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mrvacommander/notes/cli-end-to-end-demo.org
Michael Hohn 77ce997fbb Major changes to support cli-end-to-end demonstration. See full log 
* notes/cli-end-to-end-demo.org (Database Aquisition):
  Starting description for the end-to-end demonstration workflow.
  Very simplified version of notes/cli-end-to-end.org

* docker-compose-demo.yml (services):
  Make the pre-populated ql database storage an explicit container
  to get persistent data and straightforward mount semantics.

* docker-compose-demo-build.yml (services):
  Add a docker-compose configuration for *building* the demo environment.

* demo/containers/dbsdata/Dockerfile:
  Add dbsdata Docker image to hold initialized minio database file tree

* client/containers/vscode/README.org
  Update vscode container to use custom plugin for later mrva redirection
2024-10-15 10:18:42 -07:00

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# -*- coding: utf-8 -*-
#+OPTIONS: H:2 num:t \n:nil @:t ::t |:t ^:{} f:t *:t TeX:t LaTeX:t skip:nil p:nil
* End-to-end example of CLI use
This document describes a complete cycle of the MRVA workflow, but using
pre-populated data. The steps included are
1. aquiring CodeQL databases
2. selection of databases
3. configuration and use of the command-line client
4. server startup
5. submission of the jobs
6. retrieval of the results
7. examination of the results
* Start the containers
#+BEGIN_SRC sh
cd ~/work-gh/mrva/mrvacommander/
docker-compose -f docker-compose-demo.yml down --volumes --remove-orphans
docker-compose -f docker-compose-demo.yml up --build
#+END_SRC
* Database Aquisition
General database aquisition is beyond the scope of this document as it is very specific
to an organization's environment.
For this demo, the data is preloaded via container. To inspect it:
#+BEGIN_SRC sh
# On host, run
docker exec -it dbstore /bin/bash
# In the container
ls -la /data/mrvacommander/dbstore-data/qldb
# Or in one step
docker exec -it dbstore ls -la /data/mrvacommander/dbstore-data/qldb
#+END_SRC
Here we use a small sample of an example for open-source
repositories, 23 in all.
* Repository Selection
When using all of the MRVA system, we select a small subset of repositories
available to you in [[*Database Aquisition][Database Aquisition]]. For this demo we include a small
collection -- 23 repositories -- and here we further narrow the selection to 12.
The full list
#+BEGIN_SRC text
ls -1 /data/dbstore-data/qldb/
'BoomingTech$Piccoloctsj6d7177.zip'
'KhronosGroup$OpenXR-SDKctsj984ee6.zip'
'OpenRCT2$OpenRCT2ctsj975d7c.zip'
'StanfordLegion$legionctsj39cbe4.zip'
'USCiLab$cerealctsj264953.zip'
'WinMerge$winmergectsj101305.zip'
'draios$sysdigctsj12c02d.zip'
'gildor2$UEViewerctsjfefdd8.zip'
'git-for-windows$gitctsjb7c2bd.zip'
'google$orbitctsj9bbeaf.zip'
'libfuse$libfusectsj7a66a4.zip'
'luigirizzo$netmapctsj6417fa.zip'
'mawww$kakounectsjc54fab.zip'
'microsoft$node-native-keymapctsj4cc9a2.zip'
'nem0$LumixEnginectsjfab756.zip'
'pocoproject$pococtsj26b932.zip'
'quickfix$quickfixctsjebfd13.zip'
'rui314$moldctsjfec16a.zip'
'swig$swigctsj78bcd3.zip'
'tdlib$telegram-bot-apictsj8529d9.zip'
'timescale$timescaledbctsjf617cf.zip'
'xoreaxeaxeax$movfuscatorctsj8f7e5b.zip'
'xrootd$xrootdctsje4b745.zip'
#+END_SRC
The selection of 12 repositories, from an initial collection of 6000 was made
using a collection of Python/pandas scripts made for the purpose, the [[https://github.com/hohn/mrvacommander/blob/hohn-0.1.21.2-improve-structure-and-docs/client/qldbtools/README.md#installation][qldbtools]]
package. The resulting selection, in the format expected by the VS Code
extension, follows.
#+BEGIN_SRC text
cat /data/qldbtools/scratch/vscode-selection.json
{
"version": 1,
"databases": {
"variantAnalysis": {
"repositoryLists": [
{
"name": "mirva-list",
"repositories": [
"xoreaxeaxeax/movfuscatorctsj8f7e5b",
"microsoft/node-native-keymapctsj4cc9a2",
"BoomingTech/Piccoloctsj6d7177",
"USCiLab/cerealctsj264953",
"KhronosGroup/OpenXR-SDKctsj984ee6",
"tdlib/telegram-bot-apictsj8529d9",
"WinMerge/winmergectsj101305",
"timescale/timescaledbctsjf617cf",
"pocoproject/pococtsj26b932",
"quickfix/quickfixctsjebfd13",
"libfuse/libfusectsj7a66a4"
]
}
],
"owners": [],
"repositories": []
}
},
"selected": {
"kind": "variantAnalysisUserDefinedList",
"listName": "mirva-list"
}
#+END_SRC
This selection is deceptively simple. For a full explanation, see [[file:cli-end-to-end-detailed.org::*Repository Selection][Repository
Selection]] in the detailed version of this document.
** Optional: The meaning of the names
The repository names all end with =ctsj= followed by 6 hex digits like
=ctsj4cc9a2=.
The information critial for selection of databases are the columns
1. owner
2. name
3. language
4. "sha"
5. "cliVersion"
6. "creationTime"
There are others that may be useful, but they are not strictly required.
The critical ones deserve more explanation:
1. "sha": The =git= commit SHA of the repository the CodeQL database was
created from. Required to distinguish query results over the evolution of
a code base.
2. "cliVersion": The version of the CodeQL CLI used to create the database.
Required to identify advances/regressions originating from the CodeQL binary.
3. "creationTime": The time the database was created. Required (or at least
very handy) for following the evolution of query results over time.
There is a computed column, CID. The CID column combines
- cliVersion
- creationTime
- language
- sha
into a single 6-character string via hashing. Together with (owner, repo) it
provides a unique index for every DB.
For this document, we simply use a pseudo-random selection of 11 databases via
#+BEGIN_SRC sh
./bin/mc-db-generate-selection -n 11 \
scratch/vscode-selection.json \
scratch/gh-mrva-selection.json \
< scratch/db-info-3.csv
#+END_SRC
Note that these use pseudo-random numbers, so the selection is in fact
deterministic.
* Starting the server
Clone the full repository before continuing:
#+BEGIN_SRC sh
mkdir -p ~/work-gh/mrva/
git clone git@github.com:hohn/mrvacommander.git
#+END_SRC
Make sure Docker is installed and running.
With docker-compose set up and this repository cloned, we just run
#+BEGIN_SRC sh
cd ~/work-gh/mrva/mrvacommander
docker-compose -f docker-compose-demo.yml up -d
#+END_SRC
and wait until the log output no longer changes.
Should look like
#+BEGIN_SRC text
docker-compose -f docker-compose-demo.yml up -d
[+] Running 27/6
✔ dbstore Pulled 1.1s
✔ artifactstore Pulled 1.1s
✔ mrvadata 3 layers [⣿⣿⣿] 0B/0B Pulled 263.8s
✔ server 2 layers [⣿⣿] 0B/0B Pulled 25.2s
✔ agent 5 layers [⣿⣿⣿⣿⣿] 0B/0B Pulled 24.9s
✔ client-qldbtools 11 layers [⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿] 0B/0B Pulled 20.8s
[+] Running 9/9
✔ Container mrvadata Started 0.3s
✔ Container mrvacommander-client-qldbtools-1 Started 0.3s
✔ Container mrvacommander-client-ghmrva-1 Running 0.0s
✔ Container mrvacommander-code-server-1 Running 0.0s
✔ Container artifactstore Running 0.0s
✔ Container rabbitmq Running 0.0s
✔ Container dbstore Started 0.4s
✔ Container agent Started 0.5s
✔ Container server Started 0.5s
#+END_SRC
The content is prepopulated in the =dbstore= container.
** Optional: Inspect the Backing Store
As completely optional step, you can inspect the backing store:
#+BEGIN_SRC sh
docker exec -it dbstore /bin/bash
ls /data/qldb/
# 'BoomingTech$Piccoloctsj6d7177.zip' 'mawww$kakounectsjc54fab.zip'
# 'KhronosGroup$OpenXR-SDKctsj984ee6.zip' 'microsoft$node-native-keymapctsj4cc9a2.zip'
# ...
#+END_SRC
** Optional: Inspect the MinIO DB
Another completely optional step, you can inspect the minio DB contents if you
have the minio cli installed:
#+BEGIN_SRC sh
# Configuration
MINIO_ALIAS="qldbminio"
MINIO_URL="http://localhost:9000"
MINIO_ROOT_USER="user"
MINIO_ROOT_PASSWORD="mmusty8432"
QL_DB_BUCKET_NAME="qldb"
# Check for MinIO client
if ! command -v mc &> /dev/null
then
echo "MinIO client (mc) not found."
fi
# Configure MinIO client
mc alias set $MINIO_ALIAS $MINIO_URL $MINIO_ROOT_USER $MINIO_ROOT_PASSWORD
# Show contents
mc ls qldbminio/qldb
#+END_SRC
* Running the gh-mrva command-line client
The first run uses the test query to verify basic functionality, but it returns
no results.
** Run MRVA from command line
# From ~/work-gh/mrva/gh-mrva
1. Check mrva cli
#+BEGIN_SRC sh
docker exec -it mrvacommander-client-ghmrva-1 /usr/local/bin/gh-mrva -h
#+END_SRC
2. Set up the configuration
#+BEGIN_SRC sh
docker exec -i mrvacommander-client-ghmrva-1 \
sh -c 'mkdir -p /root/.config/gh-mrva/'
cat | docker exec -i mrvacommander-client-ghmrva-1 \
sh -c 'cat > /root/.config/gh-mrva/config.yml' <<eof
codeql_path: not-used/$HOME/work-gh
controller: not-used/mirva-controller
list_file: /root/work-gh/mrva/gh-mrva/gh-mrva-selection.json
eof
# check:
docker exec -i mrvacommander-client-ghmrva-1 ls /root/.config/gh-mrva/config.yml
docker exec -i mrvacommander-client-ghmrva-1 cat /root/.config/gh-mrva/config.yml
#+END_SRC
3. Provide the repository list file
#+BEGIN_SRC sh
docker exec -i mrvacommander-client-ghmrva-1 \
sh -c 'mkdir -p /root/work-gh/mrva/gh-mrva'
cat | docker exec -i mrvacommander-client-ghmrva-1 \
sh -c 'cat > /root/work-gh/mrva/gh-mrva/gh-mrva-selection.json' <<eof
{
"mirva-list": [
"xoreaxeaxeax/movfuscatorctsj8f7e5b",
"microsoft/node-native-keymapctsj4cc9a2",
"BoomingTech/Piccoloctsj6d7177",
"USCiLab/cerealctsj264953",
"KhronosGroup/OpenXR-SDKctsj984ee6",
"tdlib/telegram-bot-apictsj8529d9",
"WinMerge/winmergectsj101305",
"timescale/timescaledbctsjf617cf",
"pocoproject/pococtsj26b932",
"quickfix/quickfixctsjebfd13",
"libfuse/libfusectsj7a66a4"
]
}
eof
#+END_SRC
4. Provide the CodeQL query
#+BEGIN_SRC sh
cat | docker exec -i mrvacommander-client-ghmrva-1 \
sh -c 'cat > /root/work-gh/mrva/gh-mrva/FlatBuffersFunc.ql' <<eof
/**
,* @name pickfun
,* @description pick function from FlatBuffers
,* @kind problem
,* @id cpp-flatbuffer-func
,* @problem.severity warning
,*/
import cpp
from Function f
where
f.getName() = "MakeBinaryRegion" or
f.getName() = "microprotocols_add"
select f, "definition of MakeBinaryRegion"
eof
#+END_SRC
5. Submit the mrva job
#+BEGIN_SRC sh
docker exec -i mrvacommander-client-ghmrva-1 /usr/local/bin/gh-mrva \
submit --language cpp --session mirva-session-1360 \
--list mirva-list \
--query /root/work-gh/mrva/gh-mrva/FlatBuffersFunc.ql
#+END_SRC
6. Check the status
#+BEGIN_SRC sh
# Check the status
docker exec -i mrvacommander-client-ghmrva-1 /usr/local/bin/gh-mrva \
status --session mirva-session-1360
#+END_SRC
7. Download the sarif files, optionally also get databases. For the current
query / database combination there are zero result hence no downloads.
#+BEGIN_SRC sh
docker exec -i mrvacommander-client-ghmrva-1 /usr/local/bin/gh-mrva \
download --session mirva-session-1360 \
--download-dbs \
--output-dir mirva-session-1360
#+END_SRC
** TODO Write query that has some results
XX:
In this case, the trivial =alu_mul=,
alu_mul for https://github.com/xoreaxeaxeax/movfuscator/blob/master/movfuscator/movfuscator.c
#+BEGIN_SRC java
/**
,* @name findalu
,* @description find calls to a function
,* @kind problem
,* @id cpp-call
,* @problem.severity warning
,*/
import cpp
from FunctionCall fc
where
fc.getTarget().getName() = "alu_mul"
select fc, "call of alu_mul"
#+END_SRC
Repeat the submit steps with this query
1. [X] --
2. [X] --
3. [ ] Provide the CodeQL query
#+BEGIN_SRC sh
cat | docker exec -i mrvacommander-client-ghmrva-1 \
sh -c 'cat > /root/work-gh/mrva/gh-mrva/Alu_Mul.ql' <<eof
/**
,* @name findalu
,* @description find calls to a function
,* @kind problem
,* @id cpp-call
,* @problem.severity warning
,*/
import cpp
from FunctionCall fc
where
fc.getTarget().getName() = "alu_mul"
select fc, "call of alu_mul"
eof
#+END_SRC
4. [-] Submit the mrva job
#+BEGIN_SRC sh
docker exec -i mrvacommander-client-ghmrva-1 /usr/local/bin/gh-mrva \
submit --language cpp --session mirva-session-1490 \
--list mirva-list \
--query /root/work-gh/mrva/gh-mrva/Alu_Mul.ql
#+END_SRC
- [X] XX:
server | 2024/09/27 20:03:16 DEBUG Processed request info location="{Key:3 Bucket:packs}" language=cpp
server | 2024/09/27 20:03:16 WARN No repositories found for analysis
server | 2024/09/27 20:03:16 DEBUG Queueing analysis jobs count=0
server | 2024/09/27 20:03:16 DEBUG Forming and sending response for submitted analysis job id=3
NO: debug in the server container
#+BEGIN_SRC sh
docker exec -it server /bin/bash
apt-get update
apt-get install delve
replace
ENTRYPOINT ["./mrva_server"]
CMD ["--mode=container"]
#+END_SRC
- [ ] XX:
The dbstore is empty -- see http://localhost:9001/browser
must populate it properly, then save the image.
5. [ ] Check the status
#+BEGIN_SRC sh
docker exec -i mrvacommander-client-ghmrva-1 /usr/local/bin/gh-mrva \
status --session mirva-session-1490
#+END_SRC
This time we have results
#+BEGIN_SRC text
...
Run name: mirva-session-1490
Status: succeeded
Total runs: 1
Total successful scans: 11
Total failed scans: 0
Total skipped repositories: 0
Total skipped repositories due to access mismatch: 0
Total skipped repositories due to not found: 0
Total skipped repositories due to no database: 0
Total skipped repositories due to over limit: 0
Total repositories with findings: 7
Total findings: 618
Repositories with findings:
quickfix/quickfixctsjebfd13 (cpp-fprintf-call): 5
libfuse/libfusectsj7a66a4 (cpp-fprintf-call): 146
xoreaxeaxeax/movfuscatorctsj8f7e5b (cpp-fprintf-call): 80
pocoproject/pococtsj26b932 (cpp-fprintf-call): 17
BoomingTech/Piccoloctsj6d7177 (cpp-fprintf-call): 10
tdlib/telegram-bot-apictsj8529d9 (cpp-fprintf-call): 247
WinMerge/winmergectsj101305 (cpp-fprintf-call): 113
#+END_SRC
6. [ ] Download the sarif files, optionally also get databases.
#+BEGIN_SRC sh
docker exec -i mrvacommander-client-ghmrva-1 /usr/local/bin/gh-mrva \
download --session mirva-session-1490 \
--download-dbs \
--output-dir mirva-session-1490
# And list them:
\ls -la *1490*
#+END_SRC
7. [ ] Use the [[https://marketplace.visualstudio.com/items?itemName=MS-SarifVSCode.sarif-viewer][SARIF Viewer]] plugin in VS Code to open and review the results.
Prepare the source directory so the viewer can be pointed at it
#+BEGIN_SRC sh
cd ~/work-gh/mrva/gh-mrva/mirva-session-1490
unzip -qd BoomingTech_Piccoloctsj6d7177_1_db BoomingTech_Piccoloctsj6d7177_1_db.zip
cd BoomingTech_Piccoloctsj6d7177_1_db/codeql_db/
unzip -qd src src.zip
#+END_SRC
Use the viewer
#+BEGIN_SRC sh
code BoomingTech_Piccoloctsj6d7177_1.sarif
# For lauxlib.c, point the source viewer to
find ~/work-gh/mrva/gh-mrva/mirva-session-1490/BoomingTech_Piccoloctsj6d7177_1_db/codeql_db/src/home/runner/work/bulk-builder/bulk-builder -name lauxlib.c
# Here: ~/work-gh/mrva/gh-mrva/mirva-session-1490/BoomingTech_Piccoloctsj6d7177_1_db/codeql_db/src/home/runner/work/bulk-builder/bulk-builder/engine/3rdparty/lua-5.4.4/lauxlib.c
#+END_SRC
8. [ ] (optional) Large result sets are more easily filtered via
dataframes or spreadsheets. Convert the SARIF to CSV if needed; see [[https://github.com/hohn/sarif-cli/][sarif-cli]].
* Running the CodeQL VS Code plugin
- [ ] XX: include the *custom* codeql plugin in the container.
* Ending the session
Shut down docker via
#+BEGIN_SRC sh
cd ~/work-gh/mrva/mrvacommander
docker-compose -f docker-compose-demo.yml down
#+END_SRC
* Footnotes
[fn:1]The =csvkit= can be installed into the same Python virtual environment as
the =qldbtools=.
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