changes to readme

Author: jacobmsft

README.md

@@ -4,7 +4,7 @@
 > Current version of CodeQL only works for interpreted languages. We will add compiled languages support on future versions.
 
 CodeQL Container is a project aimed at making it easier to start using CodeQL (https://github.com/github/codeql). This project
-contains a Docker file which builds a container with the latest version of codeql-cli and codeql queries precompiled. 
+contains a Docker file which builds a container, with the latest version of codeql-cli and codeql queries precompiled. 
 It also contains scripts to keep the toolchain in the container updated. You can use this container to:
 
 * Start using codeql-cli and run queries on your projects without installing it on your local machine.
@@ -17,47 +17,60 @@ We shall continue to add more features and would be happy to accept contribution
 
 #### Downloading a pre-built container
 We keep updating the docker image periodically and uploading it to the Microsoft Container Registry at: mcr.microsoft.com/codeql/codeql-container.
-You can run the image by running the command:
+You can pull the image by running the command:
 ```
-$ docker run --rm mcr.microsoft.com/codeql/codeql-container
+$ docker pull mcr.microsoft.com/codeql/codeql-container
 ```
 
 If you want to analyze a particular source directory with codeql, run the container as:
 ```
 $ docker run --rm --name codeql-container mcr.microsoft.com/codeql/codeql-container -v /dir/to/analyze:/opt/src -v /dir/for/results:/opt/results -e CODEQL_CLI_ARGS=<query run...>
 ```
-where /dir/to/analyze contains the source files that have to be analyzed, and /dir/for/results is where the result output 
-needs to be stored, and you can specify QL_PACKS environment variable for specific QL packs to be run on the provided code.
-For more information on CodeQL and QL packs, please visit https://www.github.com/github/codeql.
-CODEQL_CLI_ARGS are the arguments that will be directly passed on to the codeql-cli. Some examples of CODEQL_CLI_ARGS are:
+
+where /dir/to/analyze contains the source files that has to be analyzed, and /dir/for/results is where the result output 
+needs to be stored.
+CODEQL_CLI_ARGS contents will be directly passed on to the codeql-cli. Some examples of CODEQL_CLI_ARGS are:
+
 ```
 CODEQL_CLI_ARGS = database create /opt/src/source_db
 ```
-**Note:** If you map your source volume to some other mountpoint other than /opt/src, you will have to make the corresponding changes
-in the CODEQL_CLI_ARGS.
+
+> **Note:** If you map your source volume to some other mount point other than /opt/src, you will have to make the corresponding changes
+> in the CODEQL_CLI_ARGS.
 
 There are some additional docker environment variables that you can specify to control the execution of the container:
-    * CHECK_LATEST_CODEQL_CLI - If there is a newer version of codeql-cli, download and install it
-    * CHECK_LATEST_QUERIES - if there is are updates to the codeql queries repo, download and use it
-    * PRECOMPILE_QUERIES - If we downloaded new queries, precompile all new query packs (query execution will be faster)
-        WARNING: Precompiling query packs might take a few hours, depending on speed of your machine and the CPU/Memory limits (if any) 
-        you have placed on the container.
-
-Since codeql first creates a database of the code representation, and then analyzes the db for issues, we need a few commands to 
-analyze a source code repo. 
+* CHECK_LATEST_CODEQL_CLI - If there is a newer version of codeql-cli, download and install it
+* CHECK_LATEST_QUERIES - if there is are updates to the codeql queries repo, download and use it
+* PRECOMPILE_QUERIES - If we downloaded new queries, precompile all new query packs (query execution will be faster)
+> WARNING: Precompiling query packs might take a few hours, depending on speed of your machine and the CPU/Memory limits (if any) 
+> you have placed on the container.
+
+Since codeql first creates a database of the code representation, and then analyzes the said db for issues, we need to run couple commands to 
+analyze a source code project. 
 For example, if you want to analyze a python project source code placed in /dir/to/analyze (or C:\dir\to\analyze for example, in windows), 
 to analyze and get a sarif result file, you will have to run:
-$ docker run --rm --name codeql-container mcr.microsoft.com/codeql/codeql-container -v /dir/to/analyze:/opt/src -v /dir/for/results:/opt/results -e CODEQL_CLI_ARGS="database create --language=python /opt/src/source_db"
-$ docker run --rm --name codeql-container mcr.microsoft.com/codeql/codeql-container -v /dir/to/analyze:/opt/src -v /dir/for/results:/opt/results -e CODEQL_CLI_ARGS="database analyze --format=sarifv2 --output=/opt/results/issues.sarif /opt/src/source_db
 
 ```
+$ docker run --rm --name codeql-container codeql-container -v /dir/to/analyze:/opt/src -v /dir/for/results:/opt/results -e CODEQL_CLI_ARGS="database create --language=python /opt/src/source_db"
+$ docker run --rm --name codeql-container codeql-container -v /dir/to/analyze:/opt/src -v /dir/for/results:/opt/results -e CODEQL_CLI_ARGS="database upgrade source_db"
+$ docker run --rm --name codeql-container codeql-container -v /dir/to/analyze:/opt/src -v /dir/for/results:/opt/results -e CODEQL_CLI_ARGS="database analyze source_db --output=/opt/results/issues.sarif /opt/src/source_db python-security-and-quality.qls"
+```
+
+This will run the python-security-and-quality.qls query pack on the provided source code and output the results to /path/to/results/issues.sarif on the local machine.
+> [The second step above is only required if the queries are newer than the one that codeql-cli recognizes.]
+ 
 This command will run all the ql packs related to security and output the results to the results folder.
 
+For more information on CodeQL and QL packs, please visit https://www.github.com/github/codeql.
+
 #### Building the container
 Building the container should be pretty straightforward.
+
+```
 git clone ...
 cd src
 docker build . -f Dockerfile -t codeql-container
+```
 
 # Contributing