Metafacture Fix

Metafacture Fix (Metafix) is work in progress towards tools and an implementation of the Fix language for Metafacture as an alternative to configuring data transformations with Metamorph. Inspired by Catmandu Fix, Metafix processes metadata not as a continuous data stream but as discrete records. The basic idea is to rebuild constructs from the (Catmandu) Fix language like functions, selectors and binds in Java and combine with additional functionalities from the Metamorph toolbox.

See also Fix Interest Group for an initiative towards an implementation-independent specification for the Fix Language.

This repo contains the actual implementation of the Fix language as a Metafacture module and related components. It started as an Xtext web project with a Fix grammar, from which a parser, a web editor, and a language server are generated. The repo also contains an extension for VS code/codium based on that language server. (The web editor has effectively been replaced by the Metafacture Playground, but remains here for its integration into the language server, which we want to move over to the playground.)

Setup

Note: If you're using Windows, configure Git option core.autocrlf before cloning: git config --global core.autocrlf false.

Clone the Git repository:

git clone https://github.com/metafacture/metafacture-fix.git

Go to the Git repository root:

cd metafacture-fix/

Run the tests (in metafix/src/test/java) and checks (.editorconfig, config/checkstyle/checkstyle.xml):

./gradlew clean check

To execute a Fix (embedded in a Flux) via CLI:

./gradlew :metafix-runner:run --args="$PWD/path/to.flux"

(To import the projects in Eclipse, choose File > Import > Existing Gradle Project and select the metafacture-fix directory.)

Usage

The repo contains and uses a new Metafix stream module for Metafacture which plays the role of the Metamorph module in Fix-based Metafacture workflows. For the current implementation of the Metafix stream module see the tests in metafix/src/test/java. To play around with some examples, check out the Metafacture Playground. For real-world usage samples see openRub.fix and duepublico.fix. For reference documentation, see Functions and cookbook.

Extension

The project metafix-vsc provides an extension for Visual Studio Code / Codium for fix via the language server protocol (LSP). In the current state the extension supports auto completion, simple syntax highlighting and auto closing brackets and quotes. This project was created using this tutorial and the corresponding example.

Build extension:

Important

There is a problem when building the extension on Windows and installing the extension on a Linux system afterwards. In some cases the Xtext Server won't start. So if you want to use the extension not only on Windows, build the extension on a Linux system or on a Linux Subsystem on Windows.

1. Install Visual Studio Code / alternative: VS Codium
2. Install Node.js (including npm)
3. In metafacture-fix execute: Unix: ./gradlew installServer Windows: .\gradlew.bat installServer
4. In metafix-vsc/ execute (tip: if you use windows, install cygwin to execute npm commands): npm install

To start the extension in development mode (starting a second code/codium instance), follow A. To create a vsix file to install the extension permanently follow B.

A) Run in dev mode:

1. Open metafix-vsc/ in Visual Studio Code / Codium
2. Launch vscode extension by pressing F5 (opens new window of Visual Studio Code)
3. Open new file (file-ending .fix) or open existing fix-file (see sample below)

B) Install vsix file:

1. Install vsce: npm install -g vsce
2. In metafix-vsc/ execute: vsce package vsce will create a vsix file in the vsc directory which can be used for installation:
3. Open VS Code / Codium
4. Click 'Extensions' section
5. Click menu bar and choose 'Install from VSIX...'

Web editor

Start the web server:

./gradlew jettyRun

Visit http://localhost:8080/, and paste this into the editor:

# Fix is a macro-language for data transformations

# Simple fixes

add_field("hello", "world")
remove_field("my.deep.nested.junk")
copy_field("stats", "output.$append")

# Conditionals

if exists("error")
  set_field("is_valid", "no")
  log("error")
elsif exists("warning")
  set_field("is_valid", "yes")
  log("warning")
else
  set_field("is_valid", "yes")
end

# Loops

do list(path: "foo", "var": "$i")
  add_field("$i.bar", "baz")
end

Content assist is triggered with Ctrl-Space. The input above is also used in FixParsingTest.java.

Run workflows on the web server, passing data, flux, and fix:

http://localhost:8080/xtext-service/run?data='1'{'a': '5', 'z': 10}&flux=as-lines|decode-formeta|fix|encode-formeta(style="multiline")&fix=map(a,b) map(_else)

Functions and cookbook

Best practices and guidelines for working with Metafacture Fix

• We recommend to use double quotation marks for arguments and values in functions, binds and conditionals.
• If using a list bind with a variable, the var option requires quotation marks (do list(path: "<sourceField>", "var": "<variableName>")).
• Fix turns repeated fields into arrays internally but only marked arrays (with [] at the end of the field name) are also emitted as "arrays" (entities with indexed literals), all other arrays are emitted as repeated fields.
• Every Fix file should end with a final newline.

Glossary

Array wildcards

Array wildcards resemble Catmandu's concept of wildcards.

When working with arrays and repeated fields you can use wildcards instead of an index number to select elements of an array.

Wildcard	Meaning
*	Selects all elements of an array.
$first	Selects only the first element of an array.
$last	Selects only the last element of an array.
$prepend	Selects the position before the first element of an array. Can only be used when adding new elements to an array.
$append	Selects the position after the last element of an array. Can only be used when adding new elements to an array.

Path wildcards

Path wildcards resemble Metamorph's concept of wildcards. They are not supported in Catmandu (it has specialized Fix functions instead).

You can use path wildcards to select fields matching a pattern. They only match path segments (field names), though, not whole paths of nested fields. These wildcards cannot be used to add new elements.

Wildcard	Meaning
*	Placeholder for zero or more characters.
?	Placeholder for exactly one character.
|	Alternation of multiple patterns.
[...]	Enumeration of characters.

Functions

Script-level functions

include

Includes a Fix file and executes it as if its statements were written in place of the function call.

Parameters:

• path (required): Path to Fix file (if the path starts with a ., it is resolved relative to the including file's directory; otherwise, it is resolved relative to the current working directory).

Options:

• All options are made available as "dynamic" local variables in the included Fix file.

include("<path>"[, <dynamicLocalVariables>...])

Java Code

log

Sends a message to the logs.

Parameters:

• logMessage (required): Message to log.

Options:

• level: Log level to log at (one of DEBUG, INFO, WARN or ERROR). (Default: INFO)

log("<logMessage>"[, level: "<logLevel>"])

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nothing

Does nothing. It is used for benchmarking in Catmandu.

nothing()

Example in Playground

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put_filemap

Defines an external map for lookup from a file or a URL. Maps with more than 2 columns are supported but are reduced to a defined key and a value column.

put_filemap("<sourceFile>", "<mapName>", sep_char: "\t")

Example in Playground

The separator (sep_char) will vary depending on the source file, e.g.:

Type	Separator
CSV	, or ;
TSV	\t

Options:

• allow_empty_values: Sets whether to allow empty values in the filemap or to ignore these entries. (Default: false)
• compression: Sets the compression of the file.
• decompress_concatenated: Flags whether to use decompress concatenated file compression.
• encoding: Sets the encoding used to open the resource.
• expected_columns: Sets number of expected columns; lines with different number of columns are ignored. Set to -1 to disable the check and allow arbitrary number of columns. (Default: 2)
• key_column: Defines the column to be used for keys. Uses zero index. (Default: 0)
• value_column: Defines the column to be used for values. Uses zero index. (Default: 1)

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put_map

Defines an internal map for lookup from key/value pairs.

put_map("<mapName>",
  "dog": "mammal",
  "parrot": "bird",
  "shark": "fish"
)

Example in Playground

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put_rdfmap

Defines an external RDF map for lookup from a file or an HTTP(S) resource. As the RDF map is reducing RDF triples to a key/value map it is mandatory to set the target. The targeted RDF property can optionally be bound by an RDF language tag.

put_rdfmap("<rdfResource>", "<rdfMapName>", target: "<rdfProperty>")
put_rdfmap("<rdfResource>", "<rdfMapName>", target: "<rdfProperty>", select_language: "<rdfLanguageTag>")

Example in Playground

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put_var

Defines a single global variable that can be referenced with $[<variableName>].

put_var("<variableName>", "<variableValue>")

Example in Playground

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put_vars

Defines multiple global variables that can be referenced with $[<variableName>].

put_vars(
  "<variableName_1>": "<variableValue_1>",
  "<variableName_2>": "<variableValue_2>"
)

Example in Playground

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to_var

Defines a single global variable that can be referenced with $[<variableName>] and assigns the value of the <sourceField>.

to_var("<sourceField>", "<variableName>")

Options:

• default: Default value if source field does not exist. The option needs to be written in quotation marks because it is a reserved word in Java. (Default: Empty string)

Example in Playground

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Record-level functions

add_array

Creates a new array (with optional values).

add_array("<targetFieldName>")
add_array("<targetFieldName>", "<value_1>"[, ...])

Example in Playground

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add_field

Creates a field with a defined value.

add_field("<targetFieldName>", "<fieldValue>")

Example in Playground

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add_hash

Creates a new hash (with optional values).

add_hash("<targetFieldName>")
add_hash("<targetFieldName>", "subfieldName": "<subfieldValue>"[, ...])

Example in Playground

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array

Converts a hash/object into an array.

array("<sourceField>")

E.g.:

array("foo")
# {"name":"value"} => ["name", "value"]

Example in Playground

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call_macro

Calls a named macro, i.e. a list of statements that have been previously defined with the do put_macro bind.

Parameters:

• name (required): Unique name of the macro.

Options:

• All options are made available as "dynamic" local variables in the macro.

do put_macro("<macroName>"[, <staticLocalVariables>...])
  ...
end
call_macro("<macroName>"[, <dynamicLocalVariables>...])

Example in Playground

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copy_field

Copies a field from an existing field.

copy_field("<sourceField>", "<targetField>")

Example in Playground

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format

Replaces the value with a formatted (sprintf-like) version.

---- TODO: THIS NEEDS MORE CONTENT -----

format("<sourceField>", "<formatString>")

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hash

Converts an array into a hash/object.

hash("<sourceField>")

E.g.:

hash("foo")
# ["name", "value"] => {"name":"value"}

Example in Playground

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move_field

Moves a field from an existing field. Can be used to rename a field.

move_field("<sourceField>", "<targetField>")

Example in Playground

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parse_text

Parses a text into an array or hash of values.

---- TODO: THIS NEEDS MORE CONTENT -----

parse_text("<sourceField>", "<parsePattern>")

Example in Playground

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paste

Joins multiple field values into a new field. Can be combined with additional literal strings.

The default join_char is a single space. Literal strings have to start with ~.

paste("<targetField>", "<sourceField_1>"[, ...][, "join_char": ", "])

E.g.:

# a: eeny
# b: meeny
# c: miny
# d: moe
paste("my.string", "~Hi", "a", "~how are you?")
# "my.string": "Hi eeny how are you?"

Example in Playground

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print_record

Prints the current record as JSON either to standard output or to a file.

Parameters:

• prefix (optional): Prefix to print before the record; may include format directives for counter and record ID (in that order). (Default: Empty string)

Options:

• append: Whether to open files in append mode if they exist. (Default: false)
• compression (file output only): Compression mode. (Default: auto)
• destination: Destination to write the record to; may include format directives for counter and record ID (in that order). (Default: stdout)
• encoding (file output only): Encoding used by the underlying writer. (Default: UTF-8)
• footer: Footer which is written at the end of the output. (Default: \n)
• header: Header which is written at the beginning of the output. (Default: Empty string)
• id: Field name which contains the record ID; if found, will be available for inclusion in prefix and destination. (Default: _id)
• internal: Whether to print the record's internal representation instead of JSON. (Default: false)
• pretty: Whether to use pretty printing. (Default: false)
• separator: Separator which is written after the record. (Default: \n)

print_record(["<prefix>"][, <options>...])

E.g.:

print_record("%d) Before transformation: ")
print_record(destination: "record-%2$s.json", id: "001", pretty: "true")
print_record(destination: "record-%03d.json.gz", header: "After transformation: ")

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random

Creates (or replaces) a field with a random number (less than the specified maximum).

random("<targetField>", "<maximum>")

Example in Playground

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remove_field

Removes a field.

remove_field("<sourceField>")

Example in Playground

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rename

Replaces a regular expression pattern in subfield names of a field. Does not change the name of the source field itself.

rename("<sourceField>", "<regexp>", "<replacement>")

Example in Playground

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retain

Deletes all fields except the ones listed (incl. subfields).

retain("<sourceField_1>"[, ...])

Example in Playground

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set_array

Currently alias for add_array.

We advise you to use add_array instead of set_array due to changing behaviour in an upcoming release. For more information see: #309

set_field

Currently alias for add_field.

We advise you to use add_field instead of set_field due to changing behaviour in an upcoming release. For more information see: #309

set_hash

Currently alias for add_hash.

We advise you to use add_hash instead of set_hash due to changing behaviour in an upcoming release. For more information see: #309

timestamp

Creates (or replaces) a field with the current timestamp.

Options:

• format: Date and time pattern as in java.text.SimpleDateFormat. (Default: timestamp)
• timezone: Time zone as in java.util.TimeZone. (Default: UTC)
• language: Language tag as in java.util.Locale. (Default: The locale of the host system)

timestamp("<targetField>"[, format: "<formatPattern>"][, timezone: "<timezoneCode>"][, language: "<languageCode>"])

Example in Playground

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vacuum

Deletes empty fields, arrays and objects.

vacuum()

Example in Playground

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Field-level functions

append

Adds a string at the end of a field value.

append("<sourceField>", "<appendString>")

Example in Playground

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capitalize

Upcases the first character in a field value.

capitalize("<sourceField>")

Example in Playground

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count

Counts the number of elements in an array or a hash and replaces the field value with this number.

count("<sourceField>")

Example in Playground

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downcase

Downcases all characters in a field value.

downcase("<sourceField>")

Example in Playground

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filter

Only keeps field values that match the regular expression pattern. Works only with array of strings/repeated fields.

filter("<sourceField>", "<regexp>")

Example in Playground

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flatten

Flattens a nested array field.

flatten("<sourceField>")

Example in Playground

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from_json

Replaces the string with its JSON deserialization.

Options:

• error_string: Error message as a placeholder if the JSON couldn't be parsed. (Default: null)

from_json("<sourceField>"[, error_string: "<errorValue>"])

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index

Returns the index position of a substring in a field and replaces the field value with this number.

index("<sourceField>", "<substring>")

Example in Playground

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isbn

Extracts an ISBN and replaces the field value with the normalized ISBN; optionally converts and/or validates the ISBN.

Options:

• to: ISBN format to convert to (either ISBN10 or ISBN13). (Default: Only normalize ISBN)
• verify_check_digit: Whether the check digit should be verified. (Default: false)
• error_string: Error message as a placeholder if the ISBN couldn't be validated. (Default: null)

isbn("<sourceField>"[, to: "<isbnFormat>"][, verify_check_digit: "<boolean>"][, error_string: "<errorValue>"])

Example in Playground

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join_field

Joins an array of strings into a single string.

join_field("<sourceField>", "<separator>")

Example in Playground

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lookup

Looks up matching values in a map and replaces the field value with this match. External files, internal maps as well as RDF resources can be used.

Parameters:

• path (required): Field path to look up.
• map (optional): Name or path of the map in which to look up values.

Options:

• default: Default value to use for unknown values. The option needs to be written in quotation marks because it is a reserved word in Java. (Default: Old value)
• delete: Whether to delete unknown values. (Default: false)
• print_unknown: Whether to print unknown values. (Default: false)

Additional options when printing unknown values:

• append: Whether to open files in append mode if they exist. (Default: true)
• compression (file output only): Compression mode. (Default: auto)
• destination: Destination to write unknown values to; may include format directives for counter and record ID (in that order). (Default: stdout)
• encoding (file output only): Encoding used by the underlying writer. (Default: UTF-8)
• footer: Footer which is written at the end of the output. (Default: \n)
• header: Header which is written at the beginning of the output. (Default: Empty string)
• id: Field name which contains the record ID; if found, will be available for inclusion in prefix and destination. (Default: _id)
• prefix: Prefix to print before the unknown value; may include format directives for counter and record ID (in that order). (Default: Empty string)
• separator: Separator which is written after the unknown value. (Default: \n)

lookup("<sourceField>"[, <mapName>][, <options>...])

E.g.:

# local (unnamed) map
lookup("path.to.field", key_1: "value_1", ...)

# internal (named) map
put_map("internal-map", key_1: "value_1", ...)
lookup("path.to.field", "internal-map")

# external file map (implicit)
lookup("path.to.field", "path/to/file", sep_char: ";")

# external file map (explicit)
put_filemap("path/to/file", "file-map", sep_char: ";")
lookup("path.to.field", "file-map")

# RDF map (explicit)
put_rdfmap("path/to/file", "rdf-map", target: "<rdfProperty>")
lookup("path.to.field", "rdf-map")

# with default value
lookup("path.to.field", "map-name", "default": "NA")

# with printing unknown values to a file
lookup("path.to.field", "map-name", print_unknown: "true", destination: "unknown.txt")

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prepend

Adds a string at the beginning of a field value.

prepend("<sourceField>", "<prependString>")

Example in Playground

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replace_all

Replaces a regular expression pattern in field values with a replacement string. Regexp capturing is possible; refer to capturing groups by number ($<number>) or name (${<name>}).

replace_all("<sourceField>", "<regexp>", "<replacement>")

Example in Playground

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reverse

Reverses the character order of a string or the element order of an array.

reverse("<sourceField>")

Example in Playground

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sort_field

Sorts strings in an array. Alphabetically and A-Z by default. Optional numerical and reverse sorting.

sort_field("<sourceField>")
sort_field("<sourceField>", reverse: "true")
sort_field("<sourceField>", numeric: "true")

Example in Playground

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split_field

Splits a string into an array and replaces the field value with this array.

split_field("<sourceField>", "<separator>")

Example in Playground

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substring

Replaces a string with its substring as defined by the start position (offset) and length.

substring("<sourceField>", "<startPosition>", "<length>")

Example in Playground

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sum

Sums numbers in an array and replaces the field value with this number.

sum("<sourceField>")

Example in Playground

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to_json

Replaces the value with its JSON serialization.

Options:

• error_string: Error message as a placeholder if the JSON couldn't be generated. (Default: null)
• pretty: Whether to use pretty printing. (Default: false)

to_json("<sourceField>"[, pretty: "<boolean>"][, error_string: "<errorValue>"])

Example in Playground

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to_base64

Replaces the value with its Base64 encoding.

Options:

-url_safe: Perform URL-safe encoding (uses Base64URL format). (Default: false)

to_base64("<sourceField>"[, url_safe: "<boolean>"])

Example in Playground

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trim

Deletes whitespace at the beginning and the end of a field value.

trim("<sourceField>")

Example in Playground

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uniq

Deletes duplicate values in an array.

uniq("<sourceField>")

Example in Playground

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upcase

Upcases all characters in a field value.

upcase("<sourceField>")

Example in Playground

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uri_encode

Encodes a field value as URI. Aka percent-encoding.

Options:

• plus_for_space: Sets whether "space" ( ) will be substituted by a "plus" (+) or be percent escaped (%20). (Default: true)
• safe_chars: Sets characters that won't be escaped. Safe characters are the ranges 0..9, a..z and A..Z. These are always safe and should not be specified. (Default: .-*_)

uri_encode("<sourceField>"[, <options>...])

E.g.:

uri_encode("path.to.field", plus_for_space:"false", safe_chars:"")

Example in Playground

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Selectors

reject

Ignores records that match a condition.

if <condition>
  reject()
end

Example in Playground

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Binds

do list

Iterates over each element of an array. In contrast to Catmandu, it can also iterate over a single object or string.

Java Code

do list(path: "<sourceField>")
  ...
end

Example in Playground

Only the current element is accessible in this case (as the root element).

When specifying a variable name for the current element, the record remains accessible as the root element and the current element is accessible through the variable name:

do list(path: "<sourceField>", "var": "<variableName>")
  ...
end

Example in Playground

do list_as

Iterates over each named element of an array (like do list with a variable name). If multiple arrays are given, iterates over the corresponding elements from each array (i.e., all elements with the same array index, skipping elements whose arrays have already been exhausted).

Example in Playground

Java Code

do list_as(element_1: "<sourceField_1>"[, ...])
  ...
end

E.g.:

# "ccm:university":["https://ror.org/0304hq317"]
# "ccm:university_DISPLAYNAME":["Gottfried Wilhelm Leibniz Universität Hannover"]
set_array("sourceOrga[]")
do list_as(orgId: "ccm:university[]", orgName: "ccm:university_DISPLAYNAME[]")
  copy_field(orgId, "sourceOrga[].$append.id")
  copy_field(orgName, "sourceOrga[].$last.name")
end
# {"sourceOrga":[{"id":"https://ror.org/0304hq317","name":"Gottfried Wilhelm Leibniz Universität Hannover"}]}

do once

Executes the statements only once (when the bind is first encountered), not repeatedly for each record.

do once()
  ...
end

Example in Playground

Java Code

In order to execute multiple blocks only once, tag them with unique identifiers:

do once("maps setup")
  ...
end
do once("vars setup")
  ...
end

do put_macro

Defines a named macro, i.e. a list of statements that can be executed later with the call_macro function.

Variables can be referenced with $[<variableName>], in the following order of precedence:

1. "dynamic" local variables, passed as options to the call_macro function;
2. "static" local variables, passed as options to the do put_macro bind;
3. global variables, defined via put_var/put_vars.

Parameters:

• name (required): Unique name of the macro.

Options:

• All options are made available as "static" local variables in the macro.

do put_macro("<macroName>"[, <staticLocalVariables>...])
  ...
end
call_macro("<macroName>"[, <dynamicLocalVariables>...])

Example in Playground

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Conditionals

Conditionals start with if in case of affirming the condition or unless rejecting the condition.

Conditionals require a final end.

Additional conditionals can be set with elsif and else.

if <condition(params, ...)>
  ...
end

unless <condition(params, ...)>
  ...
end

if <condition(params, ...)>
  ...
elsif
  ...
else
  ...
end

contain

all_contain

Executes the functions if/unless the field contains the value. If it is an array or a hash all field values must contain the string.

Example in Playground

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any_contain

Executes the functions if/unless the field contains the value. If it is an array or a hash one or more field values must contain the string.

Example in Playground

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none_contain

Executes the functions if/unless the field does not contain the value. If it is an array or a hash none of the field values may contain the string.

Example in Playground

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str_contain

Executes the functions if/unless the first string contains the second string.

Example in Playground

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equal

all_equal

Executes the functions if/unless the field value equals the string. If it is an array or a hash all field values must equal the string.

Example in Playground

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any_equal

Executes the functions if/unless the field value equals the string. If it is an array or a hash one or more field values must equal the string.

Example in Playground

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none_equal

Executes the functions if/unless the field value does not equal the string. If it is an array or a hash none of the field values may equal the string.

Example in Playground

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str_equal

Executes the functions if/unless the first string equals the second string.

Example in Playground

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exists

Executes the functions if/unless the field exists.

if exists("<sourceField>")

Example in Playground

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in

Executes the functions if/unless the field value is contained in the value of the other field.

Also aliased as is_contained_in.

Example in Playground

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is_contained_in

Alias for in.

is_array

Executes the functions if/unless the field value is an array.

Example in Playground

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is_empty

Executes the functions if/unless the field value is empty.

Example in Playground

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is_false

Executes the functions if/unless the field value equals false or 0.

Example in Playground

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is_hash

Alias for is_object.

Example in Playground

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is_number

Executes the functions if/unless the field value is a number.

Example in Playground

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is_object

Executes the functions if/unless the field value is a hash (object).

Also aliased as is_hash.

is_string

Executes the functions if/unless the field value is a string (and not a number).

Example in Playground

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is_true

Executes the functions if/unless the field value equals true or 1.

Example in Playground

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match

all_match

Executes the functions if/unless the field value matches the regular expression pattern. If it is an array or a hash all field values must match the regular expression pattern.

Example in Playground

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any_match

Executes the functions if/unless the field value matches the regular expression pattern. If it is an array or a hash one or more field values must match the regular expression pattern.

Example in Playground

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none_match

Executes the functions if/unless the field value does not match the regular expression pattern. If it is an array or a hash none of the field values may match the regular expression pattern.

Example in Playground

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str_match

Executes the functions if/unless the string matches the regular expression pattern.

Example in Playground

Java Code

Xtext

This repo has been originally set up with Xtext 2.17.0 and Eclipse for Java 2019-03, following https://www.eclipse.org/Xtext/documentation/104_jvmdomainmodel.html.