add README

Author: stevekm

scripts/README.md

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+# Helper Scripts
+
+## Dumping Database Fixtures
+
+In order to dump JSON copies of database fixtures, you should first have loaded a copy of a production database backup into your Beagle PostgreSQL database instance.
+
+The included `dump_db_fixtures.py` script can be used to some types of fixtures. See `dump_db_fixtures.py -h` for the most up to date details.
+
+### Dump Requests
+
+A request can be dumped with `dump_db_fixtures.py request <request_id>`. This will output a JSON for the File entries associated with the request, and a JSON for the FileMetadata entries. Use the `--santize` flag to replace personal information in the fixtures (e.g. people's names and email addresses) with fake ones. Currently, `--sanitize`
+
+Example:
+
+```
+$ ./dump_db_fixtures.py request 09603_I --sanitize
+
+$ ls
+09603_I.file.json
+09603_I.filemetadata.json
+```
+
+- NOTE: `dump_db_fixtures.py` should be run from your Beagle dev environment since it requires Python 3 + Django. If you installed with the `Makefile` in the `beagle` root directory, from there you can just use `make bash` to load your dev instance environment to run the script with.
+
+## Sanitize Fixtures
+
+Fixtures for use in the repo should be further sanitized to remove sample ID's and replace CMO ID's.
+
+Some easy helper scripts have been included for this purpose.
+
+Use the script `get_fields_to_sanitize.sh` to print out a list of all recognized CMO ID's and sample ID's in the JSON you generated with `dump_db_fixtures.py`
+
+```
+$ ./get_fields_to_sanitize.sh 09603_I.filemetadata.json
+# a list of id's
+```
+
+Use the list of ID's that are printed out to create a `patterns.tsv` file in this same directory. This will be used for the `sanitize.sh` script later. The `patterns.tsv` file should be formatted like this:
+
+```
+old_pattern1	new_pattern1
+old_pattern2	new_pattern2
+```
+
+A quick & easy way to do this is to utilize both Excel and a raw text editor (`nano`, Atom, Sublime, etc.). You can copy the terminal output from `get_fields_to_sanitize.sh` into Excel, then in the adjacent column fill in dummy identifiers such as `Sample1`, `Sample2`, etc.. For CMO ID's, you can generate fake ones with the included `generate_cmo_id.py` script. Once you have two columns, simple highlight them in Excel (just the two columns, not the entire sheet) and paste them into `nano`/Atom/Sublime/etc. and they should be entered as tab delimited text which you can save with the filename of `patterns.tsv`
+
+- TODO: write a script to do this instead
+
+Once `patterns.tsv` is present, you can run the `sanitize.sh` script on your JSON to replace all the old patterns with new ones.
+
+
+```
+./sanitize.sh 09603_I.filemetadata.json
+```
+
+For good measure, double check the contents of the JSON to verify that it looks correct before commiting it. The JSON should be moved to the appropriate `fixtures` directory. 

scripts/example.patterns.tsv

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+C-ABCDEF-P001-d	Sample1
+C-FB3D87	C-47D8BA