Repository: tern-tools/tern

Issue:
Tern has no concept of WORKDIR directory (required to collect go module info)
**Describe the bug**
Most golang Dockerfiles will have a `WORKDIR` where the go modules get installed. i.e.

```
# Start from the latest golang base image
FROM golang:1.14-alpine as builder

# Set the Current Working Directory inside the container
WORKDIR /app

# Copy go mod and sum files
COPY go.mod go.sum ./

# Download all dependencies. Dependencies will be cached if the go.mod and go.sum files are not changed
RUN go mod download

# Copy the source from the current directory to the Working Directory inside the container
COPY . .

# Build the Go app
RUN CGO_ENABLED=0 GOOS=linux go build -v -a -installsuffix cgo -o swag cmd/swag/main.go
```

If a `WORKDIR` is established, all the proceeding `RUN` , `CMD` , `ADD` , `COPY` , or `ENTRYPOINT` commands will be executed in this `WORKDIR`. Tern currently has no concept of a `WORKDIR`. This is an issue when it comes to analyzing the go modules in a docker image because the go command is only present in the `WORKDIR`, compared to most package manager utilities that are universally available in the image. The command `go list -m all | tail -n +2 | cut -d ' ' -f1` which attempts to collect the module names, will return `Command failed. go list -m: not using modules` if not executed from the proper WORKDIR directory. However, if you change the `base.yml` command to cd into the `WORKDIR` first, then the command executes without errors. cd-ing into the `WORKDIR` directory is not something we can do from `base.yml` because we won't know the name of the `WORKDIR` directory and there is currently no way to reference this.

**To Reproduce**
Steps to reproduce the behavior:
1. Add `go` package manager to base.yml and snippets.yml.
2. Run tern on a go image (similar to Dockerfile above)
3. If you change `base.yml` to cd into the `WORKDIR` first by running `cd /app; /usr/local/go/bin/go list -m all | tail -n +2 | cut -d ' ' -f1` to collect go modules, the command will work and Tern will output the go modules in the report. If you only use `/usr/local/go/bin/go list -m all | tail -n +2 | cut -d ' ' -f1` the command will fail.
4. See error/output below.

**Error in terminal**
Output when you cd into the WORKDIR first in `base.yml`:
```
 File licenses found in Layer:  None
        Packages found in Layer:  github.com/BurntSushi/toml-v0.3.1, github.com/KyleBanks/depth-v1.2.1,
 github.com/PuerkitoBio/purell-v1.1.1, github.com/PuerkitoBio/urlesc-v0.0.0-20170810143723-de5bf2ad4578,
 github.com/alecthomas/template-v0.0.0-20190718012654-fb15b899a751, github.com/cpuguy83/go-md2man/v2-
v2.0.0-20190314233015-f79a8a8ca69d, github.com/davecgh/go-spew-v1.1.1, github.com/ghodss/yaml-v1.0.0, 
github.com/gin-contrib/gzip-v0.0.1, github.com/gin-contrib/sse-v0.1.0, github.com/gin-gonic/gin-v1.4.0, github.com/go-
openapi/jsonpointer-v0.19.3, github.com/go-openapi/jsonreference-v0.19.3, github.com/go-openapi/spec-v0.19.4, 
github.com/go-openapi/swag-v0.19.5, github.com/golang/protobuf-v1.3.1, github.com/json-iterator/go-v1.1.6, github.com/kr
/pretty-v0.1.0, github.com/kr/pty-v1.1.5, github.com/kr/text-v0.1.0, github.com/mailru/easyjson-v0.0.0-20190626092158-
b2ccc519800e, github.com/mattn/go-isatty-v0.0.8, github.com/modern-go/concurrent-v0.0.0-20180306012644-
bacd9c7ef1dd, github.com/modern-go/reflect2-v1.0.1, github.com/pkg/errors-v0.8.1, github.com/pmezard/go-difflib-v1.0.0, 
github.com/russross/blackfriday/v2-v2.0.1, github.com/satori/go.uuid-v1.2.0, github.com/shopspring/decimal-v1.2.0, 
github.com/shurcooL/sanitized_anchor_name-v1.0.0, github.com/stretchr/objx-v0.2.0, github.com/stretchr/testify-v1.4.0,
 github.com/swaggo/files-v0.0.0-20190704085106-630677cd5c14, github.com/swaggo/gin-swagger-v1.2.0, 
github.com/ugorji/go-v1.1.5-pre, github.com/ugorji/go/codec-v1.1.5-pre, github.com/urfave/cli-v1.20.0, github.com/urfave
/cli/v2-v2.1.1, golang.org/x/crypto-v0.0.0-20190611184440-5c40567a22f8, golang.org/x/net-v0.0.0-20190827160401-
ba9fcec4b297, golang.org/x/sync-v0.0.0-20190423024810-112230192c58, golang.org/x/sys-
v0.0.0-20190616124812-15dcb6c0061f, golang.org/x/text-v0.3.2, golang.org/x/tools-
v0.0.0-20190614205625-5aca471b1d59, gopkg.in/check.v1-v1.0.0-20180628173108-788fd7840127, gopkg.in/go-
playground/assert.v1-v1.2.1, gopkg.in/go-playground/validator.v8-v8.18.2, gopkg.in/yaml.v2-v2.2.2

        Licenses found in Layer:  None
```

Output when you don't `cd` into the `WORKDIR`:
```
020-07-13 14:02:56,250 - DEBUG - rootfs - Running command: sudo unshare -pf --mount-proc=/home/rjudge/.tern/temp/mergedir/proc chroot /home/rjudge/.tern/temp/mergedir /bin/sh -c /usr/local/go/bin/go list -m all | tail -n +2 | cut -d ' ' -f1
2020-07-13 14:02:56,279 - ERROR - rootfs - Command failed. go list -m: not using modules
```

**Expected behavior**
Tern should be executing from the `WORKDIR` directory, if it exists.


Comments:

Patch:
diff --git a/tern/analyze/common.py b/tern/analyze/common.py
index df4889a..e5835c9 100644
--- a/tern/analyze/common.py
+++ b/tern/analyze/common.py
@@ -31,9 +31,11 @@ logger = logging.getLogger(constants.logger_name)
 
 
 def get_shell_commands(shell_command_line):
-    '''Given a shell command line, get a list of Command objects'''
+    '''Given a shell command line, get a list of Command objects and report on
+    branch statements'''
     statements = general.split_command(shell_command_line)
     command_list = []
+    branch_report = ''
     # traverse the statements, pick out the loop and commands.
     for stat in statements:
         if 'command' in stat:
@@ -43,7 +45,13 @@ def get_shell_commands(shell_command_line):
             for st in loop_stat:
                 if 'command' in st:
                     command_list.append(Command(st['command']))
-    return command_list
+        elif 'branch' in stat:
+            branch_report = branch_report + '\n'.join(stat['content']) + '\n\n'
+    if branch_report:
+        # add prefix
+        branch_report = '\nNon-deterministic branching statement: \n' + \
+                        branch_report
+    return command_list, branch_report
 
 
 def load_from_cache(layer, redo=False):
@@ -201,7 +209,7 @@ def get_os_release(base_layer):
     return pretty_name.strip('"')
 
 
-def collate_list_metadata(shell, listing):
+def collate_list_metadata(shell, listing, work_dir):
     '''Given the shell and the listing for the package manager, collect
     metadata that gets returned as a list'''
     pkg_dict = {}
@@ -212,7 +220,7 @@ def collate_list_metadata(shell, listing):
         return pkg_dict, msgs, warnings
     for item in command_lib.base_keys:
         if item in listing.keys():
-            items, msg = command_lib.get_pkg_attr_list(shell, listing[item])
+            items, msg = command_lib.get_pkg_attr_list(shell, listing[item], work_dir)
             msgs = msgs + msg
             pkg_dict.update({item: items})
         else:
@@ -290,7 +298,7 @@ def get_deb_package_licenses(deb_copyrights):
     return deb_licenses
 
 
-def add_base_packages(image_layer, binary, shell):
+def add_base_packages(image_layer, binary, shell, work_dir=None):
     '''Given the image layer, the binary to invoke and shell:
         1. get the listing from the base.yml
         2. Invoke any commands against the base layer
@@ -313,7 +321,7 @@ def add_base_packages(image_layer, binary, shell):
         image_layer.origins.add_notice_to_origins(
             origin_layer, Notice(snippet_msg, 'info'))
         # get all the packages in the base layer
-        pkg_dict, invoke_msg, warnings = collate_list_metadata(shell, listing)
+        pkg_dict, invoke_msg, warnings = collate_list_metadata(shell, listing, work_dir)
 
         if listing.get("pkg_format") == "deb":
             pkg_dict["pkg_licenses"] = get_deb_package_licenses(
@@ -338,7 +346,7 @@ def add_base_packages(image_layer, binary, shell):
                 listing_key=binary), 'error'))
 
 
-def fill_package_metadata(pkg_obj, pkg_listing, shell):
+def fill_package_metadata(pkg_obj, pkg_listing, shell, work_dir):
     '''Given a Package object and the Package listing from the command
     library, fill in the attribute value returned from looking up the
     data and methods of the package listing.
@@ -351,7 +359,7 @@ def fill_package_metadata(pkg_obj, pkg_listing, shell):
         pkg_listing, 'version')
     if version_listing:
         version_list, invoke_msg = command_lib.get_pkg_attr_list(
-            shell, version_listing, package_name=pkg_obj.name)
+            shell, version_listing, work_dir, package_name=pkg_obj.name)
         if version_list:
             pkg_obj.version = version_list[0]
         else:
@@ -365,7 +373,7 @@ def fill_package_metadata(pkg_obj, pkg_listing, shell):
         pkg_listing, 'license')
     if license_listing:
         license_list, invoke_msg = command_lib.get_pkg_attr_list(
-            shell, license_listing, package_name=pkg_obj.name)
+            shell, license_listing, work_dir, package_name=pkg_obj.name)
         if license_list:
             pkg_obj.license = license_list[0]
         else:
@@ -379,7 +387,7 @@ def fill_package_metadata(pkg_obj, pkg_listing, shell):
         pkg_listing, 'proj_url')
     if url_listing:
         url_list, invoke_msg = command_lib.get_pkg_attr_list(
-            shell, url_listing, package_name=pkg_obj.name)
+            shell, url_listing, work_dir, package_name=pkg_obj.name)
         if url_list:
             pkg_obj.proj_url = url_list[0]
         else:
@@ -390,7 +398,7 @@ def fill_package_metadata(pkg_obj, pkg_listing, shell):
             origin_str, Notice(listing_msg, 'warning'))
 
 
-def get_package_dependencies(package_listing, package_name, shell):
+def get_package_dependencies(package_listing, package_name, shell, work_dir=None):
     '''The package listing is the result of looking up the command name in the
     command library. Given this listing, the package name and the shell
     return a list of package dependency names'''
@@ -398,7 +406,7 @@ def get_package_dependencies(package_listing, package_name, shell):
         package_listing, 'deps')
     if deps_listing:
         deps_list, invoke_msg = command_lib.get_pkg_attr_list(
-            shell, deps_listing, package_name=package_name)
+            shell, deps_listing, work_dir, package_name=package_name)
         if deps_list:
             return list(set(deps_list)), ''
         return [], invoke_msg
@@ -457,6 +465,7 @@ def consolidate_commands(command_list):
         new_list.append(command_list.pop(0))
 
     while command_list:
+        # match the first command with its following commands.
         first = command_list.pop(0)
         for _ in range(0, len(command_list)):
             second = command_list.pop(0)
@@ -465,8 +474,11 @@ def consolidate_commands(command_list):
                 new_list.append(second)
             else:
                 if not first.merge(second):
-                    command_list.append(first)
-                new_list.append(first)
+                    # Unable to merge second, we should keep second command.
+                    command_list.append(second)
+        # after trying to merge with all following commands, add first command
+        # to the new_dict.
+        new_list.append(first)
     return new_list
 
 
@@ -478,7 +490,7 @@ def filter_install_commands(shell_command_line):
         3. Return installed command objects, and messages for ignored commands
         and unrecognized commands'''
     report = ''
-    command_list = get_shell_commands(shell_command_line)
+    command_list, branch_report = get_shell_commands(shell_command_line)
     for command in command_list:
         command_lib.set_command_attrs(command)
     ignore_msgs, filter1 = remove_ignored_commands(command_list)
@@ -487,11 +499,12 @@ def filter_install_commands(shell_command_line):
         report = report + formats.ignored + ignore_msgs
     if unrec_msgs:
         report = report + formats.unrecognized + unrec_msgs
-
+    if branch_report:
+        report = report + branch_report
     return consolidate_commands(filter2), report
 
 
-def add_snippet_packages(image_layer, command, pkg_listing, shell):
+def add_snippet_packages(image_layer, command, pkg_listing, shell, work_dir):
     '''Given an image layer object, a command object, the package listing
     and the shell used to invoke commands, add package metadata to the layer
     object. We assume the filesystem is already mounted and ready
@@ -524,7 +537,7 @@ def add_snippet_packages(image_layer, command, pkg_listing, shell):
     # get package metadata for each package name
     for pkg_name in unique_pkgs:
         pkg = Package(pkg_name)
-        fill_package_metadata(pkg, pkg_invoke, shell)
+        fill_package_metadata(pkg, pkg_invoke, shell, work_dir)
         image_layer.add_package(pkg)
 
 
diff --git a/tern/analyze/docker/analyze.py b/tern/analyze/docker/analyze.py
index 6c2bccc..b112edb 100644
--- a/tern/analyze/docker/analyze.py
+++ b/tern/analyze/docker/analyze.py
@@ -106,7 +106,12 @@ def analyze_subsequent_layers(image_obj, shell, master_list, redo, dfobj=None,
                               dfile_lock=False):
     # get packages for subsequent layers
     curr_layer = 1
+    work_dir = None
     while curr_layer < len(image_obj.layers):  # pylint:disable=too-many-nested-blocks
+        # If workdir changes, update value accordingly
+        # so we can later execute base.yml commands from the workdir.
+        if image_obj.layers[curr_layer].get_layer_workdir() is not None:
+            work_dir = image_obj.layers[curr_layer].get_layer_workdir()
         # if there is no shell, try to see if it exists in the current layer
         if not shell:
             shell = common.get_shell(image_obj.layers[curr_layer])
@@ -126,7 +131,7 @@ def analyze_subsequent_layers(image_obj, shell, master_list, redo, dfobj=None,
                 if isinstance(pkg_listing, str):
                     try:
                         common.add_base_packages(
-                            image_obj.layers[curr_layer], pkg_listing, shell)
+                            image_obj.layers[curr_layer], pkg_listing, shell, work_dir)
                     except KeyboardInterrupt:
                         logger.critical(errors.keyboard_interrupt)
                         abort_analysis()
@@ -134,7 +139,7 @@ def analyze_subsequent_layers(image_obj, shell, master_list, redo, dfobj=None,
                     try:
                         common.add_snippet_packages(
                             image_obj.layers[curr_layer], command, pkg_listing,
-                            shell)
+                            shell, work_dir)
                     except KeyboardInterrupt:
                         logger.critical(errors.keyboard_interrupt)
                         abort_analysis()
diff --git a/tern/classes/image_layer.py b/tern/classes/image_layer.py
index 46a74ad..484b802 100644
--- a/tern/classes/image_layer.py
+++ b/tern/classes/image_layer.py
@@ -327,3 +327,10 @@ class ImageLayer:
                 file_data.set_checksum('sha256', attrs_tuple[2])
                 file_data.extattrs = attrs_tuple[0]
                 self.add_file(file_data)
+
+    def get_layer_workdir(self):
+        # If the layer is created by a WORKDIR command then return the workdir
+        match = re.search(r"\bWORKDIR\ (\/\w+)+\b", self.created_by)
+        if match:
+            return match.group().split()[1]
+        return None
diff --git a/tern/command_lib/command_lib.py b/tern/command_lib/command_lib.py
index c28c1b1..d3dc999 100644
--- a/tern/command_lib/command_lib.py
+++ b/tern/command_lib/command_lib.py
@@ -205,7 +205,7 @@ def invoke_in_rootfs(snippet_list, shell, package=''):
         raise
 
 
-def get_pkg_attr_list(shell, attr_dict, package_name='', chroot=True,
+def get_pkg_attr_list(shell, attr_dict, work_dir, package_name='', chroot=True,  # pylint:disable=too-many-arguments
                       override=''):
     '''The command library has package attributes listed like this:
         {invoke: {1: {container: [command1, command2]},
@@ -225,6 +225,9 @@ def get_pkg_attr_list(shell, attr_dict, package_name='', chroot=True,
             if 'container' in attr_dict['invoke'][step].keys():
                 snippet_list = attr_dict['invoke'][step]['container']
                 result = ''
+                # If work_dir exist cd into it
+                if work_dir is not None:
+                    snippet_list.insert(0, 'cd ' + work_dir)
                 # if we need to run in a chroot environment
                 if chroot:
                     try:
diff --git a/tern/tools/verify_invoke.py b/tern/tools/verify_invoke.py
index 95a6265..d016430 100644
--- a/tern/tools/verify_invoke.py
+++ b/tern/tools/verify_invoke.py
@@ -28,6 +28,15 @@ def look_up_lib(keys):
     return subd
 
 
+def get_workdir(image_obj):
+    # get the workdir from the image config where the commands will be executed
+    config = image_obj.get_image_config(image_obj.get_image_manifest())
+    workdir = config['config']['WorkingDir']
+    if workdir == '':
+        return None
+    return workdir
+
+
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(
         description='''
@@ -78,8 +87,9 @@ if __name__ == '__main__':
             info_dict = look_up_lib(args.keys)
         # try to invoke the commands
         try:
+            work_dir = get_workdir(image_obj)
             result = command_lib.get_pkg_attr_list(
-                args.shell, info_dict, args.package)
+                args.shell, info_dict, work_dir, args.package)
             print('Output list: ' + ' '.join(result[0]))
             print('Error messages: ' + result[1])
             print('Number of elements: ' + str(len(result[0])))


Test patch:
diff --git a/tests/test_analyze_common.py b/tests/test_analyze_common.py
index e40445c..82aba50 100644
--- a/tests/test_analyze_common.py
+++ b/tests/test_analyze_common.py
@@ -32,10 +32,18 @@ class TestAnalyzeCommon(unittest.TestCase):
         del self.test_dockerfile
 
     def testGetShellCommands(self):
-        command = common.get_shell_commands("yum install nfs-utils")
+        command, _ = common.get_shell_commands("yum install nfs-utils")
         self.assertEqual(type(command), list)
         self.assertEqual(len(command), 1)
         self.assertEqual(command[0].options, self.command1.options)
+        # test on branching command
+        branching_script = "if [ -z $var ]; then yum install nfs-utils; fi"
+        branch_command, report = common.get_shell_commands(branching_script)
+        self.assertEqual(type(branch_command), list)
+        # we will ignore branching command, so len should be 0
+        self.assertEqual(len(branch_command), 0)
+        # and the report should not be None
+        self.assertTrue(report)
 
     def testLoadFromCache(self):
         '''Given a layer object, populate the given layer in case the cache isn't empty'''