From 950898df6928c0cdec4f40238eb4da4ec6901bde Mon Sep 17 00:00:00 2001
From: Arun Isaac
Date: Thu, 25 Feb 2021 14:10:50 +0530
Subject: Move generate-cwl to its own repository

---
 scripts/fastq2fasta.scm  |   6 +-
 scripts/generate-cwl.scm | 183 -----------------------------------------------
 scripts/yaml.scm         |  85 ----------------------
 3 files changed, 2 insertions(+), 272 deletions(-)
 delete mode 100644 scripts/generate-cwl.scm
 delete mode 100644 scripts/yaml.scm

diff --git a/scripts/fastq2fasta.scm b/scripts/fastq2fasta.scm
index 9eaa88f..c014852 100644
--- a/scripts/fastq2fasta.scm
+++ b/scripts/fastq2fasta.scm
@@ -2,11 +2,9 @@
 ;; fastq2fasta.cwl workflow
 ;;
 
-(add-to-load-path "./scripts")
-
 (use-modules (srfi srfi-26)
-             (generate-cwl)
-             (yaml))
+             (generate-cwl generate-cwl)
+             (generate-cwl yaml))
 
 (define threads
   (input "threads"
diff --git a/scripts/generate-cwl.scm b/scripts/generate-cwl.scm
deleted file mode 100644
index 1a26dfb..0000000
--- a/scripts/generate-cwl.scm
+++ /dev/null
@@ -1,183 +0,0 @@
-;;
-;; CWL generator
-;;
-;; This file implements a generator to generate CWL files.
-
-(define-module (generate-cwl)
-  #:use-module (rnrs records syntactic)
-  #:use-module (srfi srfi-1)
-  #:use-module (srfi srfi-71)
-  #:use-module (ice-9 match)
-  #:export (clitool
-            workflow
-            input
-            output
-            step
-            workflow-output))
-
-(define-record-type (<input> make-input input?)
-  (fields (immutable id input-id)
-          (immutable type input-type)
-          (immutable default input-default)
-          (immutable label input-label)
-          (immutable other input-other)))
-
-(define-record-type unspecified-default)
-
-(define* (input id #:key type label (default (make-unspecified-default)) (other '()))
-  "Build and return an <input> object."
-  (make-input id type default label other))
-
-(define-record-type (<output> make-output output?)
-  (fields (immutable id output-id)
-          (immutable type output-type)
-          (immutable binding output-binding)
-          (immutable other output-other)))
-
-(define* (output id #:key type binding (other '()))
-  "Build and return an <output> object."
-  (make-output id type binding other))
-
-(define* (parse-arguments args #:optional (position 1))
-  "Parse ARGS, a list of command line arguments and return a parse
-tree of labelled arguments. POSITION is an internal recursion
-variable."
-  (match args
-    (((? string? head) tail ...)
-     (if (string-prefix? "-" head)
-         (match tail
-           ((tail-head tail ...)
-            (cons (list 'keyword head tail-head)
-                  (parse-arguments tail position))))
-         (error "Unrecognized argument" head)))
-    ((head tail ...)
-     (cons (list 'positional position head)
-           (parse-arguments tail (1+ position))))
-    (() '())))
-
-(define (parse-command args)
-  "Parse ARGS, a list of command line arguments and return two
-lists---the base command and the actual arguments."
-  (let ((base-command arguments
-                      (break (match-lambda
-                               ((arg next)
-                                (and (string? arg)
-                                     (string-prefix? "-" arg)
-                                     (input? next))))
-                             (map list args (drop args 1)))))
-    (values (append (map (match-lambda
-                           ((arg next) arg))
-                         base-command)
-                    (if (input? (last args))
-                        (list)
-                        (take-right args 1)))
-            (parse-arguments
-             (append (map (match-lambda
-                            ((arg next) arg))
-                          arguments)
-                     (if (input? (last args))
-                         (take-right args 1)
-                         (list)))))))
-
-(define (input->tree input)
-  "Convert INPUT, an <input> object, to a tree."
-  `(,(input-id input)
-    ,@(filter identity
-              (list (and (input-type input)
-                         (cons 'type (input-type input)))
-                    (and (input-label input)
-                         (cons 'label (input-label input)))
-                    (and (not (unspecified-default? (input-default input)))
-                         (cons 'default (input-default input)))))
-    ,@(input-other input)))
-
-(define* (clitool args #:key (additional-inputs '()) (outputs '()) stdout stderr (other '()))
-  "Build a CommandLineTool class CWL workflow."
-  (let ((base-command arguments (parse-command args)))
-    `((cwl-version . "v1.1")
-      (class . Command-line-tool)
-      ,@other
-      (base-command . ,(list->vector base-command))
-      ,@(let ((inputs (append arguments additional-inputs)))
-          (if (not (null? inputs))
-              `((inputs . ,(map (match-lambda
-                                  (('keyword prefix input)
-                                   (append (input->tree input)
-                                           `((input-binding (prefix . ,prefix)))))
-                                  (('positional position input)
-                                   (append (input->tree input)
-                                           `((input-binding (position . ,position)))))
-                                  (input
-                                   (input->tree input)))
-                                inputs)))
-              (list)))
-      ,@(if (or (not (null? outputs)) stdout stderr)
-            `((outputs . ,(map (lambda (output)
-                                 `(,(output-id output)
-                                   ,@(filter identity
-                                             (list (and (output-type output)
-                                                        (cons 'type (output-type output)))
-                                                   (and (output-binding output)
-                                                        (cons 'output-binding (output-binding output)))))
-                                   ,@(output-other output)))
-                               outputs)))
-            (list))
-      ,@(if stdout
-            `((stdout . ,stdout))
-            '())
-      ,@(if stderr
-            `((stderr . ,stderr))
-            '()))))
-
-(define-record-type (<workflow-output> make-workflow-output workflow-output?)
-  (fields (immutable id workflow-output-id)
-          (immutable type workflow-output-type)
-          (immutable source workflow-output-source)
-          (immutable other workflow-output-other)))
-
-(define* (workflow-output id #:key type source (other '()))
-  "Build and return a <workflow-output> object."
-  (make-workflow-output id type source other))
-
-(define-record-type (<step> step step?)
-  (fields (immutable id step-id)
-          (immutable run step-run)
-          (immutable in step-in)
-          (immutable out step-out)))
-
-(define* (workflow steps outputs #:key (other '()))
-  "Build a Workflow class CWL workflow."
-  `((cwlVersion . "v1.1")
-    (class . Workflow)
-    ,@other
-    (inputs . ,(delete-duplicates
-                (map input->tree
-                     (append
-                      (append-map (lambda (step)
-                                    (filter-map (match-lambda
-                                                  ((id . (? input? input)) input)
-                                                  (_ #f))
-                                                (step-in step)))
-                                  steps)
-                      (filter-map (lambda (output)
-                                    (and (input? (workflow-output-source output))
-                                         (workflow-output-source output)))
-                                  outputs)))))
-    (outputs . ,(map (lambda (output)
-                       `(,(workflow-output-id output)
-                         (type . ,(workflow-output-type output))
-                         (output-source . ,(match (workflow-output-source output)
-                                             ((? string? source) source)
-                                             ((? input? input) (input-id input))))))
-                     outputs))
-    (steps . ,(map (lambda (step)
-                     `(,(step-id step)
-                       (in . ,(map (match-lambda
-                                     ((id . input)
-                                      (cons id (if (input? input)
-                                                   (input-id input)
-                                                   input))))
-                                   (step-in step)))
-                       (out . ,(list->vector (step-out step)))
-                       (run . ,(step-run step))))
-                   steps))))
diff --git a/scripts/yaml.scm b/scripts/yaml.scm
deleted file mode 100644
index f940911..0000000
--- a/scripts/yaml.scm
+++ /dev/null
@@ -1,85 +0,0 @@
-;;
-;; scm->yaml
-;;
-;; This file implements a library to convert a scm tree to yaml.
-
-(define-module (yaml)
-  #:use-module (ice-9 match)
-  #:export (scm->yaml))
-
-(define (kebab->camel string)
-  "Convert STRING from kebab case to CAMEL case."
-  (match (string-split string #\-)
-    ((head tail ...)
-     (string-concatenate
-      (cons head (map string-titlecase tail))))))
-
-(define (display-atom atom port)
-  "Display ATOM in PORT converting from kebab case to camel case if
-ATOM is a symbol."
-  (cond
-   ((symbol? atom)
-    (display (string->symbol (kebab->camel (symbol->string atom))) port))
-   ((number? atom)
-    (display atom port))
-   ((string? atom)
-    ;; Escape string with double quotes if
-    ;; - every character is a digit or period, and the unescaped
-    ;; string can therefore be misinterpreted as a number
-    ;; - string contains the colon character
-    (if (or (string-every (char-set-union char-set:digit (char-set #\.)) atom)
-            (string-any #\: atom))
-        (write atom port)
-        (display atom port)))
-   ((boolean? atom)
-    (display (if atom "true" "false") port))
-   (else (error "Unknown atom" atom))))
-
-(define (indent-level port level)
-  "Emit whitespaces to PORT corresponding to nesting LEVEL."
-  (display (make-string (* 2 level) #\space) port))
-
-(define (display-array-element element port level)
-  "Display array ELEMENT to PORT at nesting LEVEL."
-  (display "- " port)
-  (scm->yaml element port (1+ level)))
-
-(define (display-dictionary-entry entry port level)
-  "Display dictionary ENTRY to PORT at nesting LEVEL."
-  (match entry
-    ((key . value)
-     (display-atom key port)
-     (display ":" port)
-     (match value
-       ((or #(_ ...)
-            ((_ . _) (_ . _) ...))
-        (newline port)
-        (indent-level port (1+ level))
-        (scm->yaml value port (1+ level)))
-       (_ (display " " port)
-          (scm->yaml value port level))))))
-
-(define* (scm->yaml scm #:optional (port (current-output-port)) (level 0))
-  "Convert SCM, an S-expression tree, to YAML and display to
-PORT. LEVEL is an internal recursion variable."
-  (match scm
-    (#(head tail ...)
-     (display-array-element head port level)
-     (for-each (lambda (element)
-                 (indent-level port level)
-                 (display-array-element element port level))
-               tail))
-    (#()
-     (display "[]" port))
-    ((head tail ...)
-     (display-dictionary-entry head port level)
-     (for-each (lambda (entry)
-                 (indent-level port level)
-                 (display-dictionary-entry entry port level))
-               tail))
-    (()
-     (display "{}" port)
-     (newline port))
-    (symbol
-     (display-atom symbol port)
-     (newline port))))
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