# -*- coding: utf-8 -*-

* End-to-end example of CLI use
  This document describes a complete cycle of the MRVA workflow.  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

* 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/dbstore-data/
    ls  /data/dbstore-data/qldb/ | wc -l
  #+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.

  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
   1. Install mrva cli
      #+BEGIN_SRC sh 
        mkdir -p ~/work-gh/mrva && cd ~/work-gh/mrva
        git clone https://github.com/hohn/gh-mrva.git
        cd ~/work-gh/mrva/gh-mrva && git checkout mrvacommander-end-to-end

        # Build it
        go mod edit -replace="github.com/GitHubSecurityLab/gh-mrva=$HOME/work-gh/mrva/gh-mrva"
        go build .

        # Sanity check
        ./gh-mrva -h
      #+END_SRC

   2. Set up the configuration
      #+BEGIN_SRC sh 
        mkdir -p ~/.config/gh-mrva
        cat > ~/.config/gh-mrva/config.yml <<eof
        # The following options are supported
        # codeql_path: Path to CodeQL distribution (checkout of codeql repo)
        # controller: NWO of the MRVA controller to use.  Not used here.
        # list_file: Path to the JSON file containing the target repos

        # XX:
        codeql_path: $HOME/work-gh/not-used
        controller: not-used/mirva-controller
        list_file: $HOME/work-gh/mrva/gh-mrva/gh-mrva-selection.json
        eof
      #+END_SRC

   3. Submit the mrva job
      #+BEGIN_SRC sh 
        cp ~/work-gh/mrva/mrvacommander/client/qldbtools/scratch/gh-mrva-selection.json \
           ~/work-gh/mrva/gh-mrva/gh-mrva-selection.json 

        cd ~/work-gh/mrva/gh-mrva/
        ./gh-mrva submit --language cpp --session mirva-session-1360    \
                  --list mirva-list                                     \
                  --query ~/work-gh/mrva/gh-mrva/FlatBuffersFunc.ql
      #+END_SRC

   4. Check the status
      #+BEGIN_SRC sh 
        cd ~/work-gh/mrva/gh-mrva/

        # Check the status
        ./gh-mrva status --session mirva-session-1360
      #+END_SRC

   5. Download the sarif files, optionally also get databases.  For the current
      query / database combination there are zero result hence no downloads.
      #+BEGIN_SRC sh 
        cd ~/work-gh/mrva/gh-mrva/
        # Just download the sarif files
        ./gh-mrva download --session mirva-session-1360 \
                  --output-dir mirva-session-1360

        # Download the sarif files and CodeQL dbs
        ./gh-mrva download --session mirva-session-1360 \
                  --download-dbs \
                  --output-dir mirva-session-1360
      #+END_SRC

** Write query that has some results
   First, get the list of paths corresponding to the previously selected
   databases. 
   #+BEGIN_SRC sh 
     cd ~/work-gh/mrva/mrvacommander/client/qldbtools 
     ./bin/mc-rows-from-mrva-list scratch/gh-mrva-selection.json \
                                  scratch/db-info-3.csv > scratch/selection-full-info
     csvcut -c path scratch/selection-full-info 
   #+END_SRC

   Use one of these databases to write a query.  It need not produce results.  
   #+BEGIN_SRC sh 
     cd ~/work-gh/mrva/gh-mrva/
     code gh-mrva.code-workspace
   #+END_SRC
   In this case, the trivial =findPrintf=:
   #+BEGIN_SRC java
     /**
      ,* @name findPrintf
      ,* @description find calls to plain fprintf
      ,* @kind problem
      ,* @id cpp-fprintf-call
      ,* @problem.severity warning
      ,*/

     import cpp

     from FunctionCall fc
     where
       fc.getTarget().getName() = "fprintf"
     select fc, "call of fprintf"
   #+END_SRC


   Repeat the submit steps with this query
   1. -- 
   2. --
   3. Submit the mrva job
      #+BEGIN_SRC sh 
        cp ~/work-gh/mrva/mrvacommander/client/qldbtools/scratch/gh-mrva-selection.json \
           ~/work-gh/mrva/gh-mrva/gh-mrva-selection.json 

        cd ~/work-gh/mrva/gh-mrva/
        ./gh-mrva submit --language cpp --session mirva-session-1480    \
                  --list mirva-list                                     \
                  --query ~/work-gh/mrva/gh-mrva/Fprintf.ql
      #+END_SRC
   4. Check the status
      #+BEGIN_SRC sh 
        cd ~/work-gh/mrva/gh-mrva/
        ./gh-mrva status --session mirva-session-1480
      #+END_SRC

      This time we have results
      #+BEGIN_SRC text
        ...
        Run name: mirva-session-1480
        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
   5. Download the sarif files, optionally also get databases.  
      #+BEGIN_SRC sh 
        cd ~/work-gh/mrva/gh-mrva/
        # Just download the sarif files
        ./gh-mrva download --session mirva-session-1480 \
                  --output-dir mirva-session-1480

        # Download the sarif files and CodeQL dbs
        ./gh-mrva download --session mirva-session-1480 \
                  --download-dbs \
                  --output-dir mirva-session-1480

        # And list them:
        \ls -la *1480*
        -rwxr-xr-x@  1 hohn  staff    1915857 Aug 16 14:10 BoomingTech_Piccoloctsj6d7177_1.sarif
        drwxr-xr-x@  3 hohn  staff         96 Aug 16 14:15 BoomingTech_Piccoloctsj6d7177_1_db
        -rwxr-xr-x@  1 hohn  staff   89857056 Aug 16 14:11 BoomingTech_Piccoloctsj6d7177_1_db.zip
        -rwxr-xr-x@  1 hohn  staff    3105663 Aug 16 14:10 WinMerge_winmergectsj101305_1.sarif
        -rwxr-xr-x@  1 hohn  staff  227812131 Aug 16 14:12 WinMerge_winmergectsj101305_1_db.zip
        -rwxr-xr-x@  1 hohn  staff     193976 Aug 16 14:10 libfuse_libfusectsj7a66a4_1.sarif
        -rwxr-xr-x@  1 hohn  staff   12930693 Aug 16 14:10 libfuse_libfusectsj7a66a4_1_db.zip
        -rwxr-xr-x@  1 hohn  staff    1240694 Aug 16 14:10 pocoproject_pococtsj26b932_1.sarif
        -rwxr-xr-x@  1 hohn  staff  158924920 Aug 16 14:12 pocoproject_pococtsj26b932_1_db.zip
        -rwxr-xr-x@  1 hohn  staff     888494 Aug 16 14:10 quickfix_quickfixctsjebfd13_1.sarif
        -rwxr-xr-x@  1 hohn  staff   75023303 Aug 16 14:11 quickfix_quickfixctsjebfd13_1_db.zip
        -rwxr-xr-x@  1 hohn  staff    1487363 Aug 16 14:10 tdlib_telegram-bot-apictsj8529d9_1.sarif
        -rwxr-xr-x@  1 hohn  staff  373477635 Aug 16 14:14 tdlib_telegram-bot-apictsj8529d9_1_db.zip
        -rwxr-xr-x@  1 hohn  staff     103657 Aug 16 14:10 xoreaxeaxeax_movfuscatorctsj8f7e5b_1.sarif
        -rwxr-xr-x@  1 hohn  staff    9464225 Aug 16 14:10 xoreaxeaxeax_movfuscatorctsj8f7e5b_1_db.zip
      #+END_SRC

   6. 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-1480

        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-1480/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-1480/BoomingTech_Piccoloctsj6d7177_1_db/codeql_db/src/home/runner/work/bulk-builder/bulk-builder/engine/3rdparty/lua-5.4.4/lauxlib.c
      #+END_SRC

   7. (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]].

   


* Footnotes
[fn:1]The =csvkit= can be installed into the same Python virtual environment as
the =qldbtools=.
