From bf9ec3d91a79414deac039f7bf83352a9b0a9a85 Mon Sep 17 00:00:00 2001
From: Kyle Meyer <kyle@kyleam.com>
Date: Wed, 29 Sep 2021 18:48:59 -0400
Subject: Update to Org 9.5

---
 lisp/org/ob-java.el | 480 +++++++++++++++++++++++++++++++++++++++++++++++-----
 1 file changed, 442 insertions(+), 38 deletions(-)

(limited to 'lisp/org/ob-java.el')

diff --git a/lisp/org/ob-java.el b/lisp/org/ob-java.el
index b1d517e94aa..60ef33bc6e4 100644
--- a/lisp/org/ob-java.el
+++ b/lisp/org/ob-java.el
@@ -1,8 +1,10 @@
-;;; ob-java.el --- Babel Functions for Java          -*- lexical-binding: t; -*-
+;;; ob-java.el --- org-babel functions for java evaluation -*- lexical-binding: t -*-
 
 ;; Copyright (C) 2011-2021 Free Software Foundation, Inc.
 
-;; Author: Eric Schulte
+;; Authors: Eric Schulte
+;;          Dan Davison
+;; Maintainer: Ian Martins <ianxm@jhu.edu>
 ;; Keywords: literate programming, reproducible research
 ;; Homepage: https://orgmode.org
 
@@ -23,8 +25,7 @@
 
 ;;; Commentary:
 
-;; Currently this only supports the external compilation and execution
-;; of java code blocks (i.e., no session support).
+;; Org-Babel support for evaluating java source code.
 
 ;;; Code:
 (require 'ob)
@@ -32,52 +33,455 @@
 (defvar org-babel-tangle-lang-exts)
 (add-to-list 'org-babel-tangle-lang-exts '("java" . "java"))
 
+(defvar org-babel-temporary-directory) ; from ob-core
+
+(defvar org-babel-default-header-args:java '((:results . "output")
+					     (:dir . "."))
+  "Default header args for java source blocks.
+The docs say functional mode should be the default [1], but
+ob-java didn't originally support functional mode, so we keep
+scripting mode as the default for now to maintain previous
+behavior.
+
+Most languages write tempfiles to babel's temporary directory,
+but ob-java originally had to write them to the current
+directory, so we keep that as the default behavior.
+
+[1] https://orgmode.org/manual/Results-of-Evaluation.html")
+
+(defconst org-babel-header-args:java '((imports . :any))
+  "Java-specific header arguments.")
+
 (defcustom org-babel-java-command "java"
   "Name of the java command.
-May be either a command in the path, like java
-or an absolute path name, like /usr/local/bin/java
-parameters may be used, like java -verbose"
+May be either a command in the path, like java or an absolute
+path name, like /usr/local/bin/java.  Parameters may be used,
+like java -verbose."
   :group 'org-babel
-  :version "24.3"
+  :package-version '(Org . "9.5")
   :type 'string)
 
 (defcustom org-babel-java-compiler "javac"
   "Name of the java compiler.
-May be either a command in the path, like javac
-or an absolute path name, like /usr/local/bin/javac
-parameters may be used, like javac -verbose"
+May be either a command in the path, like javac or an absolute
+path name, like /usr/local/bin/javac.  Parameters may be used,
+like javac -verbose."
+  :group 'org-babel
+  :package-version '(Org . "9.5")
+  :type 'string)
+
+(defcustom org-babel-java-hline-to "null"
+  "Replace hlines in incoming tables with this when translating to java."
   :group 'org-babel
-  :version "24.3"
+  :package-version '(Org . "9.5")
   :type 'string)
 
+(defcustom org-babel-java-null-to 'hline
+  "Replace `null' in java tables with this before returning."
+  :group 'org-babel
+  :package-version '(Org . "9.5")
+  :type 'symbol)
+
+(defconst org-babel-java--package-re (rx line-start (0+ space) "package"
+					 (1+ space) (group (1+ (in alnum ?_ ?.))) ; capture the package name
+					 (0+ space) ?\; line-end)
+  "Regexp for the package statement.")
+(defconst org-babel-java--imports-re (rx line-start (0+ space) "import"
+                                         (opt (1+ space) "static")
+					 (1+ space) (group (1+ (in alnum ?_ ?. ?*))) ; capture the fully qualified class name
+					 (0+ space) ?\; line-end)
+  "Regexp for import statements.")
+(defconst org-babel-java--class-re (rx line-start (0+ space) (opt (seq "public" (1+ space)))
+				       "class" (1+ space)
+				       (group (1+ (in alnum ?_))) ; capture the class name
+				       (0+ space) ?{)
+  "Regexp for the class declaration.")
+(defconst org-babel-java--main-re (rx line-start (0+ space) "public"
+				      (1+ space) "static"
+				      (1+ space) "void"
+				      (1+ space) "main"
+				      (0+ space) ?\(
+				      (0+ space) "String"
+				      (0+ space) (1+ (in alnum ?_ ?\[ ?\] space)) ; "[] args" or "args[]"
+				      (0+ space) ?\)
+				      (0+ space) (opt "throws" (1+ (in alnum ?_ ?, ?. space)))
+				      ?{)
+  "Regexp for the main method declaration.")
+(defconst org-babel-java--any-method-re (rx line-start
+					    (0+ space) (opt (seq (1+ alnum) (1+ space)))   ; visibility
+					    (opt (seq "static" (1+ space)))                ; binding
+					    (1+ (in alnum ?_ ?\[ ?\]))                     ; return type
+                                            (1+ space) (1+ (in alnum ?_))                  ; method name
+					    (0+ space) ?\(
+					    (0+ space) (0+ (in alnum ?_ ?\[ ?\] ?, space)) ; params
+					    (0+ space) ?\)
+					    (0+ space) (opt "throws" (1+ (in alnum ?_ ?, ?. space)))
+					    ?{)
+  "Regexp for any method.")
+(defconst org-babel-java--result-wrapper "\n    public static String __toString(Object val) {
+        if (val instanceof String) {
+            return \"\\\"\" + val + \"\\\"\";
+        } else if (val == null) {
+            return \"null\";
+        } else if (val.getClass().isArray()) {
+            StringBuffer sb = new StringBuffer();
+            Object[] vals = (Object[])val;
+            sb.append(\"[\");
+            for (int ii=0; ii<vals.length; ii++) {
+                sb.append(__toString(vals[ii]));
+                if (ii<vals.length-1)
+                    sb.append(\",\");
+            }
+            sb.append(\"]\");
+            return sb.toString();
+        } else if (val instanceof List) {
+            StringBuffer sb = new StringBuffer();
+            List vals = (List)val;
+            sb.append(\"[\");
+            for (int ii=0; ii<vals.size(); ii++) {
+                sb.append(__toString(vals.get(ii)));
+                if (ii<vals.size()-1)
+                    sb.append(\",\");
+            }
+            sb.append(\"]\");
+            return sb.toString();
+        } else {
+            return String.valueOf(val);
+        }
+    }
+
+    public static void main(String[] args) throws IOException {
+        BufferedWriter output = new BufferedWriter(new FileWriter(\"%s\"));
+        output.write(__toString(_main(args)));
+        output.close();
+    }"
+  "Code to inject into a class so that we can capture the value it returns.
+This implementation was inspired by ob-python, although not as
+elegant.  This modified the source block to write out the value
+it wants to return to a temporary file so that ob-java can read
+it back.  The name of the temporary file to write must be
+replaced in this string.")
+
 (defun org-babel-execute:java (body params)
-  (let* ((classname (or (cdr (assq :classname params))
-			(error
-			 "Can't compile a java block without a classname")))
-	 (packagename (file-name-directory classname))
-	 (src-file (concat classname ".java"))
-	 (cmpflag (or (cdr (assq :cmpflag params)) ""))
-	 (cmdline (or (cdr (assq :cmdline params)) ""))
-	 (cmdargs (or (cdr (assq :cmdargs params)) ""))
-	 (full-body (org-babel-expand-body:generic body params)))
-    (with-temp-file src-file (insert full-body))
-    (org-babel-eval
-     (concat org-babel-java-compiler " " cmpflag " " src-file) "")
+  "Execute a java source block with BODY code and PARAMS params."
+  (let* (;; allow header overrides
+         (org-babel-java-compiler
+          (or (cdr (assq :javac params))
+              org-babel-java-compiler))
+         (org-babel-java-command
+          (or (cdr (assq :java params))
+              org-babel-java-command))
+         ;; if true, run from babel temp directory
+         (run-from-temp (not (cdr (assq :dir params))))
+         ;; class and package
+         (fullclassname (or (cdr (assq :classname params))
+                            (org-babel-java-find-classname body)))
+         ;; just the class name
+         (classname (car (last (split-string fullclassname "\\."))))
+         ;; just the package name
+         (packagename (if (string-match-p "\\." fullclassname)
+                          (file-name-base fullclassname)))
+         ;; the base dir that contains the top level package dir
+         (basedir (file-name-as-directory (if run-from-temp
+                                              (if (file-remote-p default-directory)
+                                                  (concat
+                                                   (file-remote-p default-directory)
+                                                   org-babel-remote-temporary-directory)
+                                                org-babel-temporary-directory)
+                                            default-directory)))
+         ;; the dir to write the source file
+         (packagedir (if (and (not run-from-temp) packagename)
+                         (file-name-as-directory
+                          (concat basedir (replace-regexp-in-string "\\\." "/" packagename)))
+                       basedir))
+         ;; the filename of the source file
+         (src-file (concat packagedir classname ".java"))
+         ;; compiler flags
+         (cmpflag (or (cdr (assq :cmpflag params)) ""))
+         ;; runtime flags
+         (cmdline (or (cdr (assq :cmdline params)) ""))
+         ;; command line args
+         (cmdargs (or (cdr (assq :cmdargs params)) ""))
+         ;; the command to compile and run
+         (cmd (concat org-babel-java-compiler " " cmpflag " "
+                      (org-babel-process-file-name src-file 'noquote)
+                      " && " org-babel-java-command
+                      " -cp " (org-babel-process-file-name basedir 'noquote)
+                      " " cmdline " " (if run-from-temp classname fullclassname)
+                      " " cmdargs))
+         ;; header args for result processing
+         (result-type (cdr (assq :result-type params)))
+         (result-params (cdr (assq :result-params params)))
+         (result-file (and (eq result-type 'value)
+                           (org-babel-temp-file "java-")))
+         ;; the expanded body of the source block
+         (full-body (org-babel-expand-body:java body params)))
+
     ;; created package-name directories if missing
-    (unless (or (not packagename) (file-exists-p packagename))
-      (make-directory packagename 'parents))
-    (let ((results (org-babel-eval (concat org-babel-java-command
-                                           " " cmdline " " classname " " cmdargs) "")))
-      (org-babel-reassemble-table
-       (org-babel-result-cond (cdr (assq :result-params params))
-	 (org-babel-read results t)
-         (let ((tmp-file (org-babel-temp-file "c-")))
-           (with-temp-file tmp-file (insert results))
-           (org-babel-import-elisp-from-file tmp-file)))
-       (org-babel-pick-name
-        (cdr (assq :colname-names params)) (cdr (assq :colnames params)))
-       (org-babel-pick-name
-        (cdr (assq :rowname-names params)) (cdr (assq :rownames params)))))))
+    (unless (or (not packagedir) (file-exists-p packagedir))
+      (make-directory packagedir 'parents))
+
+    ;; write the source file
+    (setq full-body (org-babel-java--expand-for-evaluation
+                     full-body run-from-temp result-type result-file))
+    (with-temp-file src-file (insert full-body))
+
+    ;; compile, run, process result
+    (org-babel-reassemble-table
+     (org-babel-java-evaluate cmd result-type result-params result-file)
+     (org-babel-pick-name
+      (cdr (assoc :colname-names params)) (cdr (assoc :colnames params)))
+     (org-babel-pick-name
+      (cdr (assoc :rowname-names params)) (cdr (assoc :rownames params))))))
+
+;; helper functions
+
+(defun org-babel-java-find-classname (body)
+  "Try to find fully qualified class name in BODY.
+Look through BODY for the package and class.  If found, put them
+together into a fully qualified class name and return.  Else just
+return class name.  If that isn't found either, default to Main."
+  (let ((package (if (string-match org-babel-java--package-re body)
+                     (match-string 1 body)))
+        (class (if (string-match org-babel-java--class-re body)
+                   (match-string 1 body))))
+    (or (and package class (concat package "." class))
+        (and class class)
+        (and package (concat package ".Main"))
+        "Main")))
+
+(defun org-babel-java--expand-for-evaluation (body suppress-package-p result-type result-file)
+  "Expand source block for evaluation.
+In order to return a value we have to add a __toString method.
+In order to prevent classes without main methods from erroring we
+add a dummy main method if one is not provided.  These
+manipulations are done outside of `org-babel--expand-body' so
+that they are hidden from tangles.
+
+BODY is the file content before instrumentation.
+
+SUPPRESS-PACKAGE-P if true, suppress the package statement.
+
+RESULT-TYPE is taken from params.
+
+RESULT-FILE is the temp file to write the result."
+  (with-temp-buffer
+    (insert body)
+
+    ;; suppress package statement
+    (goto-char (point-min))
+    (when (and suppress-package-p
+               (re-search-forward org-babel-java--package-re nil t))
+      (replace-match ""))
+
+    ;; add a dummy main method if needed
+    (goto-char (point-min))
+    (when (not (re-search-forward org-babel-java--main-re nil t))
+      (org-babel-java--move-past org-babel-java--class-re)
+      (insert "\n    public static void main(String[] args) {
+        System.out.print(\"success\");
+    }\n\n"))
+
+    ;; special handling to return value
+    (when (eq result-type 'value)
+      (goto-char (point-min))
+      (org-babel-java--move-past org-babel-java--class-re)
+      (insert (format org-babel-java--result-wrapper
+                      (org-babel-process-file-name result-file 'noquote)))
+      (search-forward "public static void main(") ; rename existing main
+      (replace-match "public static Object _main("))
+
+    ;; add imports
+    (org-babel-java--import-maybe "java.util" "List")
+    (org-babel-java--import-maybe "java.util" "Arrays")
+    (org-babel-java--import-maybe "java.io" "BufferedWriter")
+    (org-babel-java--import-maybe "java.io" "FileWriter")
+    (org-babel-java--import-maybe "java.io" "IOException")
+
+    (buffer-string)))
+
+(defun org-babel-java--move-past (re)
+  "Move point past the first occurrence of the given regexp RE."
+  (while (re-search-forward re nil t)
+    (goto-char (1+ (match-end 0)))))
+
+(defun org-babel-java--import-maybe (package class)
+  "Import from PACKAGE the given CLASS if it is used and not already imported."
+  (let (class-found import-found)
+    (goto-char (point-min))
+    (setq class-found (re-search-forward class nil t))
+    (goto-char (point-min))
+    (setq import-found
+          (re-search-forward (concat "^import .*" package ".*\\(?:\\*\\|" class "\\);") nil t))
+    (when (and class-found (not import-found))
+      (org-babel-java--move-past org-babel-java--package-re)
+      (insert (concat "import " package "." class ";\n")))))
+
+(defun org-babel-expand-body:java (body params)
+  "Expand BODY with PARAMS.
+BODY could be a few statements, or could include a full class
+definition specifying package, imports, and class.  Because we
+allow this flexibility in what the source block can contain, it
+is simplest to expand the code block from the inside out."
+  (let* ((fullclassname (or (cdr (assq :classname params)) ; class and package
+                            (org-babel-java-find-classname body)))
+         (classname (car (last (split-string fullclassname "\\.")))) ; just class name
+         (packagename (if (string-match-p "\\." fullclassname)       ; just package name
+                          (file-name-base fullclassname)))
+         (var-lines (org-babel-variable-assignments:java params))
+         (imports-val (assq :imports params))
+         (imports (if imports-val
+                      (split-string (org-babel-read (cdr imports-val) nil) " ")
+                    nil)))
+    (with-temp-buffer
+      (insert body)
+
+      ;; wrap main.  If there are methods defined, but no main method
+      ;; and no class, wrap everything in a generic main method.
+      (goto-char (point-min))
+      (when (and (not (re-search-forward org-babel-java--main-re nil t))
+                 (not (re-search-forward org-babel-java--any-method-re nil t)))
+        (org-babel-java--move-past org-babel-java--package-re) ; if package is defined, move past it
+        (org-babel-java--move-past org-babel-java--imports-re) ; if imports are defined, move past them
+        (insert "public static void main(String[] args) {\n")
+        (indent-code-rigidly (point) (point-max) 4)
+        (goto-char (point-max))
+        (insert "\n}"))
+
+      ;; wrap class.  If there's no class, wrap everything in a
+      ;; generic class.
+      (goto-char (point-min))
+      (when (not (re-search-forward org-babel-java--class-re nil t))
+        (org-babel-java--move-past org-babel-java--package-re) ; if package is defined, move past it
+        (org-babel-java--move-past org-babel-java--imports-re) ; if imports are defined, move past them
+        (insert (concat "\npublic class " (file-name-base classname) " {\n"))
+        (indent-code-rigidly (point) (point-max) 4)
+        (goto-char (point-max))
+        (insert "\n}"))
+      (goto-char (point-min))
+
+      ;; insert variables from source block headers
+      (when var-lines
+        (goto-char (point-min))
+        (org-babel-java--move-past org-babel-java--class-re)   ; move inside class
+        (insert (mapconcat 'identity var-lines "\n"))
+        (insert "\n"))
+
+      ;; add imports from source block headers
+      (when imports
+        (goto-char (point-min))
+        (org-babel-java--move-past org-babel-java--package-re) ; if package is defined, move past it
+        (insert (mapconcat (lambda (package) (concat "import " package ";")) imports "\n") "\n"))
+
+      ;; add package at the top
+      (goto-char (point-min))
+      (when (and packagename (not (re-search-forward org-babel-java--package-re nil t)))
+        (insert (concat "package " packagename ";\n")))
+
+      ;; return expanded body
+      (buffer-string))))
+
+(defun org-babel-variable-assignments:java (params)
+  "Return a list of java statements assigning the block's variables.
+variables are contained in PARAMS."
+  (mapcar
+   (lambda (pair)
+     (let* ((type-data (org-babel-java-val-to-type (cdr pair)))
+            (basetype (car type-data))
+            (var-to-java (lambda (var) (funcall #'org-babel-java-var-to-java var basetype))))
+       (format "    static %s %s = %s;"
+               (cdr type-data)                     ; type
+               (car pair)                          ; name
+               (funcall var-to-java (cdr pair))))) ; value
+   (org-babel--get-vars params)))
+
+(defun org-babel-java-var-to-java (var basetype)
+  "Convert an elisp value to a java variable.
+Convert an elisp value, VAR, of type BASETYPE into a string of
+java source code specifying a variable of the same value."
+  (cond ((and (sequencep var) (not (stringp var)))
+         (let ((var-to-java (lambda (var) (funcall #'org-babel-java-var-to-java var basetype))))
+           (concat "Arrays.asList(" (mapconcat var-to-java var ", ") ")")))
+        ((eq var 'hline) org-babel-java-hline-to)
+        ((eq basetype 'integerp) (format "%d" var))
+        ((eq basetype 'floatp) (format "%f" var))
+        ((eq basetype 'stringp) (if (and (stringp var) (string-match-p ".\n+." var))
+                                    (error "Java does not support multiline string literals")
+                                  (format "\"%s\"" var)))))
+
+(defun org-babel-java-val-to-type (val)
+  "Determine the type of VAL.
+Return (BASETYPE . LISTTYPE), where BASETYPE is a symbol
+representing the type of the individual items in VAL, and
+LISTTYPE is a string name of the type parameter for a container
+for BASETYPE items."
+  (let* ((basetype (org-babel-java-val-to-base-type val))
+         (basetype-str (pcase basetype
+                         (`integerp "Integer")
+                         (`floatp "Double")
+                         (`stringp "String")
+                         (_ (error "Unknown type %S" basetype)))))
+    (cond
+     ((and (listp val) (listp (car val))) ; a table
+      (cons basetype (format "List<List<%s>>" basetype-str)))
+     ((or (listp val) (vectorp val))      ; a list declared in the source block header
+      (cons basetype (format "List<%s>" basetype-str)))
+     (t                                   ; return base type
+      (cons basetype basetype-str)))))
+
+(defun org-babel-java-val-to-base-type (val)
+  "Determine the base type of VAL.
+VAL may be
+`integerp' if all base values are integers
+`floatp' if all base values are either floating points or integers
+`stringp' otherwise."
+  (cond
+   ((integerp val) 'integerp)
+   ((floatp val) 'floatp)
+   ((or (listp val) (vectorp val))
+    (let ((type nil))
+      (mapc (lambda (v)
+              (pcase (org-babel-java-val-to-base-type v)
+                (`stringp (setq type 'stringp))
+                (`floatp
+                 (when (or (not type) (eq type 'integerp))
+                   (setq type 'floatp)))
+                (`integerp
+                 (unless type (setq type 'integerp)))))
+            val)
+      type))
+   (t 'stringp)))
+
+(defun org-babel-java-table-or-string (results)
+  "Convert RESULTS into an appropriate elisp value.
+If the results look like a list or vector, then convert them into an
+Emacs-lisp table, otherwise return the results as a string."
+  (let ((res (org-babel-script-escape results)))
+    (if (listp res)
+        (mapcar (lambda (el) (if (eq 'null el)
+                                 org-babel-java-null-to
+                               el))
+                res)
+      res)))
+
+(defun org-babel-java-evaluate (cmd result-type result-params result-file)
+  "Evaluate using an external java process.
+CMD the command to execute.
+
+If RESULT-TYPE equals `output' then return standard output as a
+string.  If RESULT-TYPE equals `value' then return the value
+returned by the source block, as elisp.
+
+RESULT-PARAMS input params used to format the response.
+
+RESULT-FILE filename of the tempfile to store the returned value in
+for `value' RESULT-TYPE.  Not used for `output' RESULT-TYPE."
+  (let ((raw (pcase result-type
+               (`output (org-babel-eval cmd ""))
+               (`value (org-babel-eval cmd "")
+                       (org-babel-eval-read-file result-file)))))
+    (org-babel-result-cond result-params raw
+                           (org-babel-java-table-or-string raw))))
 
 (provide 'ob-java)
 
-- 
cgit v1.2.3


From 2075411edbad954c0fdf2aa141757d834a6708b7 Mon Sep 17 00:00:00 2001
From: Mattias Engdegård <mattiase@acm.org>
Date: Thu, 30 Sep 2021 17:13:12 +0200
Subject: Fix regexp snags in org

* lisp/org/org-element.el (org-element-citation-key-re):
* lisp/org/ox-org.el (org-org-identity):
Remove repeated chars in alternatives.
* lisp/org/ob-java.el (org-babel-execute:java):
Remove superfluous backslash.
* lisp/org/ob-java.el (org-babel-java--main-re)
(org-babel-java--any-method-re): Remove (0+ space) expressions
subsumed by adjacent expressions.
---
 lisp/org/ob-java.el     | 44 +++++++++++++++++++++++---------------------
 lisp/org/org-element.el |  2 +-
 lisp/org/ox-org.el      |  2 +-
 3 files changed, 25 insertions(+), 23 deletions(-)

(limited to 'lisp/org/ob-java.el')

diff --git a/lisp/org/ob-java.el b/lisp/org/ob-java.el
index 60ef33bc6e4..dd3538743db 100644
--- a/lisp/org/ob-java.el
+++ b/lisp/org/ob-java.el
@@ -96,27 +96,29 @@ like javac -verbose."
 				       (group (1+ (in alnum ?_))) ; capture the class name
 				       (0+ space) ?{)
   "Regexp for the class declaration.")
-(defconst org-babel-java--main-re (rx line-start (0+ space) "public"
-				      (1+ space) "static"
-				      (1+ space) "void"
-				      (1+ space) "main"
-				      (0+ space) ?\(
-				      (0+ space) "String"
-				      (0+ space) (1+ (in alnum ?_ ?\[ ?\] space)) ; "[] args" or "args[]"
-				      (0+ space) ?\)
-				      (0+ space) (opt "throws" (1+ (in alnum ?_ ?, ?. space)))
-				      ?{)
+(defconst org-babel-java--main-re
+  (rx line-start (0+ space) "public"
+      (1+ space) "static"
+      (1+ space) "void"
+      (1+ space) "main"
+      (0+ space) ?\(
+      (0+ space) "String"
+      (1+ (in alnum ?_ ?\[ ?\] space)) ; "[] args" or "args[]"
+      ?\)
+      (0+ space) (opt "throws" (1+ (in alnum ?_ ?, ?. space)))
+      ?{)
   "Regexp for the main method declaration.")
-(defconst org-babel-java--any-method-re (rx line-start
-					    (0+ space) (opt (seq (1+ alnum) (1+ space)))   ; visibility
-					    (opt (seq "static" (1+ space)))                ; binding
-					    (1+ (in alnum ?_ ?\[ ?\]))                     ; return type
-                                            (1+ space) (1+ (in alnum ?_))                  ; method name
-					    (0+ space) ?\(
-					    (0+ space) (0+ (in alnum ?_ ?\[ ?\] ?, space)) ; params
-					    (0+ space) ?\)
-					    (0+ space) (opt "throws" (1+ (in alnum ?_ ?, ?. space)))
-					    ?{)
+(defconst org-babel-java--any-method-re
+  (rx line-start
+      (0+ space) (opt (seq (1+ alnum) (1+ space)))   ; visibility
+      (opt (seq "static" (1+ space)))                ; binding
+      (1+ (in alnum ?_ ?\[ ?\]))                     ; return type
+      (1+ space) (1+ (in alnum ?_))                  ; method name
+      (0+ space) ?\(
+      (0+ (in alnum ?_ ?\[ ?\] ?, space)) ; params
+      ?\)
+      (0+ space) (opt "throws" (1+ (in alnum ?_ ?, ?. space)))
+      ?{)
   "Regexp for any method.")
 (defconst org-babel-java--result-wrapper "\n    public static String __toString(Object val) {
         if (val instanceof String) {
@@ -192,7 +194,7 @@ replaced in this string.")
          ;; the dir to write the source file
          (packagedir (if (and (not run-from-temp) packagename)
                          (file-name-as-directory
-                          (concat basedir (replace-regexp-in-string "\\\." "/" packagename)))
+                          (concat basedir (replace-regexp-in-string "\\." "/" packagename)))
                        basedir))
          ;; the filename of the source file
          (src-file (concat packagedir classname ".java"))
diff --git a/lisp/org/org-element.el b/lisp/org/org-element.el
index ed684df17bf..f8334ccbc60 100644
--- a/lisp/org/org-element.el
+++ b/lisp/org/org-element.el
@@ -118,7 +118,7 @@
 ;; to current setup.
 
 (defconst org-element-citation-key-re
-  (rx "@" (group (one-or-more (any word "-.:?!`'/*@+|(){}<>&_^$#%&~"))))
+  (rx "@" (group (one-or-more (any word "-.:?!`'/*@+|(){}<>&_^$#%~"))))
   "Regexp matching a citation key.
 Key is located in match group 1.")
 
diff --git a/lisp/org/ox-org.el b/lisp/org/ox-org.el
index 11d9c09ebff..fcf876854fd 100644
--- a/lisp/org/ox-org.el
+++ b/lisp/org/ox-org.el
@@ -141,7 +141,7 @@ CONTENTS and INFO are ignored."
 CONTENTS is its contents, as a string or nil.  INFO is ignored."
   (let ((case-fold-search t))
     (replace-regexp-in-string
-     "^[ \t]*#\\+attr_[-_a-za-z0-9]+:\\(?: .*\\)?\n" ""
+     "^[ \t]*#\\+attr_[-_a-z0-9]+:\\(?: .*\\)?\n" ""
      (org-export-expand blob contents t))))
 
 (defun org-org-headline (headline contents info)
-- 
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