Re: [O] [bug, patch, ox] INCLUDE and footnotes

[Rasmus]

Hi,

Thanks for the comments.  I managed to make the patch less complicated.

Nicolas Goaziou <address@hidden> writes:

>> +      (let* ((lines (and lines (split-string lines "-")))
>> +         (lbeg (and lines (string-to-number (car lines))))
>> +         (lend (and lines (string-to-number (cadr lines)))))
>
> This is not needed. `point-min' and `point-max' refer to the boundaries
> of the area to be included. It avoids relying on the expensive
> `line-number-at-pos' function later.
>
> Moreover, I suggest store (point-max) as a marker since you are going to
> modify contents of the buffer (e.g., adding ID to labels).

I did not know markers but they seem perfect in this case.  The manual
mentions setting markers to nil after use.  I guess it's not necessary
here since they are in a (let ⋯)?

>> +    (goto-char (point-min))
>> +    (while (re-search-forward org-footnote-re nil t)
>> +      (let* ((reference (org-element-context))
>> +             (type (org-element-type reference))
>> +             (footnote-type (org-element-property :type reference))
>> +             (label (org-element-property :label reference)))
>> +        (when (eq type 'footnote-reference)
>
> The order is confusing here. First you check if you're really at
> a footnote reference, then you bind LABEL and FOOTNOTE-TYPE. Actually,
> the latter doesn't even need to bound since you use it only once.

I check if I'm at a footnote reference 'cause I never want to deal with a
footnote-*definition* directly.  AFAIK org-footnote-re matches both.  It
seems a footnote-reference can never be at the beginning of line, but I
would still prefer a more explicit test through org-element.

>> +          (goto-char (org-element-property :begin reference))
>> +          (when label
>> +            (forward-char 4)
>> +            (insert (format "%d-" id))
>
> This looks wrong. Labels can be "1", "fn:label" or even "fn:" in
> anonymous footnotes. You need to check if label matches "\\`[0-9]+\\'",
> in which case prepending "fn:" is also necessary.

Ah, that explains the "\\`[0-9]+\\'" that always confused me.

>> +                  (let ((definition (org-element-context)))
>> +                    (when (and lines
>> +                               (or (< lend (line-number-at-pos
>> +                                            (org-element-property
>> +                                             :contents-begin definition)))
>> +                                   (> lbeg (line-number-at-pos
>> +                                            (org-element-property
>> +                                             :contents-begin definition)))))
>> +                      (puthash (org-element-property :label definition)
>> +                               (org-element-normalize-string
>> +                                (buffer-substring
>> +                                 (org-element-property
>> +                                  :contents-begin definition)
>> +                                 (org-element-property
>> +                                  :contents-end definition)))
>> +                               footnotes)))))))))))
>
> You don't need this part. Basically move to the definition of the
> current reference in a wide buffer. If you're not within narrowed
> boundaries stored before, put it in the hash table. Otherwise, skip it.
> It doesn't require `org-element-context' or `line-number-at-pos'.

OK.  I do it in a differently now, relying on org-footnote-get-definition.
Or do you have something more low-level in mind?  

The only "bug" *I'm aware of* is that it will pick up the wrong new-label
for footnote for something like [fn:ref with space].  But this is anyway
not a proper label, I think.  Is that OK?

Thanks,
Rasmus

-- 
Sådan en god dansk lagereddike kan man slet ikke bruge mere

>From 36bde4b87a1b3405ab80867d66b074722a251837 Mon Sep 17 00:00:00 2001
From: rasmus <address@hidden>
Date: Tue, 9 Dec 2014 12:40:52 +0100
Subject: [PATCH 1/2] ox.el: Fix footnote-bug in #+INCLUDE-keyword

* ox.el (org-export--prepare-file-contents): Preserve footnotes
when using the LINES argument.  New optional argument FOOTNOTES.
 (org-export-expand-include-keyword): New optional argument
 FOOTNOTES.
* test-ox.el (test-org-export/expand-include): Add test for INCLUDE with :lines 
and footnotes.
---
 lisp/ox.el              | 82 ++++++++++++++++++++++++++++++++++---------------
 testing/lisp/test-ox.el | 32 +++++++++++++++++--
 2 files changed, 87 insertions(+), 27 deletions(-)

diff --git a/lisp/ox.el b/lisp/ox.el
index 9d9e794..11b9a29 100644
--- a/lisp/ox.el
+++ b/lisp/ox.el
@@ -3052,17 +3052,20 @@ locally for the subtree through node properties."
                   (car key)
                   (if (org-string-nw-p val) (format " %s" val) ""))))))))
 
-(defun org-export-expand-include-keyword (&optional included dir)
+(defun org-export-expand-include-keyword (&optional included dir footnotes)
   "Expand every include keyword in buffer.
 Optional argument INCLUDED is a list of included file names along
 with their line restriction, when appropriate.  It is used to
 avoid infinite recursion.  Optional argument DIR is the current
 working directory.  It is used to properly resolve relative
-paths."
+paths.  Optional argument FOOTNOTES is a hash-table used for
+storing and resolving footnotes.  It is created automatically."
   (let ((case-fold-search t)
        (file-prefix (make-hash-table :test #'equal))
-       (current-prefix 0))
+       (current-prefix 0)
+       (footnotes (or footnotes (make-hash-table :test #'equal))))
     (goto-char (point-min))
+    ;; Expand INCLUDE keywords.
     (while (re-search-forward "^[ \t]*#\\+INCLUDE:" nil t)
       (let ((element (save-match-data (org-element-at-point))))
        (when (eq (org-element-type element) 'keyword)
@@ -3155,15 +3158,24 @@ paths."
                               file location only-contents lines)
                            lines)))
                     (org-mode)
-                    (insert
-                     (org-export--prepare-file-contents
-                      file lines ind minlevel
-                      (or (gethash file file-prefix)
-                          (puthash file (incf current-prefix) file-prefix)))))
+                     (insert (org-export--prepare-file-contents
+                             file lines ind minlevel
+                             (or (gethash file file-prefix)
+                                 (puthash file (incf current-prefix) 
file-prefix))
+                             footnotes)))
                   (org-export-expand-include-keyword
                    (cons (list file lines) included)
-                   (file-name-directory file))
-                  (buffer-string)))))))))))))
+                   (file-name-directory file)
+                   footnotes)
+                  (buffer-string)))))
+              ;; Expand footnotes after all files have been
+              ;; included.  Footnotes are stored at end of buffer.
+             (when (and (not included) (> (hash-table-count footnotes) 0))
+               (org-with-wide-buffer
+                (goto-char (point-max))
+                (unless (bolp) (insert "\n"))
+                (maphash (lambda (ref def) (insert (format "[%s] %s\n" ref 
def)))
+                         footnotes)))))))))))
 
 (defun org-export--inclusion-absolute-lines (file location only-contents lines)
   "Resolve absolute lines for an included file with file-link.
@@ -3227,8 +3239,8 @@ Return a string of lines to be included in the format 
expected by
                       (while (< (point) end) (incf counter) (forward-line))
                       counter))))))))
 
-(defun org-export--prepare-file-contents (file &optional lines ind minlevel id)
-  "Prepare the contents of FILE for inclusion and return them as a string.
+(defun org-export--prepare-file-contents (file &optional lines ind minlevel id 
footnotes)
+  "Prepare contents of FILE for inclusion and return it as a string.
 
 When optional argument LINES is a string specifying a range of
 lines, include only those lines.
@@ -3246,7 +3258,11 @@ file should have.
 Optional argument ID is an integer that will be inserted before
 each footnote definition and reference if FILE is an Org file.
 This is useful to avoid conflicts when more than one Org file
-with footnotes is included in a document."
+with footnotes is included in a document.
+
+Optional argument FOOTNOTES is a hash-table to store footnotes in
+the included document.
+"
   (with-temp-buffer
     (insert-file-contents file)
     (when lines
@@ -3309,18 +3325,34 @@ with footnotes is included in a document."
     ;; become file specific and cannot collide with footnotes in other
     ;; included files.
     (when id
-      (goto-char (point-min))
-      (while (re-search-forward org-footnote-re nil t)
-       (let ((reference (org-element-context)))
-         (when (memq (org-element-type reference)
-                     '(footnote-reference footnote-definition))
-           (goto-char (org-element-property :begin reference))
-           (forward-char)
-           (let ((label (org-element-property :label reference)))
-             (cond ((not label))
-                   ((org-string-match-p "\\`[0-9]+\\'" label)
-                    (insert (format "fn:%d-" id)))
-                   (t (forward-char 3) (insert (format "%d-" id)))))))))
+      (let ((marker-min (point-min-marker))
+           (marker-max (point-max-marker)))
+       (goto-char (point-min))
+       (while (re-search-forward org-footnote-re nil t)
+         (let* ((reference (org-element-context))
+                (label (org-element-property :label reference))
+                (digit-label (and label (org-string-match-p "\\`[0-9]+\\'" 
label))))
+           (when (eq (org-element-type reference) 'footnote-reference)
+             (goto-char (1+ (org-element-property :begin reference)))
+             (when label
+               (let ((new-label
+                      (buffer-substring-no-properties
+                       (point)
+                       (progn (if digit-label (insert (format "fn:%d-" id))
+                                (forward-char 3)
+                                (insert (format "%d-" id)))
+                              (1- (search-forward "]"))))))
+                 (unless (eq (org-element-property :type reference) 'inline)
+                   (org-with-wide-buffer
+                    (let* ((definition (org-footnote-get-definition label))
+                           (beginning (set-marker (make-marker) (nth 1 
definition))))
+                      (goto-char (1+ beginning))
+                      (if digit-label (insert (format "fn:%d-" id))
+                        (forward-char 3)
+                        (insert (format "%d-" id)))
+                      (when (or (< beginning marker-min) (> beginning 
marker-max))
+                        (puthash new-label (nth 3 definition)
+                                 footnotes))))))))))))
     (org-element-normalize-string (buffer-string))))
 
 (defun org-export-execute-babel-code ()
diff --git a/testing/lisp/test-ox.el b/testing/lisp/test-ox.el
index 9a0e787..37e2e23 100644
--- a/testing/lisp/test-ox.el
+++ b/testing/lisp/test-ox.el
@@ -904,12 +904,13 @@ Footnotes[fn:1], [fn:test] and [fn:inline:anonymous 
footnote].
                        (org-element-property :label ref)))))))))))))
   ;; Footnotes labels are not local to each include keyword.
   (should
-   (= 3
+   (= 4
       (length
        (delete-dups
        (let ((contents "
-Footnotes[fn:1], [fn:test] and [fn:inline:anonymous footnote].
+Footnotes[fn:1], [fn:test], [2] and [fn:inline:anonymous footnote].
 \[fn:1] Footnote 1
+\[2] Footnote 2
 \[fn:test] Footnote \"test\""))
          (org-test-with-temp-text-in-file contents
            (let ((file (buffer-file-name)))
@@ -919,6 +920,33 @@ Footnotes[fn:1], [fn:test] and [fn:inline:anonymous 
footnote].
                (org-element-map (org-element-parse-buffer)
                    'footnote-reference
                  (lambda (ref) (org-element-property :label ref)))))))))))
+  ;; Footnotes are supported by :lines-like elements and unnecessary
+  ;; footnotes are dropped.
+  (should
+   (= 4
+      (length
+       (delete-dups
+       (let ((contents "
+* foo
+Footnotes[fn:1]
+* bar
+Footnotes[fn:2], foot[fn:test], digit only[3], and [fn:inline:anonymous 
footnote]
+
+\[fn:1] Footnote 1
+\[fn:2] Footnote 1
+* Footnotes
+\[fn:test] Footnote \"test\"
+\[3] Footnote 3
+"))
+         (org-test-with-temp-text-in-file contents
+           (let ((file (buffer-file-name)))
+             (org-test-with-temp-text
+                 (format "#+INCLUDE: \"%s::*bar\"
+" file)
+               (org-export-expand-include-keyword)
+               (org-element-map (org-element-parse-buffer)
+                   'footnote-definition
+                 (lambda (ref) (org-element-property :label ref)))))))))))
   ;; If only-contents is non-nil only include contents of element.
   (should
    (equal
-- 
2.2.1