General Layout
An Instruction JSON file contains a series of instructions - declarations of what should go into a specific Intermediate File (see IFLs, the consumers of the files, for more details).
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Above is an example of the structure of an instruction file. Here the file specifies three tables, each referencing a part of the overall data structure. As you can see, each Table has a series of Columns, where the column objects specify how to interpret the input files to generate them.
File Header
source
Source is the source file (or folder) for the table.
destination
Destination is the output destination for the intermediate file.
delimiter
(Mostly used by the CSV loader) Delimiter used to separate entries in the file. Ex( | , :)
fileType
The input file type. Generic, HapMap, VCF are currently supported filetypes. Each filetype comes with different behind the scenes code to deal with that type, and supports a different subset of column types.
Table
Each 'table' contains several elements, as well as several columns specifying what columns of data to be pulled.
table
Name of the Intermediate File to be generated, also the name of the table the data will be loaded into. Used to determine where data is stored.
VCF Options
Options for filtering the VCF before loading.
Dataset Id
The ID of the dataset if there is a dataset to be loaded in this request.
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Email address to send the load status to
Columns
| Code Block |
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"columnType" : |
Many types, for Generic we have ROW, COLUMN, CONSTANT or BOTH
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BOTH every entry contains the rest of the row of input (Helpful for variant call part)
"rCoord" :
Row coordinate of starting point
"cCoord" :
Column coordinate of starting point
"name" :
Name of the column, ignored in subcolumns
"filterFrom" :
String to filter 'from'. Starts the string at the first occurrence of filter.
"filterTo" :
String to filter 'to'. Ends the string at the first occurance of filter.
"constantValue" :
A constant value - if this column is of type constant this is the value that appears
"subcolumn" :
True if this is a subcolumn
"subcolumnDelimiter" :
The character that combines the subcolumn to the column before it
"metaDataId" :
This is currently not used
Lifecycle
An instruction file is created either by passing a POJO to the web services serialized, or through calls to the web services directly. As they are represented as objects in the gobii-model project, they can be thought of both as .json files and as Java objects, however the names and constraints remain the same.
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