sorer 0.1.0

A schema on read file parser
Documentation
# SoRer
`SoRer`, short for schema-on-read-er, is a program that can read files in
the SoR format and build columnar dataframes based on a dynamically
inferred schema.

`SoRer` was built with speed and memory efficiency in mind so it can handle
processing files that are too large to fit into RAM.

On our 2 year old desktop computer with a SATA SSD (meaning our testing is
likely near being bottlenecked by ssd read speeds) and 4 cores (4 threads),
`SoRer` can parse at ~`400 MB/s` on a large test file with 8 columns, two of
each data type with random values (which can be generated by running
`cargo run --release --bin generate` (warning don't do this inside of Docker,
you must install rust if you want to do this due to file i/o overhead when
using Docker). In a best case scenario, on a large file with 3 columns of
random bools, it can parse at over `700 MB/s`

![Perf](perf.png)

# Usage
## Building SoRer
`SoRer` can be built on any computer by running the command: `make build`
from the root of this repository. This builds a Docker image tagged as `sorer`.
It also builds the executable for `sorer`, located at
`/sorer/target/release/sorer` and copies over the executable to the current directory.

Tests can be ran by running the command `make test`. The program can be ran
against a small test file named `sor.txt` by running the command: `make run`.

Note that ideally the best way to run our program is bare metal due to 
overhead for using Docker (especially on Windows or Mac). You can do that by
installing `rust` by running the following command:

`curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh`

Follow the printed instructions to source the cargo environment variables after
installing.

Then build `sorer` by running `cargo build --release`. You may test the
program after installing `rust` by running `cargo test`. Documentation may 
be built by running `cargo doc --no-deps --open`.

## SoRer Documentation

Documentation can be built by running the command `make doc`. This builds the
documentation and copies it to `./doc/` on the host filesystem in this directory.
This documentation can be viewed by opening `./doc/sorer/index.html` in
your broswer.

## Running SoRer
`SoRer` is ran as a command line tool that prints its results to `stdout`.

The command line arguments are summarized in the below table

| argument  | value type  | required?  | description  |
|:-:|:-:|---|---|
| -f   | \<string\>  | yes  | path to SoR file  |
| -from  | \<uint\>  | no  | starting position in file (in bytes)  |
| -len  | \<uint\>  |  no | number of bytes to read  |
| -print_col_type  | \<uint\>  | depends  | print the type of a column: BOOL, INT, FLOAT, STRING |
| -print_col_idx  | \<uint\> \<uint\>  | depends  | the first argument is the column, the second is the offset   |
| -is_missing_idx  | \<uint\> \<uint\>  | depends  | is there a missing field in the specified column offset  |

When `<val>` in `-from <val>` is greater than 0, then the file is read
starting from the first complete line after `<val>`.

When `<val>` in `-len <val>` is greater than 0, then the file is read
up until the last complete line.

After running `make build`, running `make bash` will mount the current 
the current directory to the docker container and start bash. If you
want to test any large files, you should do `make build` first, then copy
the files into this directory, then run `make bash`. Once you're in bash,
you can interact with `sorer` as usual:

E.g.: `./sorer -f sor.txt -from 0 -len 100000 -print_col_idx 0 0`


# SoR Files
A SoR file is stored as plain text. Files consists of a sequence of rows,
each row must be separated by the newline character, "\n".
Each row is a sequence of fields, each field starting with "<" and ending
with ">". Spaces around delimiters are ignored.

# SoR Fields
A field can be either missing a value, or contain a value of one of four
 SoR types:
- `String`
- `Float`
- `Integer`
- `Bool`

|Type   |Allowed values   |
|:-:|:-:|
| String  | Either as a sequences of characters without spaces or as a double quote delimited sequence of characters with spaces. Line breaks are not allowed in Strings. Can't be longer than 255 characters.  | Float  | Any C++ float    |
| Integer  | Any C++ integer, ie a sequence of digits with an optional leading sign (must not be separated by whitespace)   |
|bool   | {1, 0}  |
| Missing (aka Null)  | must be empty, ie "<>"  |


## Valid Examples of SoR Fields

The following is an example of a row with four fields:

`< 1 > < hi >< +2.2 >   < " bye ">`
 
The following is an example of a row with explicit missing fields:
 
`<1> <bye> <> <>`
 
The following is also valid:
 
`<> <> <> <>`

## Invalid Examples of SoR Fields

```c
<1. 2>       // space after dot

<bye world>  // string with spaces and without quotes

<+ 1>        // space after the +
```

NOTE: If a SoR file contains an invalid field, the row will be discarded
 for both schema inference and data parsing.

# Schema Inference
The schema that `SoRer` generates depends on the data types contained in
the row with the most number of fields in the first 500 rows (or 
the whole file, whichever comes first), irregardless of
the `-from` command line argument. The data type chosen for
each column in the schema depends on the precedence of the data type. 
Based on this data type precedence, a schema is inferred and then applied
to all fields in that column.

The Data Type precedence is as follows:
1. `String`
2. `Float`
3. `Integer`
4. `Bool`

This means that if any value is a `String`, the whole column is parsed
into a `String` type. Otherwise, if any of the values is a `Float`, then the
column is of `Float` type. Otherwise, if you find a value with a sign or a
value larger than `1`, then the column is `Integer`. Otherwise the column
is a `Bool` type.

## Rows that don't match the schema
If a row that doesn't match the schema is found after the schema is
inferred (meaning after the first 500 lines), then the row is discarded.
An example is if a schema is parsed as `<int> <int>`,  but a line coming
after the first 500 has `<string> <int>`, then it will be discarded.

**Note** however, that it is valid for two rows in the same file to have a
different number of fields and still be considered to match the schema. 
For rows with more fields than the schema, the extra fields will be 
discarded but the row will still be parsed as long as the other fields
match the schema.
 
E.g. The schema: `<int> <bool>` and a row: `<12> <0> <discarded>`
parses to `<12><0>`
 
 
If a row has less fields without explicit missing fields (i.e. "<>"), aka
implicit missing fields, `SoRer` will attempt to parse the fields 
according to the schema and fill in explicit missing fields at the end
of the row until it matches the number of fields in the schema.
 
E.g. The schema: `<int> <bool> <string>` and a row: `<12>`
parses to `<12><><>`