Merge branch 'main' into 'tdd_file_writer'

Added documentation for arrays and code generation for CP-DSL.

See merge request !19

README.md

@@ -12,6 +12,8 @@ This project contains multiple DSLs for ocean and earth system models.
 - TDD-DSL testing DSL for test-driven development
 - BGC-DSL language to specify biogeochemical models
 
+Documentation can be found in the `doc`.
+
 ## License
 
 Apache 2.0

doc/common/unit-system.md

+# OceanDSL Unit System
+
+Units in OceanDSL can be any combination of SI or custom units using
+standard prefixes, such as k for kilo or m for milli. They can have
+exponents to express areas, volumes or other higher dimensions.
+
+As some values can be unit-less, it is possible to specify a variable,
+function or value without a unit. To express more complex unit, it
+is necessary to create composite units, such as kg m² / s².
+
+Units are used to ensure that only valid numbers are assigned to values.
+The OceanDSL DSLs allow to convert compatible units. That means if a parameter
+is declared as using meter, but the assigned value is specified with the unit
+km, the value is automatically converted to meter.
+Similarly, Celsius and Kelvin are converted accordingly.
+
+## Grammar
+
+```antlr
+// ----------------------
+// Units
+// ----------------------
+
+// substance is of type substanceDeclaration
+unit:
+	':' units=unitElement+ (substance=ID)? |
+	'::'
+;
+
+unitElement:
+	prefixUnit | groupUnit | exponentUnit
+;
+
+// removed unit-label for UNIT_STRING, here
+prefixUnit:
+	(UNIT_STRING | custom=CUSTOM_STRING)
+;
+
+groupUnit:
+	'(' elements+=unitElement+ ')'
+;
+
+exponentUnit:
+    unit=unitElement '^' exponent=NUMBER
+
+```
+
+The rule `unit` allows to compose a unit out of one or more unit
+elements, or skip the unit with `::`.
+The ability to have a sequence of units in `groupUnit` and `unit`
+seems to be unnecessary complicated, but from a users point of view, it
+allows you to avoid braces for more basic composites, such as Nm and kg m²/s².
+The former would be two `prefixUnit`s and the latter one with `kg` followed by
+two `exponentUnit`s, i.e., `m ^ 2` and `s ^-2`.
+The negative index value expresses the fraction (/).
+
+Each unit can have an substance identifier. This is used in BGC-DSL to ensure
+that substances are not mixed.
+In future, this could be extended to allow certain mixtures to create new
+kind of substances.
+
+A unit is comprised at least of one `unitElement`. Each `unitElement` is either
+a `prefixUnit`, an `groupUnit` or an `exponentUnit`.
+
+A `prefixUnit` is either an SI unit with or without an SI prefix, or a
+custom unit identifier. It can be used to specify simple units of measurement.
+
+`groupUnit` allows to group `unitElement`s together. This can be helpful to
+express more complex units which may arose during calculations. For example, the
+kg m^2 s^2 unit can also be written as kg (m s^-1)^2. While this might not
+seem to be necessary in many cases, we have found examples in the literature
+that required grouping.
+
+`exponentUnit` is used to express any unit with an exponent, e.g., m^2.
+The exponent numbers can be positive or negative.
+
+
+## SI Unit Parsing
+
+SI units comprise of an optional prefix and one or more character to define a
+base unit.
+
+Prefixes are: https://www.nist.gov/pml/owm/metric-si-prefixes
+- Q R Y Z E P T G M k h da d c m my n p f a z y r q
+Units are: https://en.wikipedia.org/wiki/International_System_of_Units
+- s m g A K mol cd Hz J C W rad sr N Pa V F Ohm S Wb T H °C lm lx Bq Gy Sv kat
+
+**Rules**
+Here is a list of mapping rules for SI unit string. ($ indicates line end)
+m -> meter
+mm -> milli mmeter
+mmol -> milli mol
+my -> micro
+
+**Note:** The original Java code can be found here. However, it is more
+complicated as it is also able to process exponents and other symbols.
+https://git.se.informatik.uni-kiel.de/oceandsl/cp-dsl/-/blob/master/bundles/org.oceandsl.configuration/src/org/oceandsl/configuration/parser/UnitParser.java
+
+
+## Representation
+
+The grammar implies a specific CST structure for units. Here we go beyond this,
+as it better represents basic units and prefixes.
+
+```
+class Unit
+  units : List<UnitElement>
+
+abstract class UnitElement
+```
+
+**Discuss:** Should we use one `PrefixUnit` class for SI and custom units?
+
+*Option* joined class
+```
+class PrefixUnit extends UnitElement
+  basicUnit : EUnit
+  prefix : EPRefix
+  unitName : String
+```
+
+*Option* separate class
+```
+class PrefixUnit extends UnitElement
+
+class PrefixSIUnit extends PrefixUnit
+  basicUnit : EUnit
+  prefix : EPRefix
+
+class PrefixCustomUnit extends PrefixUnit
+  unitName : String
+```
+
+**Discuss:** Should custom units also have a prefix and how do we process these?
+
+*Option* separate class where both can use prefixes
+```
+class PrefixUnit extends UnitElement
+  prefix : EPRefix
+  
+class PrefixSIUnit extends PrefixUnit
+  basicUnit : EUnit
+
+class PrefixCustomUnit extends PrefixUnit
+  unitName : String
+```
+
+Classes for units with exponent and grouped units.
+
+```
+class ExponentUnit extends UnitElement
+  unit : UnitElement
+  exponent : integer
+  
+class GroupUnit extends UnitElement
+  units : List<UnitElement>
+```
+
+## Semantics
+
+Unit semantics are similar to normal type system semantics, however, there are
+also some subtle differences. Therefore, we explain basic semantic rules here.
+Please note that units can be much more complicated (see normalization).
+
+T,R,S are unit type placeholders
+t,r,s are variables, functions or values
+
+### Expression: t + r
+
+```
+t : T + r : T
+-------------
+  t + r : T
+```
+
+This expresses that in an addition both need to have the same unit.
+Regarding substances, the substance can be different, as it is possible that
+different substances are mixed. They can even create new substances.
+
+### Expression: t - r
+
+```
+t : T - r : T
+-------------
+  t - r : T
+```
+
+This expresses that in a subtraction both need to have the same unit.
+
+### Expression: t * r
+
+```
+t : T * r : R
+-------------
+t * r : T * R
+```
+
+In case the base type of T and R are the same, the unit can be merged, e.g.,
+when multiplying two length (m), the result is area (m^2).
+
+```
+                    t * r : T * R and base(T) == base(R)
+----------------------------------------------------------------------------
+t * r : S and base(S) == base(T) and exponent(S) = exponent(T) + exponent(R)
+```
+
+In other cases the unit expression becomes more complex.
+
+### Expression: t / r
+
+Analog the the multiplication, the division leads to a new composite type which
+could be merged when both types have the same base unit.
+
+```
+t : T / r : R
+-------------
+t / r : T / R
+```
+
+### Expression: f(x_1,...,x_n)
+
+Functions have already a unit type assigned or it can be derived from their
+expression. Furthermore, each parameter has a unit assigned.
+For mathematical built-in functions, they do not have a type and assume the
+type specified by the input type.
+Therefore, all input units must be the same unit or without a unit.
+
+### expression: t^i
+
+Exponents require that t has a unit or no unit, but i is a unit less integer
+value.
+
+```
+                        t : T ^ i : I
+------------------------------------------------------------------
+t ^ i : S with base(S) = base(T) and exponent(S) = exponent(T) * i
+```
+
+## Normalization
+
+Based on the syntax, the same unit can be expressed in different ways. This
+can happen due to the sequence of basic units and grouping. The goal of the
+normalization is to have one sequence of exponent units which is sorted in
+the same order.
+
+Discuss: Shall we do unit normalization in expression, e.g.,
+1 m^3 + 1 l would be codes as 1 m^3 + 0.001 m^3.
+
+The normalization works therefore in two phases.
+1. All groups get removed.
+2. Merge nested `exponentUnit`s.
+3. The remaining units are sorted.
+4. Units with the same base unit get combined.
+
+### Group elimination
+
+There are two cases of groups.
+(a) Group which is the child of an `exponentUnit`
+(b) Group which is the child of another `groupUnit` or `unit`
+
+In case (a) each child of the group element, is embedded by a `exponentUnit`.
+For example, kg (m s^-1)^2 becomes kg m^2 s^-1^2.
+In case (b) the `groupUnit` can be merged directly with the parent `groupUnit` 
+or `unit`.
+
+### Exponent Merging
+
+For all `exponentUnit`s in the unit sequence, it is checked whether there is
+a nested `exponentUnit`. To eliminate one nesting the outer `exponentUnit`'s 
+exponent is multiplied with the exponent of the inner `exponentUnit` and the
+inner `exponentUnit`'s unit becomes the outer `exponentUnit`'s unit.
+This is repeated until all `exponentUnit`s only contain one `prefixUnit`.
+
+### Sort Units
+
+We iterate over the remaining sequence and replace every `prefixUnit` for an
+`exponentUnit` with the exponent value of 1 and set the `prefixUnit` as its 
+`unit`.
+Then we sort the units on the basis of `prefixUnit`s, i.e., in case in a
+sequence, we find a m and a m^2 they are sorted next to each other.
+
+Discuss: Do we ignore prefixes at this point or must we consider prefixes as
+well?
+
+### Merge Base Units
+
+Finally, we run over the sequence and look for each value whether the next
+value is of the same `prefixUnit` and merge their exponent accordingly, i.e.,
+we create the sum of the exponents.
+We then replace the two `exponentUnit`s by one with the same `prefixUnit` as
+the original and the sum of both exponents.
+Then we repeat this with the next `exponentUnit`.
+In case the exponent becomes zero both `exponentUnit`s are removed and nothing
+is added.

doc/cp-dsl/array.md

+# Arrays in CP-DSL
+
+Arrays are a common element of programming languages and are widely used to
+configure functions in earth system models. In the past, arrays were merely
+blocks of memory split in identical elements of one type. They could be
+multidimensional which then require a more complex way to map indices to
+memory location, e.g., `int[2][4]` would either require two blocks of 4
+integers or 4 blocks of 2 integers. The location function would be
+
+```location(i_0,i_1) = (i_0*4+i_1)*sizeof(int)```
+
+This becomes more complex when arrays are dynamic, i.e., they are defined
+with dimensions `d_0 ... d_n-1`, but the respective sizes for each dimension are
+unknown at compile time. For two dimensions, this would look like
+
+```location(i_0,i_1) = (i_0*d_1+i_1)*sizeof(int)```
+
+This implies an order where the second dimension (d_1) has scalar elements, and
+the first dimension (d_0) is a list of array of dimension d_1. Thus, the index
+must be multiplied by the length of d_1.
+
+```math
+location(i_0,...,i_n) = sizeof(int) * \sum_{j=0}^{n} i_j * \prod_{k=j+1}^{n} d_k
+```
+
+The CP-DSL supports dynamic arrays. Thus, dimension sizes can change and are
+not fixed in size in the declaration model. Therefore, we can use lists or maps
+to implement them. 
+
+## Features of Arrays
+
+Arrays can have multiple dimensions. These dimensions can be declared as fixed
+in size or dynamic in size in the declaration model. The fixed size can be
+defined as size or range.
+- size, e.g., `int[5]`, which defines an integer array with values for
+  0 to 4. 
+- range, e.g., `int[2:6]`, which defines an array with elements from
+  2 to 6.
+
+Dynamic arrays start if not specified differently with the index 0. However,
+there can also be constraints: 
+- `int[]`, starts its values from index 0 upwards
+- `int[2:]`, starts its values from index 2 upwards
+- `int [:4]`, limits the indices to 4 starting from 0, e.g., '[0,1,2,3,4]'
+
+The declaration model declares the dimensions, size constraints and base type of
+an array. In the configuration model, an array element selector can select a
+subset of an array, e.g., declaration model `int[1:10] data` declares the
+attribute data as an integer array with the indices 1 to 10. There is no
+element at index 0. The configuration model assignment
+
+```
+data[2:5] = [ 1,2,3,4 ]
+```
+
+assigns to the attribute **data** 4 values to the indices 2 to 5 of the declared
+array. This implies elements 1,6,7,8,9 and 10 are uninitialized.
+
+The specified **values** (here 1,2,3,4) in the configuration model must match
+the **sizes** of the remaining dimensions based on the configuration model
+modifiers (here the range from 2:5). There the values are moved in the
+assignment to the correct indices. The above example
+`data[2:5] = [ 1,2,3,4 ]` creates a value array with 4 numbers that are
+internally a list of values starting at index 0 up to 3.
+`data[2:5]` is an array selector on data, which selects the indices 2 to 5
+from the data array. The assignment then places the values 2 to 5 accordingly,
+i.e., the element with index 0 of the value array is assigned to `data[2]`,
+element 1 is assigned to `data[3]` and so on.
+
+In addition to ranges, element selectors can also select single elements. For
+example, `data[2] = 4` assigns the scalar value 4 to the element with the index
+number 2 of the data array. Thus, it is possible in our DSL to initialize 
+arrays in CP-DSL as follows:
+
+- `data[2] = 1`
+- `data[3] = 2`
+- `data[5:6] = [ 3, 4 ]`
+
+This allows for empty elements in arrays. Not all programming languages
+allow for empty cells in arrays, especially not with primitive data
+types. Thus, this generates a information indicator in the editor. As some
+configurations use this feature, we cannot prohibit such specifications.
+
+## Implementation
+
+The template compiler needs a model for arrays that retains the ranges and
+indices to each value. Therefore, the internal representation of arrays
+follow the concept of an associative array or map, where indices are map
+keys. This has also an impact on for-loops. The template DSL implements a
+for-loop that iterates over an array initializing three values available in the
+expression of the loop. These are `it` containing one element value of the
+array, `icount` containing the loop counter (starting always with 0), and the
+index number 'i#'.
+
+Here, the loop iterates over all elements declared in declarations. However,
+*it* will only contain a value for those that have a value assigned, *i#* will
+contain the respective index value, and *icount* the relevant loop counter.
+
+Array values can also be accessed directly in a template by parameter name and
+an index, e.g., `data[4]`. Here, this would return the element with the index 4
+from the array data. Using our example above, `data[4]` has no assigned value.
+Thus, it would be undefined. When converted to string, this produces the value
+`undef`. However, to be able to distinguish whether a value exists or is
+undefined, the user can use the function exists, which returns `true` in case a
+value is present.
+

doc/cp-dsl/code-generation.md

+# Code Generation
+
+The CP-DSL comprises a declaration, a configuration and a template DSL.
+The declaration DSL declares features, parameter groups, parameters, default 
+values for parameters and dependencies between features. The default values
+can use expressions to compute their values, which is helpful when parameters
+depend on each other. The configuration DSL allows to select features and
+assign values to parameters. Here, defaults can be replaced by actual
+assignments.
+To provide the template DSL with an easy-to-access data model, we compute an
+interim model containing all resolved values and type descriptors. The
+current implementation uses X stages to compose the interim model and generate
+template output.
+
+Initially, we create a model containing all parameters groups, parameters and
+features. The latter all in a deactivated state. Then the parameters get their 
+assigned default expressions or values. This is necessary, as the expression 
+might need (re-)evaluation after configuration values have been assigned.
+In case there are circular references between parameters, the declaration DSL
+editor would have reported them.
+
+Secondly, the configuration is applied to the interim model. Here,
+parameter become their configured values or expressions. These can also include
+references to other parameters, and this may also cause circular dependencies.
+The generator checks this and reports an error if circular dependencies are found.
+
+Thirdly, the expressions for each parameter are evaluated and only the resulting
+value is stored in the interim model.
+
+Fourthly, all templates related to the declaration model are processed based on
+the interim model.
+
+# Interim Model
+
+InterimModel
+
+- name : String // experiment name from the configuration model
+- declaration : DeclarationModel 
+- parameterGroups : ParameterGroup[]
+- features : Feature[]
+
+ParameterGroup
+
+- name : String
+- declaration : ParameterGroupDeclaration
+- parameters : Parameter[]
+
+Feature
+
+- name : String
+- parameterGroups : ParameterGroup[]
+- features : Feature[]
+- declaration : FeatureDeclaration
+- active : Boolean
+
+Parameter
+
+- name : String
+- declaration : ParameterDeclaration
+- computedValue: ValueContainer
+- dataEntries : ParameterEntry
+- specifiedType : TypeAssignment // type including the restrictions due to
+                                    the selector used in the configuration. This
+                                    is used to support the type cast during
+                                    computation of the value for the parameter
+
+ParameterEntry
+
+- expression : Expression
+- selectors : Selector
+
+ValueContainer (generic type)
++ ScalarValue
++ ArrayValue
+
+ScalarValue
+- value : Value
+
+ArrayValue
+
+- values : IndexToValueContainerMap
+- lowerBound : long
+- upperBound : long
+
+IndexToValueContainerMap
+
+- key : long
+- value : ValueContainer
+
+# Processing Declaration Model
+
+- InterimModel is created and the back reference (DeclarationModel) is set
+- for each ParameterGroupDeclaration a interim:ParameterGroup is created and
+  the back reference (ParameterGroupDeclaration) is set.
+- for each Parameter in each ParameterGroupDeclaration a corresponding entry
+  is created and linked back
+- the same applies to all Features
+
+Each interim::Parameter will have set 
+- name
+- declaration
+- dataEntries (one entry from the Declaration model)
+- specifiedType (??)
+
+# Processing Configuration Model
+
+- Walk over the InterimModel and 
+  - add parameter values from the configuration and add them to dataEntries
+  - activate and deactivate features
+  
+# Computing Values in the Interim Model
+
+In this task, all value expression must be computed. This is done for each
+parameter.
+
+
+
+
+
+  

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+      <circle r="15" clip-path="url(#clipPath2)" cx="1150" cy="284" stroke="none"/>
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+    <g text-rendering="geometricPrecision" stroke-miterlimit="1.45" shape-rendering="geometricPrecision" transform="matrix(1,0,0,1,-351,-115)" stroke-linecap="butt">
+      <circle fill="none" r="15" clip-path="url(#clipPath2)" cx="1150" cy="284"/>
+      <text x="1105.0477" xml:space="preserve" y="331.484" clip-path="url(#clipPath2)" font-family="sans-serif" stroke="none">Compute Result</text>
+      <text x="1132.3059" xml:space="preserve" y="347.8281" clip-path="url(#clipPath2)" font-family="sans-serif" stroke="none">Model</text>
+    </g>
+    <g fill="rgb(255,204,0)" text-rendering="geometricPrecision" shape-rendering="geometricPrecision" transform="matrix(1,0,0,1,-351,-115)" stroke="rgb(255,204,0)">
+      <path d="M887.5 402 L1131.5 402 L1131.5 417 L1146.5 417 L1146.5 482 L887.5 482 Z" stroke="none" clip-path="url(#clipPath2)"/>
+      <path fill="white" d="M1131.5 402 L1131.5 417 L1146.5 417 Z" clip-path="url(#clipPath2)" fill-rule="evenodd" stroke="none"/>
+    </g>
+    <g text-rendering="geometricPrecision" stroke-miterlimit="1.45" shape-rendering="geometricPrecision" transform="matrix(1,0,0,1,-351,-115)" stroke-linecap="butt">
+      <path fill="none" d="M887.5 402 L1131.5 402 L1131.5 417 L1146.5 417 L1146.5 482 L887.5 482 Z" clip-path="url(#clipPath2)"/>
+      <path fill="none" d="M1131.5 402 L1131.5 417 L1146.5 417 Z" clip-path="url(#clipPath2)" fill-rule="evenodd"/>
+      <text x="895.4331" xml:space="preserve" y="430.3119" clip-path="url(#clipPath2)" font-family="sans-serif" stroke="none">Technically the interim model/symbol table</text>
+      <text x="902.6392" xml:space="preserve" y="446.656" clip-path="url(#clipPath2)" font-family="sans-serif" stroke="none">and the resolved model can be the same</text>
+      <text x="975.4017" xml:space="preserve" y="463.0002" clip-path="url(#clipPath2)" font-family="sans-serif" stroke="none">data structure.</text>
+      <path fill="none" d="M461 284 L526 284" clip-path="url(#clipPath2)"/>
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+      <path fill="none" d="M460.9844 350 L517 350 L538.9657 304.6957" clip-path="url(#clipPath2)"/>
+      <path d="M542.4559 297.4972 L532.7215 306.1136 L538.5294 305.5955 L541.7197 310.4763 Z" clip-path="url(#clipPath2)" stroke="none"/>
+      <path fill="none" d="M564 284 L636 284" clip-path="url(#clipPath2)"/>
+      <path d="M644 284 L632 279 L635 284 L632 289 Z" clip-path="url(#clipPath2)" stroke="none"/>
+      <path fill="none" d="M768 284 L838.5 284" clip-path="url(#clipPath2)"/>
+      <path d="M846.5 284 L834.5 279 L837.5 284 L834.5 289 Z" clip-path="url(#clipPath2)" stroke="none"/>
+      <path fill="none" d="M762 211 L807 211 L847.7404 265.5698" clip-path="url(#clipPath2)"/>
+      <path d="M852.5264 271.9803 L849.354 259.3733 L847.1422 264.7685 L841.3409 265.3557 Z" clip-path="url(#clipPath2)" stroke="none"/>
+      <path fill="none" d="M762 145 L813 145 L853.9228 262.284" clip-path="url(#clipPath2)"/>
+      <path d="M856.5583 269.8374 L857.3259 256.86 L853.5933 261.3398 L847.8842 260.1545 Z" clip-path="url(#clipPath2)" stroke="none"/>
+      <path fill="none" d="M876.5 284 L947 284" clip-path="url(#clipPath2)"/>
+      <path d="M955 284 L943 279 L946 284 L943 289 Z" clip-path="url(#clipPath2)" stroke="none"/>
+      <path fill="none" d="M1079 284 L1127 284" clip-path="url(#clipPath2)"/>
+      <path d="M1135 284 L1123 279 L1126 284 L1123 289 Z" clip-path="url(#clipPath2)" stroke="none"/>
+      <path fill="none" d="M1165 284 L1213 284" clip-path="url(#clipPath2)"/>
+      <path d="M1221 284 L1209 279 L1212 284 L1209 289 Z" clip-path="url(#clipPath2)" stroke="none"/>
+      <path fill="none" stroke-dasharray="6,2" d="M887.5018 442 L784 442 L713.4051 299" clip-path="url(#clipPath2)"/>
+      <path fill="none" stroke-dasharray="6,2" d="M1017 401.9985 L1017 299" clip-path="url(#clipPath2)"/>
+      <path fill="none" stroke-dasharray="6,2" d="M1146.4939 442 L1208 442 L1273.1646 299" clip-path="url(#clipPath2)"/>
+    </g>
+  </g>
+</svg>

doc/cp-dsl/template-dsl.md

+# Template Language
+
+The template language allows to define file templates based on a declaration
+model. It supports two template types:
+- File templates which will generate files
+- Text templates which allow to produce text and allow to subdivide the file
+  generation
+  
+## Basic File Structure
+
+Each template file starts with a preamble specifying the declaration model to
+use.
+
+```
+for DeclarationModelName
+```
+
+After that any number of file and sub templates can be specified.
+
+## File Template
+
+A file template starts with the keyword *file*.
+
+```
+file "filename expression" : "body expression"
+file "filename expression" when exists(exampleGroup) : "body expression"
+```
+
+The first example produces a file regardless of the content of the configuration
+file. The second example requests that an element *exampleGroup* exists.
+
+## Text Template
+
+A text template starts with the keyword *template* followed by a list of
+optional parameters and a template body.
+
+```
+template basic "body expression"
+template withParameters (ParameterGroup group) "body expression"
+```
+
+## Expressions
+
+File names, conditionals and template bodys are expressions in the template
+language. In text and file templates the expression must be a text string for
+file names and bodys and a boolean for conditionals.
+
+The language supports richstrings starting and ending with '''.
+Rich strings can be interupted with « » and between these french quotes, other
+expressions and commands can be inserted.
+
+```
+'''«for group.parameters join "," it.name»'''
+```
+
+## List of Expression Elements
+
+- *, /, %  *multiply, divide, modulo*
+- +, -  *add, subtract*
+- if boolean text-expression (then text-expression)?
+- for variable (join string)? text-expression
+- switch variable cases end
+- cases
+  - case case-text-expression text-expression  *case for expression*
+  - is type-name text-expression  *type case expression*
+- and, or  *logical ops*
+- ==, >, <, >=, <=, !=  *compare ops*
+- !  (not)
+- use template-name (parameters)  *use another template*
+- exists(variable), isEmpty(list), size(list) *built-in functions*
+- it *referencing the loop variable*
+
+## How to get 
+
+- « and » in the editor?
+- CTRL-< and SHIFT-CTRL-< (lower left corner on the keyboard)
+