR}" -o "${INTEGRATION_PROFILE}"
 
 echo "Integration coverage profile saved to ${INTEGRATION_PROFILE}"
 
-
 echo "Combining coverage profiles..."
 tests/scripts/coverage/combine-coverage.sh
-
-

tests/scripts/coverage/run-e2e-coverage.sh

@@ -0,0 +1,20 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+ROOT_DIR=$(git rev-parse --show-toplevel)
+COVERAGE_ROOT="${COVERAGE_ROOT:-${ROOT_DIR}/coverage}"
+BUILD_DIR="${BUILD_DIR:-${ROOT_DIR}/build/coverage}"
+export PATH="${BUILD_DIR}:${PATH}"
+
+INTEGRATION_COV_DIR="${INTEGRATION_COV_DIR:-${COVERAGE_ROOT}/integration/raw}"
+INTEGRATION_PROFILE="${INTEGRATION_PROFILE:-${COVERAGE_ROOT}/integration/coverage.out}"
+export GOCOVERDIR="${INTEGRATION_COV_DIR}"
+
+mkdir -p "${BUILD_DIR}" "${INTEGRATION_COV_DIR}" "$(dirname "${INTEGRATION_PROFILE}")"
+go build "${GOFLAGS[@]}" -cover -covermode=atomic -coverpkg=./... -o "${BUILD_DIR}/git-drs" .
+
+
+"${E2E_SCRIPT}"
+
+go tool covdata textfmt -i="${INTEGRATION_COV_DIR}" -o "${INTEGRATION_PROFILE}"
+echo "Integration coverage profile saved to ${INTEGRATION_PROFILE}"

tests/scripts/e2e.sh

@@ -0,0 +1,69 @@
+#!/bin/bash
+set -e
+set -x
+
+# Set repo name and remote URL
+REPO_NAME="git-drs-e2e-test"
+GIT_USER="cbds"
+
+# REMOTE_URL="https://source.ohsu.edu/$GIT_USER/$REPO_NAME"
+REMOTE_URL="git@source.ohsu.edu:$GIT_USER/$REPO_NAME.git"
+
+# Clean up if rerunning (don't fail if not removable)
+rm -rf "$REPO_NAME" || true
+
+# Create directory and initialize git
+mkdir "$REPO_NAME"
+cd "$REPO_NAME"
+
+# Step 1: Initialize Repository
+git init
+git drs init
+git drs remote add gen3 origin --cred ~/.gen3/credentials.json --project cbds-git_drs_test --bucket cbds
+
+# set branch / add remote
+git branch -M main
+git remote add origin "$REMOTE_URL"
+
+git lfs track "*.greeting"
+git add .gitattributes
+
+# Step 2: Create and Commit Initial Files
+mkdir -p data/A data/B data/C
+
+DATE="hello $(date)"
+echo $DATE > data/A/simple.greeting
+echo $DATE > data/B/simple.greeting
+echo $DATE > data/C/simple.greeting
+
+git add data/
+git commit -m "Initial commit: Add .greeting files with 'hello'"
+
+# Prompt user for remote if not set
+git push --set-upstream origin main
+
+# Step 3: Add single duplicate file (edge case)
+cp data/A/simple.greeting data/A/duplicate.greeting
+git add data/A/duplicate.greeting
+git commit -m "Add duplicate .greeting file"
+git push
+
+# Step 4: Update and Commit File Changes
+echo "A" >> data/A/simple.greeting
+echo "B" >> data/B/simple.greeting
+echo "C" >> data/C/simple.greeting
+
+git add data/
+git commit -m "Update .greeting files with folder-specific greetings"
+git push
+
+# Step 5: clone and pull
+git clone "$REMOTE_URL"
+cd "$REPO_NAME"
+git drs init
+git drs remote add gen3 origin --cred ~/.gen3/credentials.json --project cbds-git_drs_test --bucket cbds
+git lfs pull
+
+# Step 6: test data provenance 
+git checkout HEAD~1
+git lfs pull