src/abimetadata

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This module provides a command-line tool for displaying and modifying metadata in ABIF files.

The abimetadata tool allows users to:

  1. List all human-readable metadata fields in an ABIF file
  2. View the full content of a specific tag
  3. Edit the value of a tag (currently limited to string-type tags)

Command-line usage:

abimetadata <input.ab1> [options]

Options:

-h, --help
Show help message
-l, --list
List all metadata fields (default)
-t, --tag=STRING
Tag name to view or edit
-v, --value=STRING
New value for tag when editing
-o, --output=STRING
Output file for modified ABI file
--limit=INT
Limit number of tags displayed
--version
Show version information
--debug
Show additional debug information

Examples:

# List all tags
abimetadata input.ab1

# View a specific tag's full content
abimetadata input.ab1 -t SMPL1

# Edit a tag
abimetadata input.ab1 -t SMPL1 -v "New Sample Name" -o modified.ab1

Types

Config = object
  inputFile*: string         ## Path to the input ABIF file
  outputFile*: string        ## Path to the output file (when editing)
  tag*: string               ## Tag name to view or edit
  value*: string             ## New value for tag (when editing)
  listTags*: bool            ## Whether to list all tags (default behavior)
  debug*: bool               ## Whether to show debug information
  limit*: int                ## Maximum number of tags to display (0 = no limit)
  showVersion*: bool         ## Whether to show version information
Configuration for the abimetadata tool. Contains command-line options and settings. Source   Edit  

Procs

proc canDisplayTag(tagName: string; entry: DirectoryEntry): bool {....raises: [],
    tags: [], forbids: [].}

Determines if a tag can be displayed based on its name and properties.

Parameters: tagName: The name of the tag entry: The DirectoryEntry for the tag

Returns: true if the tag can be displayed, false otherwise

Source   Edit   
proc displaySingleTag(trace: ABIFTrace; tagName: string; debug: bool) {.
    ...raises: [KeyError], tags: [ReadIOEffect], forbids: [].}

Displays the full content of a single tag.

Parameters: trace: The ABIFTrace containing the tag tagName: The name of the tag to display debug: Whether to show debug information

Source   Edit   
proc formatTagValue(tagName: string; entry: DirectoryEntry; trace: ABIFTrace): string {.
    ...raises: [], tags: [ReadIOEffect], forbids: [].}

Formats a tag's value for display, with possible truncation for long values.

Parameters: tagName: The name of the tag entry: The DirectoryEntry for the tag trace: The ABIFTrace containing the tag

Returns: The tag's value as a string, possibly truncated for display

Source   Edit   
proc getFullTagValue(tagName: string; entry: DirectoryEntry; trace: ABIFTrace): string {.
    ...raises: [], tags: [ReadIOEffect], forbids: [].}

Gets the full, untruncated value of a tag.

Parameters: tagName: The name of the tag entry: The DirectoryEntry for the tag trace: The ABIFTrace containing the tag

Returns: The tag's value as a string, formatted according to its data type

Source   Edit   
proc isHumanReadableType(tagType: ElementType): bool {....raises: [], tags: [],
    forbids: [].}

Determines if a tag type can be displayed in a human-readable format.

Parameters: tagType: The ElementType to check

Returns: true if the type is human-readable, false otherwise

Source   Edit   
proc listMetadata(trace: ABIFTrace; debug: bool; limit: int = 0) {.
    ...raises: [IOError, KeyError], tags: [WriteIOEffect, ReadIOEffect],
    forbids: [].}

Lists all human-readable metadata fields in the ABIF file.

Parameters: trace: The ABIFTrace to list metadata from debug: Whether to show debug information limit: Maximum number of tags to display (0 = no limit)

Source   Edit   
proc main() {....raises: [ValueError, OSError],
              tags: [ReadIOEffect, ReadDirEffect, WriteIOEffect, ExecIOEffect],
              forbids: [].}

Main entry point for the abimetadata program.

Handles command-line parsing and executes the appropriate action based on the provided options (list, view, or edit tags).

Source   Edit   
proc modifyTag(trace: ABIFTrace; tagName: string; newValue: string;
               outputFile: string): bool {....raises: [KeyError],
    tags: [WriteIOEffect, ExecIOEffect, ReadDirEffect, ReadIOEffect],
    forbids: [].}
Modifies the value of a tag in an ABIF file. Source   Edit   
proc parseCommandLine(): Config {....raises: [ValueError, OSError],
                                  tags: [ReadIOEffect], forbids: [].}

Parses command line arguments and returns a Config object.

This procedure:

  • Initializes Config with default values
  • Processes command-line arguments
  • Handles special flags like --version and --help
  • Validates required parameters based on operating mode

Returns: A Config object with settings based on command-line arguments

Source   Edit   
proc printHelp() {....raises: [], tags: [], forbids: [].}
Displays the help message for the abimetadata tool. Exits the program after displaying the message. Source   Edit   
proc verifyTagUpdate(inputFile, outputFile, tagName: string): bool {....raises: [],
    tags: [ReadIOEffect, WriteIOEffect], forbids: [].}

Verifies that a tag was properly updated by comparing original and modified files.

Parameters: inputFile: Path to the original ABIF file outputFile: Path to the modified ABIF file tagName: The name of the tag that was modified

Returns: true if the tag was successfully updated, false otherwise

Source   Edit   
proc verifyTagUpdateBasic(inputFile, outputFile, tagName: string;
                          newValue: string; offset: int): bool {.discardable,
    ...raises: [], tags: [ReadIOEffect], forbids: [].}
Verifies tag update by directly checking the binary content at the specified offset This simpler method just checks if we can find the expected value at the offset Source   Edit  

Made with Nim. Generated: 2025-07-23 15:08:18 UTC