From d89e3adf2c2389e159a30f94d42b9a530ff0d7ad Mon Sep 17 00:00:00 2001
From: Sijie <sijiex@lbl.gov>
Date: Mon, 4 Mar 2024 19:10:50 -0800
Subject: [PATCH 01/25] run on mongo7 without update

---
 .github/workflows/test.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index d3cc9ba..bcac2cd 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -28,9 +28,13 @@ jobs:
           - go: '1.12'
             mongo: 'mongodb-linux-x86_64-3.6.20'
             minio: '2019-05-23T00-29-34Z'
+            wired_tiger: 'true'
+          - go: '1.12'
+            mongo: 'mongodb-linux-x86_64-ubuntu2204-7.0.4'
+            minio: '2019-05-23T00-29-34Z'
             wired_tiger: 'false'
           - go: '1.12'
-            mongo: 'mongodb-linux-x86_64-3.6.20'
+            mongo: 'mongodb-linux-x86_64-ubuntu2204-7.0.4'
             minio: '2019-05-23T00-29-34Z'
             wired_tiger: 'true'
     steps:

From 6a7139510ab6254b265da89710105b8f97ae07ba Mon Sep 17 00:00:00 2001
From: Sijie <sijiex@lbl.gov>
Date: Fri, 8 Mar 2024 17:26:57 -0800
Subject: [PATCH 02/25] add function getMongoDBVer and fix --nojournal arg

---
 test/mongocontroller/controller.go | 37 ++++++++++++++++++++----------
 1 file changed, 25 insertions(+), 12 deletions(-)

diff --git a/test/mongocontroller/controller.go b/test/mongocontroller/controller.go
index 96869f7..ff26bc9 100644
--- a/test/mongocontroller/controller.go
+++ b/test/mongocontroller/controller.go
@@ -6,6 +6,7 @@ import (
 	"os/exec"
 	"path/filepath"
 	"strconv"
+	"strings"
 	"time"
 
 	"go.mongodb.org/mongo-driver/mongo"
@@ -28,7 +29,7 @@ type Params struct {
 	UseWiredTiger bool
 }
 
-// Controller is a Minio controller.
+// Controller is a Mongo controller.
 type Controller struct {
 	port            int
 	tempDir         string
@@ -53,14 +54,25 @@ func New(p Params) (*Controller, error) {
 	if err != nil {
 		return nil, err
 	}
+
 	cmdargs := []string{
 		"--port", strconv.Itoa(port),
 		"--dbpath", ddir,
-		"--nojournal",
+	}
+
+	// check mongodb version
+	ver, err := getMongoDBVer(p.ExecutablePath)
+	if err != nil {
+		return nil, err
+	}
+
+	if ver.LessThan(*semver.New("6.1")) {
+		cmdargs = append(cmdargs, "--nojournal")
 	}
 	if p.UseWiredTiger {
 		cmdargs = append(cmdargs, "--storageEngine", "wiredTiger")
 	}
+
 	cmd := exec.Command(p.ExecutablePath, cmdargs...)
 	cmd.Stdout = outfile
 	cmd.Stderr = outfile
@@ -80,18 +92,8 @@ func New(p Params) (*Controller, error) {
 	if err != nil {
 		return nil, err
 	}
-	res := client.Database("foo").RunCommand(nil, map[string]int{"buildinfo": 1})
-	if res.Err() != nil {
-		return nil, res.Err()
-	}
-	var doc map[string]interface{}
-	err = res.Decode(&doc)
-	if err != nil {
-		return nil, err
-	}
 	// wired tiger will also not include index names for 3.0, but we're not going to test
 	// that so screw it
-	ver := semver.New(doc["version"].(string))
 	return &Controller{port, tdir, cmd, ver.LessThan(*semver.New("3.2.1000"))}, nil
 }
 
@@ -121,3 +123,14 @@ func (c *Controller) Destroy(deleteTempDir bool) error {
 	}
 	return nil
 }
+
+func getMongoDBVer(ExecutablePath string) (*semver.Version, error) {
+	cmd := exec.Command(ExecutablePath, "--version")
+	stdout, err := cmd.Output()
+	if err != nil {
+		return nil, err
+	}
+	rep := strings.Replace(string(stdout), "\n", " ", -1)
+	ver := strings.Split(rep, " ")[2][1:]
+	return semver.New(ver), err
+}

From b1fc0008ed13cf2517418a8ab8da5bd2e9d8e3a2 Mon Sep 17 00:00:00 2001
From: Sijie <sijiex@lbl.gov>
Date: Fri, 8 Mar 2024 17:35:45 -0800
Subject: [PATCH 03/25] add more ref for nojournal option

---
 test/mongocontroller/controller.go | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/test/mongocontroller/controller.go b/test/mongocontroller/controller.go
index ff26bc9..08e78f8 100644
--- a/test/mongocontroller/controller.go
+++ b/test/mongocontroller/controller.go
@@ -66,7 +66,11 @@ func New(p Params) (*Controller, error) {
 		return nil, err
 	}
 
-	if ver.LessThan(*semver.New("6.1")) {
+	// Starting in MongoDB 6.1, journaling is always enabled. 
+	// As a result, MongoDB removes the storage.journal.enabled option and 
+	// the corresponding --journal and --nojournal command-line options.
+	// https://www.mongodb.com/docs/manual/release-notes/6.1/#changes-to-journaling
+	if ver.LessThan(*semver.New("6.1.0")) {
 		cmdargs = append(cmdargs, "--nojournal")
 	}
 	if p.UseWiredTiger {

From d0afe815106f8f0fec4eb477b2537f3b79c1bbef Mon Sep 17 00:00:00 2001
From: Sijie <sijiex@lbl.gov>
Date: Fri, 8 Mar 2024 23:33:36 -0800
Subject: [PATCH 04/25] remove namespace check

---
 nodestore/mongostore_test.go | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/nodestore/mongostore_test.go b/nodestore/mongostore_test.go
index 2302a91..617f924 100644
--- a/nodestore/mongostore_test.go
+++ b/nodestore/mongostore_test.go
@@ -773,7 +773,7 @@ func (t *TestSuite) TestConfigIndexes() {
 		"_id_":     false,
 		"schema_1": true,
 	}
-	t.checkIndexes("config", testDB+".config", expected)
+	t.checkIndexes("config", expected)
 }
 
 func (t *TestSuite) TestUserIndexes() {
@@ -782,7 +782,7 @@ func (t *TestSuite) TestUserIndexes() {
 		"user_1": true,
 		"id_1":   true,
 	}
-	t.checkIndexes("users", testDB+".users", expected)
+	t.checkIndexes("users", expected)
 }
 
 func (t *TestSuite) TestNodeIndexes() {
@@ -790,12 +790,11 @@ func (t *TestSuite) TestNodeIndexes() {
 		"_id_": false,
 		"id_1": true,
 	}
-	t.checkIndexes("nodes", testDB+".nodes", expected)
+	t.checkIndexes("nodes", expected)
 }
 
 func (t *TestSuite) checkIndexes(
 	collection string,
-	expectedNamespace string,
 	expectedIndexes map[string]bool) {
 	_, err := NewMongoNodeStore(t.client.Database(testDB))
 	if err != nil {
@@ -815,7 +814,6 @@ func (t *TestSuite) checkIndexes(
 			t.Fail(err.Error())
 		}
 		m := elem.Map()
-		t.Equal(expectedNamespace, m["ns"], "incorrect name space")
 		if un, ok := m["unique"]; ok {
 			names[m["name"].(string)] = un.(bool)
 		} else {

From d143ada251f4715d915ed73c0b55d25204c708bc Mon Sep 17 00:00:00 2001
From: Sijie <sijiex@lbl.gov>
Date: Fri, 8 Mar 2024 23:49:36 -0800
Subject: [PATCH 05/25] fix error

---
 nodestore/mongostore_test.go | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/nodestore/mongostore_test.go b/nodestore/mongostore_test.go
index 617f924..d42bad6 100644
--- a/nodestore/mongostore_test.go
+++ b/nodestore/mongostore_test.go
@@ -105,7 +105,8 @@ func (t *TestSuite) TestConstructFailAddConfigIndex() {
 	t.Contains(err.Error(), "E11000 duplicate key error", "incorrect error")
 	t.Contains(err.Error(), testDB+".config", "incorrect error")
 	t.Contains(err.Error(), "schema_1", "incorrect error")
-	t.Contains(err.Error(), "dup key: { : \"schema\" }", "incorrect error")
+	t.Contains(err.Error(), "dup key: { ", "incorrect error")
+	t.Contains(err.Error(), ": \"schema\" }", "incorrect error")
 }
 
 func (t *TestSuite) TestConstructFailTwoConfigDocs() {

From d1286a3d11e3a19adffac72f47b986d3ea44cc74 Mon Sep 17 00:00:00 2001
From: Sijie <sijiex@lbl.gov>
Date: Mon, 11 Mar 2024 20:40:48 -0700
Subject: [PATCH 06/25] add auth shadow jar

---
 test/kbaseauthcontroller/authjars.go | 127 ++++++++++++++-------------
 1 file changed, 64 insertions(+), 63 deletions(-)

diff --git a/test/kbaseauthcontroller/authjars.go b/test/kbaseauthcontroller/authjars.go
index af96fd9..8234db2 100644
--- a/test/kbaseauthcontroller/authjars.go
+++ b/test/kbaseauthcontroller/authjars.go
@@ -10,67 +10,68 @@ const (
 // required for the auth server.
 // might want to make the paths non-unix specific... yagni
 var jars = []string{
-	"kbase/auth2/kbase-auth2-0.2.4.jar",
-	"kbase/auth2/kbase-auth2test-0.2.4.jar",
-	//lib
-	"apache_commons/commons-codec-1.8.jar",
-	"apache_commons/commons-validator-1.5.1.jar",
-	"google/guava-18.0.jar",
-	"ini4j/ini4j-0.5.2.jar",
-	"jcommander/jcommander-1.48.jar",
-	"mongo/mongo-java-driver-3.3.0.jar",
-	"mustache/compiler-0.9.3.jar",
-	"nulab-inc/zxcvbn-1.2.2.jar",
-	//logging
-	"kbase/common/kbase-common-0.0.22.jar",
-	"jna/jna-3.4.0.jar",
-	"logback/logback-core-1.1.2.jar",
-	"logback/logback-classic-1.1.2.jar",
-	"slf4j/slf4j-api-1.7.25.jar",
-	"syslog4j/syslog4j-0.9.46.jar",
-	//yauaa
-	"yauaa/yauaa-1.3.jar",
-	"apache_commons/commons-lang3-3.5.jar",
-	"apache_commons/commons-collections4-4.1.jar",
-	"apache_commons/commons-logging-1.2.jar",
-	"kohsuke/args4j-2.33.jar",
-	"snakeyaml/snakeyaml-1.18.jar",
-	//jackson
-	"jackson/jackson-annotations-2.5.4.jar",
-	"jackson/jackson-core-2.5.4.jar",
-	"jackson/jackson-databind-2.5.4.jar",
-	"jackson/jackson-jaxrs-base-2.5.4.jar",
-	"jackson/jackson-jaxrs-json-provider-2.5.4.jar",
-	"jackson/jackson-module-jaxb-annotations-2.5.4.jar",
-	//jersey
-	"jersey/entity-filtering/jersey-entity-filtering-2.23.2.jar",
-	"jersey/entity-filtering/jersey-media-json-jackson-2.23.2.jar",
-	"jersey/mvc/jersey-mvc-2.23.2.jar",
-	"jersey/mvc/jersey-mvc-mustache-2.23.2.jar",
-	"jersey/jersey-client-2.23.2.jar",
-	"jersey/jersey-common-2.23.2.jar",
-	"jersey/jersey-container-servlet-2.23.2.jar",
-	"jersey/jersey-container-servlet-core-2.23.2.jar",
-	"jersey/jersey-guava-2.23.2.jar",
-	"jersey/jersey-media-jaxb-2.23.2.jar",
-	"jersey/jersey-server-2.23.2.jar",
-	//jerseydeps
-	"annotation/javax.annotation-api-1.2.jar",
-	"asm/asm-debug-all-5.0.4.jar",
-	"inject/javax.inject-2.5.0-b05.jar",
-	"javassist/javassist-3.20.0-GA.jar",
-	"jaxb/jaxb-api-2.2.7.jar",
-	"jaxrs/javax.ws.rs-api-2.0.1.jar",
-	"osgi/org.osgi.core-4.2.0.jar",
-	"persistence/persistence-api-1.0.jar",
-	"servlet/javax.servlet-api-3.0.1.jar",
-	"validationapi/validation-api-1.1.0.Final.jar",
-	//jerseydep_hk2
-	"hk2/aopalliance-repackaged-2.5.0-b05.jar",
-	"hk2/hk2-api-2.5.0-b05.jar",
-	"hk2/hk2-locator-2.5.0-b05.jar",
-	"hk2/hk2-utils-2.5.0-b05.jar",
-	"hk2/osgi-resource-locator-1.0.1.jar",
-	//test
-	"jetty/jetty-all-9.3.11.v20160721-uber.jar",
+	"kbase/auth2/kbase-auth2-test-shadow-all-0.7.0.jar",
+	// "kbase/auth2/kbase-auth2-0.2.4.jar",
+	// "kbase/auth2/kbase-auth2test-0.2.4.jar",
+	// //lib
+	// "apache_commons/commons-codec-1.8.jar",
+	// "apache_commons/commons-validator-1.5.1.jar",
+	// "google/guava-18.0.jar",
+	// "ini4j/ini4j-0.5.2.jar",
+	// "jcommander/jcommander-1.48.jar",
+	// "mongo/mongo-java-driver-3.3.0.jar",
+	// "mustache/compiler-0.9.3.jar",
+	// "nulab-inc/zxcvbn-1.2.2.jar",
+	// //logging
+	// "kbase/common/kbase-common-0.0.22.jar",
+	// "jna/jna-3.4.0.jar",
+	// "logback/logback-core-1.1.2.jar",
+	// "logback/logback-classic-1.1.2.jar",
+	// "slf4j/slf4j-api-1.7.25.jar",
+	// "syslog4j/syslog4j-0.9.46.jar",
+	// //yauaa
+	// "yauaa/yauaa-1.3.jar",
+	// "apache_commons/commons-lang3-3.5.jar",
+	// "apache_commons/commons-collections4-4.1.jar",
+	// "apache_commons/commons-logging-1.2.jar",
+	// "kohsuke/args4j-2.33.jar",
+	// "snakeyaml/snakeyaml-1.18.jar",
+	// //jackson
+	// "jackson/jackson-annotations-2.5.4.jar",
+	// "jackson/jackson-core-2.5.4.jar",
+	// "jackson/jackson-databind-2.5.4.jar",
+	// "jackson/jackson-jaxrs-base-2.5.4.jar",
+	// "jackson/jackson-jaxrs-json-provider-2.5.4.jar",
+	// "jackson/jackson-module-jaxb-annotations-2.5.4.jar",
+	// //jersey
+	// "jersey/entity-filtering/jersey-entity-filtering-2.23.2.jar",
+	// "jersey/entity-filtering/jersey-media-json-jackson-2.23.2.jar",
+	// "jersey/mvc/jersey-mvc-2.23.2.jar",
+	// "jersey/mvc/jersey-mvc-mustache-2.23.2.jar",
+	// "jersey/jersey-client-2.23.2.jar",
+	// "jersey/jersey-common-2.23.2.jar",
+	// "jersey/jersey-container-servlet-2.23.2.jar",
+	// "jersey/jersey-container-servlet-core-2.23.2.jar",
+	// "jersey/jersey-guava-2.23.2.jar",
+	// "jersey/jersey-media-jaxb-2.23.2.jar",
+	// "jersey/jersey-server-2.23.2.jar",
+	// //jerseydeps
+	// "annotation/javax.annotation-api-1.2.jar",
+	// "asm/asm-debug-all-5.0.4.jar",
+	// "inject/javax.inject-2.5.0-b05.jar",
+	// "javassist/javassist-3.20.0-GA.jar",
+	// "jaxb/jaxb-api-2.2.7.jar",
+	// "jaxrs/javax.ws.rs-api-2.0.1.jar",
+	// "osgi/org.osgi.core-4.2.0.jar",
+	// "persistence/persistence-api-1.0.jar",
+	// "servlet/javax.servlet-api-3.0.1.jar",
+	// "validationapi/validation-api-1.1.0.Final.jar",
+	// //jerseydep_hk2
+	// "hk2/aopalliance-repackaged-2.5.0-b05.jar",
+	// "hk2/hk2-api-2.5.0-b05.jar",
+	// "hk2/hk2-locator-2.5.0-b05.jar",
+	// "hk2/hk2-utils-2.5.0-b05.jar",
+	// "hk2/osgi-resource-locator-1.0.1.jar",
+	// //test
+	// "jetty/jetty-all-9.3.11.v20160721-uber.jar",
 }

From 95e7f5c41fd186ab3585d10179c821647af4e184 Mon Sep 17 00:00:00 2001
From: Sijie <sijiex@lbl.gov>
Date: Mon, 11 Mar 2024 21:14:19 -0700
Subject: [PATCH 07/25] finish & clean up

---
 test/kbaseauthcontroller/authjars.go   | 76 ++------------------------
 test/kbaseauthcontroller/controller.go | 12 ++--
 2 files changed, 9 insertions(+), 79 deletions(-)

diff --git a/test/kbaseauthcontroller/authjars.go b/test/kbaseauthcontroller/authjars.go
index 8234db2..455684e 100644
--- a/test/kbaseauthcontroller/authjars.go
+++ b/test/kbaseauthcontroller/authjars.go
@@ -1,77 +1,11 @@
 package kbaseauthcontroller
 
-// this file simply lists the jars that are required to run the KBase auth server in test mode.
+// this file simply lists the template and the jar in the KBase jars repo (https://github.com/kbase/jars)
+// that are required to run the KBase auth server in test mode.
 const (
 	// authTemplates is the zip file containing templates for the server
 	authTemplates = "kbase/auth2/kbase-auth2templates-0.2.4.zip"
-)
 
-// jars contains the list of jars in the KBase jars repo (https://github.com/kbase/jars)
-// required for the auth server.
-// might want to make the paths non-unix specific... yagni
-var jars = []string{
-	"kbase/auth2/kbase-auth2-test-shadow-all-0.7.0.jar",
-	// "kbase/auth2/kbase-auth2-0.2.4.jar",
-	// "kbase/auth2/kbase-auth2test-0.2.4.jar",
-	// //lib
-	// "apache_commons/commons-codec-1.8.jar",
-	// "apache_commons/commons-validator-1.5.1.jar",
-	// "google/guava-18.0.jar",
-	// "ini4j/ini4j-0.5.2.jar",
-	// "jcommander/jcommander-1.48.jar",
-	// "mongo/mongo-java-driver-3.3.0.jar",
-	// "mustache/compiler-0.9.3.jar",
-	// "nulab-inc/zxcvbn-1.2.2.jar",
-	// //logging
-	// "kbase/common/kbase-common-0.0.22.jar",
-	// "jna/jna-3.4.0.jar",
-	// "logback/logback-core-1.1.2.jar",
-	// "logback/logback-classic-1.1.2.jar",
-	// "slf4j/slf4j-api-1.7.25.jar",
-	// "syslog4j/syslog4j-0.9.46.jar",
-	// //yauaa
-	// "yauaa/yauaa-1.3.jar",
-	// "apache_commons/commons-lang3-3.5.jar",
-	// "apache_commons/commons-collections4-4.1.jar",
-	// "apache_commons/commons-logging-1.2.jar",
-	// "kohsuke/args4j-2.33.jar",
-	// "snakeyaml/snakeyaml-1.18.jar",
-	// //jackson
-	// "jackson/jackson-annotations-2.5.4.jar",
-	// "jackson/jackson-core-2.5.4.jar",
-	// "jackson/jackson-databind-2.5.4.jar",
-	// "jackson/jackson-jaxrs-base-2.5.4.jar",
-	// "jackson/jackson-jaxrs-json-provider-2.5.4.jar",
-	// "jackson/jackson-module-jaxb-annotations-2.5.4.jar",
-	// //jersey
-	// "jersey/entity-filtering/jersey-entity-filtering-2.23.2.jar",
-	// "jersey/entity-filtering/jersey-media-json-jackson-2.23.2.jar",
-	// "jersey/mvc/jersey-mvc-2.23.2.jar",
-	// "jersey/mvc/jersey-mvc-mustache-2.23.2.jar",
-	// "jersey/jersey-client-2.23.2.jar",
-	// "jersey/jersey-common-2.23.2.jar",
-	// "jersey/jersey-container-servlet-2.23.2.jar",
-	// "jersey/jersey-container-servlet-core-2.23.2.jar",
-	// "jersey/jersey-guava-2.23.2.jar",
-	// "jersey/jersey-media-jaxb-2.23.2.jar",
-	// "jersey/jersey-server-2.23.2.jar",
-	// //jerseydeps
-	// "annotation/javax.annotation-api-1.2.jar",
-	// "asm/asm-debug-all-5.0.4.jar",
-	// "inject/javax.inject-2.5.0-b05.jar",
-	// "javassist/javassist-3.20.0-GA.jar",
-	// "jaxb/jaxb-api-2.2.7.jar",
-	// "jaxrs/javax.ws.rs-api-2.0.1.jar",
-	// "osgi/org.osgi.core-4.2.0.jar",
-	// "persistence/persistence-api-1.0.jar",
-	// "servlet/javax.servlet-api-3.0.1.jar",
-	// "validationapi/validation-api-1.1.0.Final.jar",
-	// //jerseydep_hk2
-	// "hk2/aopalliance-repackaged-2.5.0-b05.jar",
-	// "hk2/hk2-api-2.5.0-b05.jar",
-	// "hk2/hk2-locator-2.5.0-b05.jar",
-	// "hk2/hk2-utils-2.5.0-b05.jar",
-	// "hk2/osgi-resource-locator-1.0.1.jar",
-	// //test
-	// "jetty/jetty-all-9.3.11.v20160721-uber.jar",
-}
+	// auth2ShadowAllJar is the jar required for the server
+	authShadowAllJar = "kbase/auth2/kbase-auth2-test-shadow-all-0.7.0.jar"
+)
diff --git a/test/kbaseauthcontroller/controller.go b/test/kbaseauthcontroller/controller.go
index ccc9795..2686158 100644
--- a/test/kbaseauthcontroller/controller.go
+++ b/test/kbaseauthcontroller/controller.go
@@ -124,15 +124,11 @@ func getClassPath(jarsDir string) (string, error) {
 	if err != nil {
 		return "", err
 	}
-	cp := []string(nil)
-	for _, j := range jars { // global variable, yech
-		jpath := path.Join(jarsDir, j)
-		if _, err := os.Stat(jpath); os.IsNotExist(err) {
-			return "", fmt.Errorf("Jar %v does not exist", jpath)
-		}
-		cp = append(cp, jpath)
+	jpath := path.Join(jarsDir, authShadowAllJar)
+	if _, err := os.Stat(jpath); os.IsNotExist(err) {
+		return "", fmt.Errorf("Jar %v does not exist", jpath)
 	}
-	return strings.Join(cp, ":"), nil
+	return jpath, nil
 }
 
 func installTemplates(jarsDir string, templateDir string) error {

From d2b48b7e2ab70b44a9b1981e0b003871d311268b Mon Sep 17 00:00:00 2001
From: Sijie <sijiex@lbl.gov>
Date: Wed, 13 Mar 2024 12:46:00 -0700
Subject: [PATCH 08/25] update test.yml, var name, and mongo connection testing

---
 .github/workflows/test.yml             |  8 --------
 test/kbaseauthcontroller/authjars.go   | 11 -----------
 test/kbaseauthcontroller/controller.go |  5 +++++
 test/mongocontroller/controller.go     | 10 ++++++++--
 4 files changed, 13 insertions(+), 21 deletions(-)
 delete mode 100644 test/kbaseauthcontroller/authjars.go

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index bcac2cd..829b409 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -25,14 +25,6 @@ jobs:
             mongo: 'mongodb-linux-x86_64-3.6.12'
             minio: '2019-05-23T00-29-34Z'
             wired_tiger: 'false'
-          - go: '1.12'
-            mongo: 'mongodb-linux-x86_64-3.6.20'
-            minio: '2019-05-23T00-29-34Z'
-            wired_tiger: 'true'
-          - go: '1.12'
-            mongo: 'mongodb-linux-x86_64-ubuntu2204-7.0.4'
-            minio: '2019-05-23T00-29-34Z'
-            wired_tiger: 'false'
           - go: '1.12'
             mongo: 'mongodb-linux-x86_64-ubuntu2204-7.0.4'
             minio: '2019-05-23T00-29-34Z'
diff --git a/test/kbaseauthcontroller/authjars.go b/test/kbaseauthcontroller/authjars.go
deleted file mode 100644
index 455684e..0000000
--- a/test/kbaseauthcontroller/authjars.go
+++ /dev/null
@@ -1,11 +0,0 @@
-package kbaseauthcontroller
-
-// this file simply lists the template and the jar in the KBase jars repo (https://github.com/kbase/jars)
-// that are required to run the KBase auth server in test mode.
-const (
-	// authTemplates is the zip file containing templates for the server
-	authTemplates = "kbase/auth2/kbase-auth2templates-0.2.4.zip"
-
-	// auth2ShadowAllJar is the jar required for the server
-	authShadowAllJar = "kbase/auth2/kbase-auth2-test-shadow-all-0.7.0.jar"
-)
diff --git a/test/kbaseauthcontroller/controller.go b/test/kbaseauthcontroller/controller.go
index 2686158..bdd07be 100644
--- a/test/kbaseauthcontroller/controller.go
+++ b/test/kbaseauthcontroller/controller.go
@@ -22,8 +22,13 @@ import (
 	"github.com/phayes/freeport"
 )
 
+// The following are required to run the KBase auth server in test mode.
 const (
 	serverClass = "us.kbase.test.auth2.StandaloneAuthServer"
+	// authTemplates is the zip file containing templates for the server
+	authTemplates = "kbase/auth2/kbase-auth2templates-0.2.4.zip"
+	// auth2ShadowAllJar is the jar required for the server
+	authShadowAllJar = "kbase/auth2/kbase-auth2-test-shadow-all-0.7.0.jar"
 )
 
 // Params are Parameters for creating a KBase Auth2 service (https://github.com/kbase/auth2)
diff --git a/test/mongocontroller/controller.go b/test/mongocontroller/controller.go
index 08e78f8..4156793 100644
--- a/test/mongocontroller/controller.go
+++ b/test/mongocontroller/controller.go
@@ -96,6 +96,12 @@ func New(p Params) (*Controller, error) {
 	if err != nil {
 		return nil, err
 	}
+
+	// test mongo connection
+	res := client.Database("foo").RunCommand(context.TODO(), map[string]int{"buildinfo": 1})
+	if res.Err() != nil {
+		return nil, res.Err()
+	}
 	// wired tiger will also not include index names for 3.0, but we're not going to test
 	// that so screw it
 	return &Controller{port, tdir, cmd, ver.LessThan(*semver.New("3.2.1000"))}, nil
@@ -128,8 +134,8 @@ func (c *Controller) Destroy(deleteTempDir bool) error {
 	return nil
 }
 
-func getMongoDBVer(ExecutablePath string) (*semver.Version, error) {
-	cmd := exec.Command(ExecutablePath, "--version")
+func getMongoDBVer(executablePath string) (*semver.Version, error) {
+	cmd := exec.Command(executablePath, "--version")
 	stdout, err := cmd.Output()
 	if err != nil {
 		return nil, err

From 2ecb09a069f0605098f8db3beaa598663eb88b38 Mon Sep 17 00:00:00 2001
From: Sijie <sijiex@lbl.gov>
Date: Wed, 13 Mar 2024 13:38:23 -0700
Subject: [PATCH 09/25] check test connection && compare mongo version

---
 test/mongocontroller/controller.go | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/test/mongocontroller/controller.go b/test/mongocontroller/controller.go
index 4156793..18f09f7 100644
--- a/test/mongocontroller/controller.go
+++ b/test/mongocontroller/controller.go
@@ -2,6 +2,7 @@ package mongocontroller
 
 import (
 	"context"
+	"fmt"
 	"os"
 	"os/exec"
 	"path/filepath"
@@ -102,6 +103,15 @@ func New(p Params) (*Controller, error) {
 	if res.Err() != nil {
 		return nil, res.Err()
 	}
+	var doc map[string]interface{}
+	err = res.Decode(&doc)
+	if err != nil {
+		return nil, err
+	}
+	if ver.String() != doc["version"].(string) {
+		return nil, fmt.Errorf("the two mongo versions should be the same: %s != %s",
+		ver.String(), doc["version"].(string))
+	}
 	// wired tiger will also not include index names for 3.0, but we're not going to test
 	// that so screw it
 	return &Controller{port, tdir, cmd, ver.LessThan(*semver.New("3.2.1000"))}, nil

From 71babb3999b38b07847f6aaa7fb724604166d584 Mon Sep 17 00:00:00 2001
From: Sijie <sijiex@lbl.gov>
Date: Thu, 14 Mar 2024 13:33:32 -0700
Subject: [PATCH 10/25] update all the way

---
 .github/workflows/test.yml             | 12 ++--
 auth/kbase_provider_test.go            |  2 +-
 service/integration_test.go            |  2 +-
 test.cfg.example                       |  5 +-
 test/kbaseauthcontroller/controller.go | 81 +++++++++++++++++---------
 test/testhelpers/config.go             | 10 ++--
 6 files changed, 69 insertions(+), 43 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 829b409..9a806ff 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -14,6 +14,9 @@ on:
       - master
       - develop
 
+env:
+  AUTH2_JAR_NAME: kbase-auth2-test-shadow-all-0.7.0.jar
+
 jobs:
   workspace_deluxe_tests:
     runs-on: ubuntu-latest
@@ -46,10 +49,9 @@ jobs:
           # move to parent dir to install binaries etc
           cd ..
 
-          # set up jars
-          # TODO switch to the auth shadow jar
-          git clone https://github.com/kbase/jars
-          export JARSDIR=`pwd`/jars/lib/jars/
+          # set up auth2 jar
+          wget -q https://github.com/kbase/jars/raw/master/lib/jars/kbase/auth2/$AUTH2_JAR_NAME
+          export AUTH2JAR=`pwd`/$AUTH2_JAR_NAME
 
           # set up mongo
           wget -q http://fastdl.mongodb.org/linux/${{matrix.mongo}}.tgz
@@ -68,7 +70,7 @@ jobs:
           sed -i "s#^test.mongo.exe.*#test.mongo.exe=$MONGOD#" test.cfg
           sed -i "s#^test.minio.exe.*#test.minio.exe=$MINIO#" test.cfg
           sed -i "s#^test.mongo.wired_tiger.*#test.mongo.wired_tiger=${{matrix.wired_tiger}}#" test.cfg
-          sed -i "s#^test.jars.dir.*#test.jars.dir=$JARSDIR#" test.cfg
+          sed -i "s#^test.auth2jar.*#test.auth2jar=$AUTH2JAR#" test.cfg
           cat test.cfg
 
       - name: Run tests
diff --git a/auth/kbase_provider_test.go b/auth/kbase_provider_test.go
index d520618..7340088 100644
--- a/auth/kbase_provider_test.go
+++ b/auth/kbase_provider_test.go
@@ -53,7 +53,7 @@ func (t *TestSuite) SetupSuite() {
 	t.mongo = mongoctl
 
 	auth, err := kbaseauthcontroller.New(kbaseauthcontroller.Params{
-		JarsDir:       tcfg.JarsDir,
+		Auth2Jar:      tcfg.Auth2JarPath,
 		MongoHost:     "localhost:" + strconv.Itoa(mongoctl.GetPort()),
 		MongoDatabase: "test_kb_auth_provider_authdb",
 		RootTempDir:   tcfg.TempDir,
diff --git a/service/integration_test.go b/service/integration_test.go
index 18034b3..ae4a07b 100644
--- a/service/integration_test.go
+++ b/service/integration_test.go
@@ -191,7 +191,7 @@ func (t *TestSuite) addTestRole(username string, role string) {
 func (t *TestSuite) setupAuth(cfg *testhelpers.TestConfig,
 ) (*kbaseauthcontroller.Controller, url.URL) {
 	auth, err := kbaseauthcontroller.New(kbaseauthcontroller.Params{
-		JarsDir:       cfg.JarsDir,
+		Auth2Jar:      cfg.Auth2JarPath,
 		MongoHost:     "localhost:" + strconv.Itoa(t.mongo.GetPort()),
 		MongoDatabase: "test_kb_auth_provider_authdb",
 		RootTempDir:   cfg.TempDir,
diff --git a/test.cfg.example b/test.cfg.example
index 6e8a729..4825897 100644
--- a/test.cfg.example
+++ b/test.cfg.example
@@ -10,9 +10,8 @@ test.mongo.exe=mongod
 # no.
 test.mongo.wired_tiger=false
 
-# The path to the jars dir inside the jars repo (https://github.com/kbase/jars), e.g.
-# [path to jars repo]/lib/jars
-test.jars.dir =
+# The path to the auth2 jar
+test.auth2jar=
 
 # Where to store temporary files generated during the test.
 test.temp.dir=temp_test_dir
diff --git a/test/kbaseauthcontroller/controller.go b/test/kbaseauthcontroller/controller.go
index bdd07be..c20fd6e 100644
--- a/test/kbaseauthcontroller/controller.go
+++ b/test/kbaseauthcontroller/controller.go
@@ -1,7 +1,6 @@
 package kbaseauthcontroller
 
 import (
-	"archive/zip"
 	"bytes"
 	"encoding/json"
 	"errors"
@@ -22,20 +21,15 @@ import (
 	"github.com/phayes/freeport"
 )
 
-// The following are required to run the KBase auth server in test mode.
 const (
 	serverClass = "us.kbase.test.auth2.StandaloneAuthServer"
-	// authTemplates is the zip file containing templates for the server
-	authTemplates = "kbase/auth2/kbase-auth2templates-0.2.4.zip"
-	// auth2ShadowAllJar is the jar required for the server
-	authShadowAllJar = "kbase/auth2/kbase-auth2-test-shadow-all-0.7.0.jar"
 )
 
 // Params are Parameters for creating a KBase Auth2 service (https://github.com/kbase/auth2)
 // controller.
 type Params struct {
-	// JarsDir is the path to the /lib/jars directory of the
-	JarsDir string
+	// Auth2Jar is the path to the kbase auth2 jar.
+	Auth2Jar string
 	// MongoHost is the mongo host.
 	MongoHost string
 	// MongoDatabase is the database to use for auth data.
@@ -53,7 +47,7 @@ type Controller struct {
 
 // New creates a new controller.
 func New(p Params) (*Controller, error) {
-	classPath, err := getClassPath(p.JarsDir)
+	classPath, err := getClassPath(p.Auth2Jar)
 	if err != nil {
 		return nil, err
 	}
@@ -63,7 +57,7 @@ func New(p Params) (*Controller, error) {
 	if err != nil {
 		return nil, err
 	}
-	err = installTemplates(p.JarsDir, templateDir)
+	err = installTemplates(p.Auth2Jar, templateDir)
 	if err != nil {
 		return nil, err
 	}
@@ -124,46 +118,77 @@ func waitForStartup(port string) error {
 	return startupErr
 }
 
-func getClassPath(jarsDir string) (string, error) {
-	jarsDir, err := filepath.Abs(jarsDir)
+func getClassPath(auth2Jar string) (string, error) {
+	jpath, err := filepath.Abs(auth2Jar)
 	if err != nil {
 		return "", err
 	}
-	jpath := path.Join(jarsDir, authShadowAllJar)
 	if _, err := os.Stat(jpath); os.IsNotExist(err) {
-		return "", fmt.Errorf("Jar %v does not exist", jpath)
+		return "", fmt.Errorf("jar %v does not exist", jpath)
 	}
 	return jpath, nil
 }
 
-func installTemplates(jarsDir string, templateDir string) error {
-	templateZip := path.Join(jarsDir, authTemplates)
-	arch, err := zip.OpenReader(templateZip) // global variable, yech
+func pullTemplatesOutofAuth2Jar(classPath string) (string, error) {
+	dirPath := filepath.Dir(classPath)
+	outfile, err := os.Create(filepath.Join(dirPath, "output.txt"))
+	if err != nil {
+		return "", err
+	}
+
+	cmdargs := []string{classPath, "-d", dirPath}
+	cmd := exec.Command("unzip", cmdargs...)
+	cmd.Stdout = outfile
+	cmd.Stderr = outfile
+	err = cmd.Start()
+	if err != nil {
+		return "", err
+	}
+
+	tpath := filepath.Join(dirPath, "kbase_auth2_templates")
+	if _, err := os.Stat(tpath); os.IsNotExist(err) {
+		return "", fmt.Errorf("the template folder %v does not exist", tpath)
+	}
+	return tpath, err
+}
+
+func installTemplates(classPath string, templateDir string) error {
+	tpath, err := pullTemplatesOutofAuth2Jar(classPath)
 	if err != nil {
 		return err
 	}
-	for _, f := range arch.File {
-		name := f.FileHeader.Name
+    files, err := os.ReadDir(tpath)
+    if err != nil {
+        return err
+    }
+	for _, f := range files {
+		name := f.Name()
 		if !strings.HasSuffix(name, "/") { // not a directory
 			name = path.Clean(name)
 			if path.IsAbs(name) || strings.HasPrefix(name, "..") {
-				return fmt.Errorf("Zip file %v contains files outside the zip directory - "+
-					"this is a sign of a malicious zip file", templateZip)
+				return fmt.Errorf("template folder %v contains files outside the directory - "+
+					"this is a sign of a malicious template folder", tpath)
 			}
-			target, err := filepath.Abs(path.Join(templateDir, name))
+			dst, err := filepath.Abs(path.Join(templateDir, name))
 			if err != nil {
 				return err
 			}
-			os.MkdirAll(path.Dir(target), 0600)
-			r, err := f.Open()
+			os.MkdirAll(path.Dir(dst), 0600)
+
+			src := filepath.Join(tpath, name)
+			source, err := os.Open(src)
+			if err != nil {
+				return err
+			}
+			defer source.Close()
+
+			destination, err := os.Create(dst)
 			if err != nil {
 				return err
 			}
-			f, err := os.Create(target)
+			defer destination.Close()
 
-			io.Copy(f, r)
-			r.Close()
-			f.Close()
+			io.Copy(destination, source)
 		}
 	}
 	return nil
diff --git a/test/testhelpers/config.go b/test/testhelpers/config.go
index 42b045f..b233e65 100644
--- a/test/testhelpers/config.go
+++ b/test/testhelpers/config.go
@@ -21,8 +21,8 @@ const (
 	TestMongoExe = "test.mongo.exe"
 	// TestUseWiredTiger denotes that the MongoDB WiredTiger storage engine should be used.
 	TestUseWiredTiger = "test.mongo.wired_tiger"
-	// TestJarsDir is the key in the config file for the path to the KBase jars directory.
-	TestJarsDir = "test.jars.dir"
+	// TestAuth2Jar is the key in the config file for the path to the KBase auth2 jar.
+	TestAuth2Jar = "test.auth2jar"
 	// TestTempDir is the key in the config file for the temporary directory.
 	TestTempDir = "test.temp.dir"
 	// TestDeleteTempDir is the key in the config file for whether the temporary directory
@@ -36,7 +36,7 @@ type TestConfig struct {
 	MinioExePath  string
 	MongoExePath  string
 	UseWiredTiger bool
-	JarsDir       string
+	Auth2JarPath  string
 	TempDir       string
 	DeleteTempDir bool
 }
@@ -71,7 +71,7 @@ func GetConfig() (*TestConfig, error) {
 	if err != nil {
 		return nil, err
 	}
-	jarsdir, err := getValue(sec, TestJarsDir, configfile, true)
+	auth2Jar, err := getValue(sec, TestAuth2Jar, configfile, true)
 	if err != nil {
 		return nil, err
 	}
@@ -88,7 +88,7 @@ func GetConfig() (*TestConfig, error) {
 			MinioExePath:  minio,
 			MongoExePath:  mongo,
 			UseWiredTiger: wiredTiger == "true",
-			JarsDir:       jarsdir,
+			Auth2JarPath:  auth2Jar,
 			TempDir:       tempDir,
 			DeleteTempDir: del != "false",
 		},

From 6dc56fcba45d0d7b4ea4886ade9f8813098222fd Mon Sep 17 00:00:00 2001
From: Sijie <sijiex@lbl.gov>
Date: Thu, 14 Mar 2024 13:38:43 -0700
Subject: [PATCH 11/25] fix spacing issue

---
 test/kbaseauthcontroller/controller.go | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/kbaseauthcontroller/controller.go b/test/kbaseauthcontroller/controller.go
index c20fd6e..3ab98e2 100644
--- a/test/kbaseauthcontroller/controller.go
+++ b/test/kbaseauthcontroller/controller.go
@@ -157,8 +157,8 @@ func installTemplates(classPath string, templateDir string) error {
 	if err != nil {
 		return err
 	}
-    files, err := os.ReadDir(tpath)
-    if err != nil {
+	files, err := os.ReadDir(tpath)
+	if err != nil {
         return err
     }
 	for _, f := range files {

From f859c671bdb3b5b08fe8c09af307708327a5a5e3 Mon Sep 17 00:00:00 2001
From: Sijie <sijiex@lbl.gov>
Date: Thu, 14 Mar 2024 13:45:26 -0700
Subject: [PATCH 12/25] switch to ioutil

---
 test/kbaseauthcontroller/controller.go | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/kbaseauthcontroller/controller.go b/test/kbaseauthcontroller/controller.go
index 3ab98e2..af1f800 100644
--- a/test/kbaseauthcontroller/controller.go
+++ b/test/kbaseauthcontroller/controller.go
@@ -157,7 +157,7 @@ func installTemplates(classPath string, templateDir string) error {
 	if err != nil {
 		return err
 	}
-	files, err := os.ReadDir(tpath)
+	files, err := ioutil.ReadDir(tpath)
 	if err != nil {
         return err
     }

From f1c744518ac821ce216a8319ca9632bb299d1640 Mon Sep 17 00:00:00 2001
From: Sijie <sijiex@lbl.gov>
Date: Thu, 14 Mar 2024 14:14:56 -0700
Subject: [PATCH 13/25] use jar xf to unzip

---
 test/kbaseauthcontroller/controller.go | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/kbaseauthcontroller/controller.go b/test/kbaseauthcontroller/controller.go
index af1f800..80d8ca7 100644
--- a/test/kbaseauthcontroller/controller.go
+++ b/test/kbaseauthcontroller/controller.go
@@ -136,8 +136,8 @@ func pullTemplatesOutofAuth2Jar(classPath string) (string, error) {
 		return "", err
 	}
 
-	cmdargs := []string{classPath, "-d", dirPath}
-	cmd := exec.Command("unzip", cmdargs...)
+	cmdargs := []string{"xf", classPath}
+	cmd := exec.Command("jar", cmdargs...)
 	cmd.Stdout = outfile
 	cmd.Stderr = outfile
 	err = cmd.Start()

From 408b570d2c3ccf8890d3164e21dfe72a11f79a6b Mon Sep 17 00:00:00 2001
From: Sijie <sijiex@lbl.gov>
Date: Thu, 14 Mar 2024 14:20:58 -0700
Subject: [PATCH 14/25] fix path bug

---
 test/kbaseauthcontroller/controller.go | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/test/kbaseauthcontroller/controller.go b/test/kbaseauthcontroller/controller.go
index 80d8ca7..a3379d3 100644
--- a/test/kbaseauthcontroller/controller.go
+++ b/test/kbaseauthcontroller/controller.go
@@ -57,7 +57,7 @@ func New(p Params) (*Controller, error) {
 	if err != nil {
 		return nil, err
 	}
-	err = installTemplates(p.Auth2Jar, templateDir)
+	err = installTemplates(classPath, templateDir)
 	if err != nil {
 		return nil, err
 	}
@@ -136,8 +136,8 @@ func pullTemplatesOutofAuth2Jar(classPath string) (string, error) {
 		return "", err
 	}
 
-	cmdargs := []string{"xf", classPath}
-	cmd := exec.Command("jar", cmdargs...)
+	cmdargs := []string{classPath, "-d", dirPath}
+	cmd := exec.Command("unzip", cmdargs...)
 	cmd.Stdout = outfile
 	cmd.Stderr = outfile
 	err = cmd.Start()

From 33d9ee77a36727bd839925148d1256fafcaa738e Mon Sep 17 00:00:00 2001
From: Sijie <sijiex@lbl.gov>
Date: Thu, 14 Mar 2024 14:28:19 -0700
Subject: [PATCH 15/25] display all files

---
 test/kbaseauthcontroller/controller.go | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/test/kbaseauthcontroller/controller.go b/test/kbaseauthcontroller/controller.go
index a3379d3..dd46bad 100644
--- a/test/kbaseauthcontroller/controller.go
+++ b/test/kbaseauthcontroller/controller.go
@@ -131,6 +131,7 @@ func getClassPath(auth2Jar string) (string, error) {
 
 func pullTemplatesOutofAuth2Jar(classPath string) (string, error) {
 	dirPath := filepath.Dir(classPath)
+	fmt.Printf("the parent dir of auth2 is located at %v", dirPath)
 	outfile, err := os.Create(filepath.Join(dirPath, "output.txt"))
 	if err != nil {
 		return "", err
@@ -145,6 +146,11 @@ func pullTemplatesOutofAuth2Jar(classPath string) (string, error) {
 		return "", err
 	}
 
+	files, _ := ioutil.ReadDir(dirPath)
+	for _, f := range files {
+		fmt.Print(f.Name())
+	}
+
 	tpath := filepath.Join(dirPath, "kbase_auth2_templates")
 	if _, err := os.Stat(tpath); os.IsNotExist(err) {
 		return "", fmt.Errorf("the template folder %v does not exist", tpath)
@@ -153,6 +159,7 @@ func pullTemplatesOutofAuth2Jar(classPath string) (string, error) {
 }
 
 func installTemplates(classPath string, templateDir string) error {
+	fmt.Printf("the auth2 is located at %v", classPath)
 	tpath, err := pullTemplatesOutofAuth2Jar(classPath)
 	if err != nil {
 		return err

From 6369af91534854d866533f75ca2e1bef11259766 Mon Sep 17 00:00:00 2001
From: Sijie <sijiex@lbl.gov>
Date: Thu, 14 Mar 2024 14:32:34 -0700
Subject: [PATCH 16/25] display with println

---
 test/kbaseauthcontroller/controller.go | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/test/kbaseauthcontroller/controller.go b/test/kbaseauthcontroller/controller.go
index dd46bad..d4180f5 100644
--- a/test/kbaseauthcontroller/controller.go
+++ b/test/kbaseauthcontroller/controller.go
@@ -131,7 +131,9 @@ func getClassPath(auth2Jar string) (string, error) {
 
 func pullTemplatesOutofAuth2Jar(classPath string) (string, error) {
 	dirPath := filepath.Dir(classPath)
+	fmt.Println("------------------------------")
 	fmt.Printf("the parent dir of auth2 is located at %v", dirPath)
+	fmt.Println("------------------------------")
 	outfile, err := os.Create(filepath.Join(dirPath, "output.txt"))
 	if err != nil {
 		return "", err
@@ -148,7 +150,7 @@ func pullTemplatesOutofAuth2Jar(classPath string) (string, error) {
 
 	files, _ := ioutil.ReadDir(dirPath)
 	for _, f := range files {
-		fmt.Print(f.Name())
+		fmt.Println(f.Name())
 	}
 
 	tpath := filepath.Join(dirPath, "kbase_auth2_templates")
@@ -159,7 +161,9 @@ func pullTemplatesOutofAuth2Jar(classPath string) (string, error) {
 }
 
 func installTemplates(classPath string, templateDir string) error {
+	fmt.Println("------------------------------")
 	fmt.Printf("the auth2 is located at %v", classPath)
+	fmt.Println("------------------------------")
 	tpath, err := pullTemplatesOutofAuth2Jar(classPath)
 	if err != nil {
 		return err

From 2c8f9d173350613ab930af670d73a341389f86b5 Mon Sep 17 00:00:00 2001
From: Sijie <sijiex@lbl.gov>
Date: Thu, 14 Mar 2024 14:41:54 -0700
Subject: [PATCH 17/25] sleep 1 sec

---
 test/kbaseauthcontroller/controller.go | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/test/kbaseauthcontroller/controller.go b/test/kbaseauthcontroller/controller.go
index d4180f5..c053450 100644
--- a/test/kbaseauthcontroller/controller.go
+++ b/test/kbaseauthcontroller/controller.go
@@ -153,6 +153,8 @@ func pullTemplatesOutofAuth2Jar(classPath string) (string, error) {
 		fmt.Println(f.Name())
 	}
 
+	time.Sleep(1 * time.Second)
+
 	tpath := filepath.Join(dirPath, "kbase_auth2_templates")
 	if _, err := os.Stat(tpath); os.IsNotExist(err) {
 		return "", fmt.Errorf("the template folder %v does not exist", tpath)

From 19ebf3b1107995a9e56a6c8d62ad09af4ed6959b Mon Sep 17 00:00:00 2001
From: Sijie <sijiex@lbl.gov>
Date: Thu, 14 Mar 2024 15:28:44 -0700
Subject: [PATCH 18/25] check kbase_auth2_templates existence

---
 test/kbaseauthcontroller/controller.go | 21 +++++++++++++--------
 1 file changed, 13 insertions(+), 8 deletions(-)

diff --git a/test/kbaseauthcontroller/controller.go b/test/kbaseauthcontroller/controller.go
index c053450..0dcd679 100644
--- a/test/kbaseauthcontroller/controller.go
+++ b/test/kbaseauthcontroller/controller.go
@@ -23,6 +23,9 @@ import (
 
 const (
 	serverClass = "us.kbase.test.auth2.StandaloneAuthServer"
+
+	// The max number of attempts to check if templates have been pulled out of the shadow jar
+	attempts = 10
 )
 
 // Params are Parameters for creating a KBase Auth2 service (https://github.com/kbase/auth2)
@@ -148,15 +151,17 @@ func pullTemplatesOutofAuth2Jar(classPath string) (string, error) {
 		return "", err
 	}
 
-	files, _ := ioutil.ReadDir(dirPath)
-	for _, f := range files {
-		fmt.Println(f.Name())
-	}
-
-	time.Sleep(1 * time.Second)
-
+	i := 0
 	tpath := filepath.Join(dirPath, "kbase_auth2_templates")
-	if _, err := os.Stat(tpath); os.IsNotExist(err) {
+	for i < attempts {
+		if _, err := os.Stat(tpath); os.IsNotExist(err) {
+			time.Sleep(1 * time.Second)
+			i += 1
+			continue
+		}
+		break
+    }
+	if i == attempts {
 		return "", fmt.Errorf("the template folder %v does not exist", tpath)
 	}
 	return tpath, err

From 04daa79e3a7206e4151d51ddb3c56b8665521b0d Mon Sep 17 00:00:00 2001
From: Sijie <sijiex@lbl.gov>
Date: Thu, 14 Mar 2024 15:34:22 -0700
Subject: [PATCH 19/25] clean up && finish

---
 test/kbaseauthcontroller/controller.go | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

diff --git a/test/kbaseauthcontroller/controller.go b/test/kbaseauthcontroller/controller.go
index 0dcd679..2003e06 100644
--- a/test/kbaseauthcontroller/controller.go
+++ b/test/kbaseauthcontroller/controller.go
@@ -134,9 +134,6 @@ func getClassPath(auth2Jar string) (string, error) {
 
 func pullTemplatesOutofAuth2Jar(classPath string) (string, error) {
 	dirPath := filepath.Dir(classPath)
-	fmt.Println("------------------------------")
-	fmt.Printf("the parent dir of auth2 is located at %v", dirPath)
-	fmt.Println("------------------------------")
 	outfile, err := os.Create(filepath.Join(dirPath, "output.txt"))
 	if err != nil {
 		return "", err
@@ -151,8 +148,9 @@ func pullTemplatesOutofAuth2Jar(classPath string) (string, error) {
 		return "", err
 	}
 
-	i := 0
 	tpath := filepath.Join(dirPath, "kbase_auth2_templates")
+
+	i := 0
 	for i < attempts {
 		if _, err := os.Stat(tpath); os.IsNotExist(err) {
 			time.Sleep(1 * time.Second)
@@ -168,9 +166,6 @@ func pullTemplatesOutofAuth2Jar(classPath string) (string, error) {
 }
 
 func installTemplates(classPath string, templateDir string) error {
-	fmt.Println("------------------------------")
-	fmt.Printf("the auth2 is located at %v", classPath)
-	fmt.Println("------------------------------")
 	tpath, err := pullTemplatesOutofAuth2Jar(classPath)
 	if err != nil {
 		return err

From 8576aab0b7facf660a854bc050046ac18c25e358 Mon Sep 17 00:00:00 2001
From: Sijie <sijiex@lbl.gov>
Date: Thu, 14 Mar 2024 15:54:58 -0700
Subject: [PATCH 20/25] move pullTemplatesOutofAuth2Jar into New

---
 test/kbaseauthcontroller/controller.go | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/test/kbaseauthcontroller/controller.go b/test/kbaseauthcontroller/controller.go
index 2003e06..18a795e 100644
--- a/test/kbaseauthcontroller/controller.go
+++ b/test/kbaseauthcontroller/controller.go
@@ -54,13 +54,17 @@ func New(p Params) (*Controller, error) {
 	if err != nil {
 		return nil, err
 	}
+	tpath, err := pullTemplatesOutofAuth2Jar(classPath)
+	if err != nil {
+		return nil, err
+	}
 	tdir := filepath.Join(p.RootTempDir, "AuthController-"+uuid.New().String())
 	templateDir := filepath.Join(tdir, "templates")
 	err = os.MkdirAll(templateDir, 0700)
 	if err != nil {
 		return nil, err
 	}
-	err = installTemplates(classPath, templateDir)
+	err = installTemplates(tpath, templateDir)
 	if err != nil {
 		return nil, err
 	}
@@ -165,11 +169,7 @@ func pullTemplatesOutofAuth2Jar(classPath string) (string, error) {
 	return tpath, err
 }
 
-func installTemplates(classPath string, templateDir string) error {
-	tpath, err := pullTemplatesOutofAuth2Jar(classPath)
-	if err != nil {
-		return err
-	}
+func installTemplates(tpath string, templateDir string) error {
 	files, err := ioutil.ReadDir(tpath)
 	if err != nil {
         return err

From 8503abaf4ad4214ba995de81692013bdfe1c241d Mon Sep 17 00:00:00 2001
From: Sijie <sijiex@lbl.gov>
Date: Fri, 15 Mar 2024 10:38:33 -0700
Subject: [PATCH 21/25] address all comments

---
 test.cfg.example                       |  2 +-
 test/kbaseauthcontroller/controller.go | 69 +++++++-------------------
 test/testhelpers/config.go             |  2 +-
 3 files changed, 20 insertions(+), 53 deletions(-)

diff --git a/test.cfg.example b/test.cfg.example
index 4825897..b58f209 100644
--- a/test.cfg.example
+++ b/test.cfg.example
@@ -10,7 +10,7 @@ test.mongo.exe=mongod
 # no.
 test.mongo.wired_tiger=false
 
-# The path to the auth2 jar
+# The path to the kbase auth2 service shadow test jar
 test.auth2jar=
 
 # Where to store temporary files generated during the test.
diff --git a/test/kbaseauthcontroller/controller.go b/test/kbaseauthcontroller/controller.go
index 18a795e..e96c140 100644
--- a/test/kbaseauthcontroller/controller.go
+++ b/test/kbaseauthcontroller/controller.go
@@ -1,6 +1,7 @@
 package kbaseauthcontroller
 
 import (
+	"archive/zip"
 	"bytes"
 	"encoding/json"
 	"errors"
@@ -23,9 +24,6 @@ import (
 
 const (
 	serverClass = "us.kbase.test.auth2.StandaloneAuthServer"
-
-	// The max number of attempts to check if templates have been pulled out of the shadow jar
-	attempts = 10
 )
 
 // Params are Parameters for creating a KBase Auth2 service (https://github.com/kbase/auth2)
@@ -50,11 +48,7 @@ type Controller struct {
 
 // New creates a new controller.
 func New(p Params) (*Controller, error) {
-	classPath, err := getClassPath(p.Auth2Jar)
-	if err != nil {
-		return nil, err
-	}
-	tpath, err := pullTemplatesOutofAuth2Jar(classPath)
+	authJarPath, err := checkAuthJarExists(p.Auth2Jar)
 	if err != nil {
 		return nil, err
 	}
@@ -64,7 +58,7 @@ func New(p Params) (*Controller, error) {
 	if err != nil {
 		return nil, err
 	}
-	err = installTemplates(tpath, templateDir)
+	err = installTemplates(authJarPath, templateDir)
 	if err != nil {
 		return nil, err
 	}
@@ -78,7 +72,7 @@ func New(p Params) (*Controller, error) {
 	}
 	strport := strconv.Itoa(port)
 	cmdargs := []string{
-		"-classpath", classPath,
+		"-classpath", authJarPath,
 		"-DAUTH2_TEST_MONGOHOST=" + p.MongoHost,
 		"-DAUTH2_TEST_MONGODB=" + p.MongoDatabase,
 		"-DAUTH2_TEST_TEMPLATE_DIR=" + templateDir,
@@ -125,7 +119,7 @@ func waitForStartup(port string) error {
 	return startupErr
 }
 
-func getClassPath(auth2Jar string) (string, error) {
+func checkAuthJarExists(auth2Jar string) (string, error) {
 	jpath, err := filepath.Abs(auth2Jar)
 	if err != nil {
 		return "", err
@@ -136,51 +130,25 @@ func getClassPath(auth2Jar string) (string, error) {
 	return jpath, nil
 }
 
-func pullTemplatesOutofAuth2Jar(classPath string) (string, error) {
-	dirPath := filepath.Dir(classPath)
-	outfile, err := os.Create(filepath.Join(dirPath, "output.txt"))
+func installTemplates(authJarPath string, templateDir string) error {
+	buff, err := ioutil.ReadFile(authJarPath)  //read the content of file
 	if err != nil {
-		return "", err
+		return err
 	}
 
-	cmdargs := []string{classPath, "-d", dirPath}
-	cmd := exec.Command("unzip", cmdargs...)
-	cmd.Stdout = outfile
-	cmd.Stderr = outfile
-	err = cmd.Start()
+	r, err := zip.NewReader(bytes.NewReader(buff), int64(len(buff)))
 	if err != nil {
-		return "", err
-	}
-
-	tpath := filepath.Join(dirPath, "kbase_auth2_templates")
-
-	i := 0
-	for i < attempts {
-		if _, err := os.Stat(tpath); os.IsNotExist(err) {
-			time.Sleep(1 * time.Second)
-			i += 1
-			continue
-		}
-		break
-    }
-	if i == attempts {
-		return "", fmt.Errorf("the template folder %v does not exist", tpath)
+		return err
 	}
-	return tpath, err
-}
 
-func installTemplates(tpath string, templateDir string) error {
-	files, err := ioutil.ReadDir(tpath)
-	if err != nil {
-        return err
-    }
-	for _, f := range files {
-		name := f.Name()
-		if !strings.HasSuffix(name, "/") { // not a directory
+	for _, f := range r.File {
+		name := f.Name
+		// not a directory
+		if !strings.HasSuffix(name, "/") && strings.HasPrefix(name, "kbase_auth2_templates") {
 			name = path.Clean(name)
-			if path.IsAbs(name) || strings.HasPrefix(name, "..") {
-				return fmt.Errorf("template folder %v contains files outside the directory - "+
-					"this is a sign of a malicious template folder", tpath)
+			if path.IsAbs(name) {
+				return fmt.Errorf("jar file %v contains files outside the directory - "+
+					"this is a sign of a malicious jar file", authJarPath)
 			}
 			dst, err := filepath.Abs(path.Join(templateDir, name))
 			if err != nil {
@@ -188,8 +156,7 @@ func installTemplates(tpath string, templateDir string) error {
 			}
 			os.MkdirAll(path.Dir(dst), 0600)
 
-			src := filepath.Join(tpath, name)
-			source, err := os.Open(src)
+			source, err := f.Open()
 			if err != nil {
 				return err
 			}
diff --git a/test/testhelpers/config.go b/test/testhelpers/config.go
index b233e65..918ca58 100644
--- a/test/testhelpers/config.go
+++ b/test/testhelpers/config.go
@@ -21,7 +21,7 @@ const (
 	TestMongoExe = "test.mongo.exe"
 	// TestUseWiredTiger denotes that the MongoDB WiredTiger storage engine should be used.
 	TestUseWiredTiger = "test.mongo.wired_tiger"
-	// TestAuth2Jar is the key in the config file for the path to the KBase auth2 jar.
+	// TestAuth2Jar is the key in the config file for the path to the KBase auth2 shadow test jar.
 	TestAuth2Jar = "test.auth2jar"
 	// TestTempDir is the key in the config file for the temporary directory.
 	TestTempDir = "test.temp.dir"

From 651d281ceaf2dd66ec3738cf60324676fd955ab9 Mon Sep 17 00:00:00 2001
From: Sijie <sijiex@lbl.gov>
Date: Fri, 15 Mar 2024 10:49:58 -0700
Subject: [PATCH 22/25] debug permission denied

---
 test/kbaseauthcontroller/controller.go | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/kbaseauthcontroller/controller.go b/test/kbaseauthcontroller/controller.go
index e96c140..cc51a9a 100644
--- a/test/kbaseauthcontroller/controller.go
+++ b/test/kbaseauthcontroller/controller.go
@@ -168,6 +168,7 @@ func installTemplates(authJarPath string, templateDir string) error {
 			}
 			defer destination.Close()
 
+			fmt.Println("pass this line")
 			io.Copy(destination, source)
 		}
 	}

From b30088a2bae9e86b0a0575b64f53b8e1e3f9cae8 Mon Sep 17 00:00:00 2001
From: Sijie <sijiex@lbl.gov>
Date: Fri, 15 Mar 2024 10:59:36 -0700
Subject: [PATCH 23/25] fix bug

---
 test/kbaseauthcontroller/controller.go | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/test/kbaseauthcontroller/controller.go b/test/kbaseauthcontroller/controller.go
index cc51a9a..d85c429 100644
--- a/test/kbaseauthcontroller/controller.go
+++ b/test/kbaseauthcontroller/controller.go
@@ -150,7 +150,7 @@ func installTemplates(authJarPath string, templateDir string) error {
 				return fmt.Errorf("jar file %v contains files outside the directory - "+
 					"this is a sign of a malicious jar file", authJarPath)
 			}
-			dst, err := filepath.Abs(path.Join(templateDir, name))
+			dst, err := filepath.Abs(path.Join(templateDir, filepath.Base(name)))
 			if err != nil {
 				return err
 			}
@@ -168,7 +168,6 @@ func installTemplates(authJarPath string, templateDir string) error {
 			}
 			defer destination.Close()
 
-			fmt.Println("pass this line")
 			io.Copy(destination, source)
 		}
 	}

From a3cc1fe25fe2b977a794fb103aabc8f1f665497b Mon Sep 17 00:00:00 2001
From: Sijie <sijiex@lbl.gov>
Date: Fri, 15 Mar 2024 11:09:24 -0700
Subject: [PATCH 24/25] replace nil by context.Background()

---
 test/mongocontroller/controller.go | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/mongocontroller/controller.go b/test/mongocontroller/controller.go
index 18f09f7..42b572e 100644
--- a/test/mongocontroller/controller.go
+++ b/test/mongocontroller/controller.go
@@ -99,7 +99,7 @@ func New(p Params) (*Controller, error) {
 	}
 
 	// test mongo connection
-	res := client.Database("foo").RunCommand(context.TODO(), map[string]int{"buildinfo": 1})
+	res := client.Database("foo").RunCommand(context.Background(), map[string]int{"buildinfo": 1})
 	if res.Err() != nil {
 		return nil, res.Err()
 	}

From 9771d7e8c791cb0b94aaef992cb154ac546ebe8f Mon Sep 17 00:00:00 2001
From: Sijie <sijiex@lbl.gov>
Date: Fri, 15 Mar 2024 13:53:32 -0700
Subject: [PATCH 25/25] fix file check

---
 test/kbaseauthcontroller/controller.go | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

diff --git a/test/kbaseauthcontroller/controller.go b/test/kbaseauthcontroller/controller.go
index d85c429..99689f5 100644
--- a/test/kbaseauthcontroller/controller.go
+++ b/test/kbaseauthcontroller/controller.go
@@ -131,22 +131,17 @@ func checkAuthJarExists(auth2Jar string) (string, error) {
 }
 
 func installTemplates(authJarPath string, templateDir string) error {
-	buff, err := ioutil.ReadFile(authJarPath)  //read the content of file
+	jar, err := zip.OpenReader(authJarPath)
 	if err != nil {
 		return err
 	}
 
-	r, err := zip.NewReader(bytes.NewReader(buff), int64(len(buff)))
-	if err != nil {
-		return err
-	}
-
-	for _, f := range r.File {
+	for _, f := range jar.File {
 		name := f.Name
 		// not a directory
 		if !strings.HasSuffix(name, "/") && strings.HasPrefix(name, "kbase_auth2_templates") {
 			name = path.Clean(name)
-			if path.IsAbs(name) {
+			if filepath.Dir(name) != "kbase_auth2_templates" {
 				return fmt.Errorf("jar file %v contains files outside the directory - "+
 					"this is a sign of a malicious jar file", authJarPath)
 			}