430 lines
18 KiB
EmacsLisp
430 lines
18 KiB
EmacsLisp
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;; -*- lexical-binding: t -*-
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;;; ob-ein.el --- org-babel functions for template evaluation
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;; Copyright (C) John M. Miller
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;; Author: John M. Miller <millejoh at mac.com>
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;;
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;;; License:
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;; This file is NOT part of GNU Emacs.
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;; ob-ein.el is free software: you can redistribute it and/or modify
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;; it under the terms of the GNU General Public License as published by
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;; the Free Software Foundation, either version 3 of the License, or
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;; (at your option) any later version.
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;; ob-ein.el is distributed in the hope that it will be useful,
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;; but WITHOUT ANY WARRANTY; without even the implied warranty of
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;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;; GNU General Public License for more details.
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;; You should have received a copy of the GNU General Public License
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;; along with ob-ein.el. If not, see <http://www.gnu.org/licenses/>.
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;;; Commentary:
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;; Support executing org-babel source blocks using EIN worksheets.
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;;; Credits:
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;; Uses code from https://github.com/gregsexton/ob-ipython (MIT License)
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;;; Code:
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(require 'ob)
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(require 'ein-utils)
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(autoload 'org-element-property "org-element")
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(autoload 'org-element-context "org-element")
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(autoload 'ein:notebooklist-new-notebook-with-name "ein-notebooklist")
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(autoload 'ein:notebooklist-login "ein-notebooklist")
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(autoload 'ein:notebook-get-opened-notebook "ein-notebook")
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(autoload 'ein:notebook-url "ein-notebook")
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(autoload 'ein:notebook-open "ein-notebook")
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(autoload 'ein:notebook-close "ein-notebook")
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(autoload 'ein:process-url-or-port "ein-process")
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(autoload 'ein:process-url-match "ein-process")
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(autoload 'ein:process-refresh-processes "ein-process")
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(autoload 'ein:jupyter-server-conn-info "ein-jupyter")
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(autoload 'ein:jupyter-server-start "ein-jupyter")
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(autoload 'ein:connect-buffer-to-notebook "ein-connect")
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(autoload 'ein:connect-run-buffer "ein-connect")
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(autoload 'ein:shared-output-get-cell "ein-shared-output")
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(autoload 'ein:shared-output-eval-string "ein-shared-output")
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(autoload 'ein:kernel-live-p "ein-kernel")
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(autoload 'ein:query-singleton-ajax "ein:query")
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(defvar *ob-ein-sentinel* "[....]"
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"Placeholder string replaced after async cell execution")
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(defcustom ob-ein-timeout-seconds 600
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"Maximum seconds to wait for block to finish (for synchronous operations)."
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:type 'integer
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:group 'ein)
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(defcustom ob-ein-languages
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'(("ein" . python)
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("ein-python" . python)
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("ein-R" . R)
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("ein-r" . R)
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("ein-julia" . julia)
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("ein-hy" . hy))
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"ob-ein has knowledge of these (ein-LANG . LANG-MODE) pairs."
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:type '(repeat (cons string symbol))
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:group 'ein)
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(defcustom ob-ein-anonymous-path ".%s.ipynb"
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"When session header doesn't specify ipynb, prosecute all interactions for a given language in this throwaway notebook (substitute %s with language)."
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:type '(string)
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:group 'ein)
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(defsubst ob-ein-anonymous-p (path)
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"Return t if PATH looks like ob-ein-anonymous-path. Fragile"
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(string-match (replace-regexp-in-string "%s" ".+"
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(replace-regexp-in-string "\\." "\\\\." ob-ein-anonymous-path))
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path))
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(defcustom ob-ein-inline-image-directory "ein-images"
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"Store ob-ein images here."
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:group 'ein
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:type '(directory))
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(defcustom ob-ein-default-header-args:ein nil
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"No documentation."
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:group 'ein
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:type '(repeat string))
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(defun ob-ein--inline-image-info (value)
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(let* ((f (md5 value))
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(d ob-ein-inline-image-directory)
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(tf (concat d "/ob-ein-" f ".png")))
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(unless (file-directory-p d)
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(make-directory d 'parents))
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tf))
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(defun ob-ein--write-base64-image (img-string file)
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(with-temp-file file
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(let ((buffer-read-only nil)
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(buffer-file-coding-system 'binary)
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(require-final-newline nil)
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(file-precious-flag t))
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(insert img-string)
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(base64-decode-region (point-min) (point-max)))))
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(defun ob-ein--return-mime-type (json file)
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(cl-loop
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for key in ein:output-types-text-preferred
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for type = (intern (format ":%s" key)) ; something like `:text'
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for value = (plist-get json type) ; FIXME: optimize
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when (plist-member json type)
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return
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(cl-case key
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((svg image/svg)
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(let ((file (or file (ob-ein--inline-image-info value))))
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(ob-ein--write-base64-image value file)
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(format "[[file:%s]]" file)))
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((png image/png jpeg image/jpeg)
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(let ((file (or file (ob-ein--inline-image-info value))))
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(ob-ein--write-base64-image value file)
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(format "[[file:%s]]" file)))
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(t (plist-get json type)))))
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(defun ob-ein--process-outputs (outputs params)
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(let ((file (cdr (assoc :image params))))
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(ein:join-str "\n"
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(cl-loop for o in outputs
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collecting (ob-ein--return-mime-type o file)))))
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(defun ob-ein--get-name-create (src-block-info)
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"Get the name of a src block or add a uuid as the name."
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(if-let ((name (cl-fifth src-block-info)))
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name
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(save-excursion
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(let ((el (org-element-context))
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(id (org-id-new 'none)))
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(goto-char (org-element-property :begin el))
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(back-to-indentation)
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(split-line)
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(insert (format "#+NAME: %s" id))
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id))))
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(defun ob-ein--babelize-lang (lang-name lang-mode)
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"Stand-up LANG-NAME as a babelized language with LANG-MODE syntax table.
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Based on ob-ipython--configure-kernel."
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(add-to-list 'org-src-lang-modes `(,lang-name . ,lang-mode))
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(defvaralias (intern (concat "org-babel-default-header-args:" lang-name))
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'ob-ein-default-header-args:ein)
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(fset (intern (concat "org-babel-execute:" lang-name))
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`(lambda (body params)
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(require (quote ,(intern (format "ob-%s" lang-mode))) nil t)
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(if (boundp 'python-indent-guess-indent-offset-verbose)
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(setq python-indent-guess-indent-offset-verbose nil))
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(let* ((parser
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(quote
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,(intern
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(format "org-babel-variable-assignments:%s" lang-mode))))
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(assignments (if (fboundp parser)
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(funcall (symbol-function parser) params)
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(ein:log 'verbose "%s: No suitable ob-%s module"
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(concat "org-babel-execute:" ,lang-name)
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(quote ,lang-mode))
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nil)))
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(ob-ein--execute-body body params assignments)))))
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(defun ob-ein--execute-body (body params assignments)
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(let* ((buffer (current-buffer))
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(processed-params (org-babel-process-params params))
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(result-params (cdr (assq :result-params params)))
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(session (or (ein:aand (cdr (assoc :session processed-params))
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(unless (string= "none" it)
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(format "%s" it)))
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ein:url-localhost))
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(lang (nth 0 (org-babel-get-src-block-info)))
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(kernelspec (or (cdr (assoc :kernelspec processed-params))
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(ein:aif (cdr (assoc lang org-src-lang-modes))
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(cons 'language (format "%s" it))
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(error "ob-ein--execute-body: %s not among %s"
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lang (mapcar #'car org-src-lang-modes)))))
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(name (ob-ein--get-name-create (org-babel-get-src-block-info)))
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(full-body (org-babel-expand-body:generic
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(encode-coding-string body 'utf-8)
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params
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assignments))
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(callback (lambda (notebook)
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(ob-ein--execute-async
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buffer
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full-body
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(ein:$notebook-kernel notebook)
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processed-params
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result-params
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name))))
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(save-excursion
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(cl-assert (not (stringp (org-babel-goto-named-src-block name))))
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(org-babel-insert-result *ob-ein-sentinel* result-params))
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(ob-ein--initiate-session session kernelspec callback)
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(if (ein:eval-if-bound 'org-current-export-file)
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(save-excursion
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(cl-loop with interval = 2000
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with pending = t
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repeat (/ (* ob-ein-timeout-seconds 1000) interval)
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do (progn
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(org-babel-goto-named-result name)
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(forward-line 1)
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(setq pending (re-search-forward
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(regexp-quote *ob-ein-sentinel*)
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(org-babel-result-end) t)))
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until (not pending)
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do (sleep-for 0 interval)
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finally return
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(if pending
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(progn
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(ein:log 'error "ob-ein--execute-body: %s timed out" name)
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"")
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(ob-ein--process-outputs
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(ein:oref-safe (ein:shared-output-get-cell) 'outputs)
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processed-params))))
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(org-babel-remove-result)
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*ob-ein-sentinel*)))
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(defsubst ob-ein--execute-async-callback (buffer params result-params name)
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"Callback of 1-arity (the shared output cell) to update org buffer when
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`ein:shared-output-eval-string' completes."
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(apply-partially
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(lambda (buffer* params* result-params* name* cell)
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(let* ((raw (ein:aif (ein:oref-safe cell 'traceback)
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(ansi-color-apply (ein:join-str "\n" it))
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(ob-ein--process-outputs
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(ein:oref-safe cell 'outputs) params*)))
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(result
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(let ((tmp-file (org-babel-temp-file "ein-")))
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(with-temp-file tmp-file raw)
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(org-babel-result-cond result-params*
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raw (org-babel-import-elisp-from-file tmp-file '(16)))))
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(info (org-babel-get-src-block-info 'light)))
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(ein:log 'debug "ob-ein--execute-async-callback %s \"%s\" %s" name* result buffer*)
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(save-excursion
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(save-restriction
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(with-current-buffer buffer*
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(unless (stringp (org-babel-goto-named-src-block name*)) ;; stringp=error
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(when info ;; kill #+RESULTS: (no-name)
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(setf (nth 4 info) nil)
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(org-babel-remove-result info))
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(org-babel-remove-result) ;; kill #+RESULTS: name
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(org-babel-insert-result
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result
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(cdr (assoc :result-params
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(cl-third (org-babel-get-src-block-info)))))
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(org-redisplay-inline-images)))))))
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buffer params result-params name))
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(defun ob-ein--execute-async (buffer body kernel params result-params name)
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"As `ein:shared-output-get-cell' is a singleton, ob-ein can only execute blocks
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one at a time. Further, we do not order the queued up blocks!"
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(deferred:$
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(deferred:next
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(deferred:lambda ()
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(let ((cell (ein:shared-output-get-cell)))
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(if (eq (slot-value cell 'callback) #'ignore)
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(let ((callback
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(ob-ein--execute-async-callback buffer params
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result-params name)))
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(setf (slot-value cell 'callback) callback))
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;; still pending previous callback
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(deferred:nextc (deferred:wait 1200) self)))))
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(deferred:nextc it
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(lambda (_x)
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(ein:shared-output-eval-string kernel body nil)))))
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(defun ob-ein--parse-session (session)
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(cl-multiple-value-bind (url-or-port _password) (ein:jupyter-server-conn-info)
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(let ((tokens (split-string session "/"))
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(parsed-url (url-generic-parse-url session)))
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(cond ((null (url-host parsed-url))
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(let* ((candidate (apply #'ein:url (car tokens) (cdr tokens)))
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(parsed-candidate (url-generic-parse-url candidate))
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(missing (url-scheme-get-property
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(url-type parsed-candidate)
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'default-port)))
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(if (and url-or-port
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(= (url-port parsed-candidate) missing))
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(apply #'ein:url url-or-port (cdr tokens))
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candidate)))
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(t (ein:url session))))))
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(defun ob-ein--initiate-session (session kernelspec callback &optional babel-info)
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"Retrieve notebook based on SESSION path and KERNELSPEC, starting jupyter instance
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if necessary. Install CALLBACK (i.e., cell execution) upon notebook retrieval."
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(let* ((nbpath (ob-ein--parse-session session))
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(info (or (org-babel-get-src-block-info) babel-info))
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(anonymous-path (format ob-ein-anonymous-path (nth 0 info)))
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(parsed-url (url-generic-parse-url nbpath))
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(slash-path (car (url-path-and-query parsed-url)))
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(path (if (string= slash-path "") anonymous-path
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(substring slash-path 1)))
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(url-or-port (if (string= slash-path "")
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nbpath
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(substring nbpath 0 (- (length slash-path)))))
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(notebook (ein:notebook-get-opened-notebook url-or-port path))
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(callback-nbopen (lambda (nb _created)
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(cl-loop repeat 50
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for live-p = (ein:kernel-live-p (ein:$notebook-kernel nb))
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until live-p
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do (sleep-for 0 300)
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finally
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do (if (not live-p)
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(ein:log 'error
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"Kernel for %s failed to launch"
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(ein:$notebook-notebook-name nb))
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(funcall callback nb)))))
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(errback-nbopen (lambda (url-or-port status-code)
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(if (eq status-code 404)
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(ein:notebooklist-new-notebook-with-name
|
||
|
|
url-or-port kernelspec path callback-nbopen t))))
|
||
|
|
(callback-login (lambda (_buffer url-or-port)
|
||
|
|
(ein:notebook-open url-or-port path kernelspec
|
||
|
|
callback-nbopen errback-nbopen t))))
|
||
|
|
(cond ((and notebook
|
||
|
|
(string= path anonymous-path)
|
||
|
|
(stringp kernelspec)
|
||
|
|
(not (equal (ein:$kernelspec-name (ein:$notebook-kernelspec notebook))
|
||
|
|
kernelspec)))
|
||
|
|
(ein:log 'debug "ob-ein--initiate-session: switching %s from %s to %s"
|
||
|
|
path (ein:$kernelspec-name (ein:$notebook-kernelspec notebook))
|
||
|
|
kernelspec)
|
||
|
|
(cl-letf (((symbol-function 'y-or-n-p) #'ignore))
|
||
|
|
(ein:notebook-close notebook)
|
||
|
|
(ein:query-singleton-ajax
|
||
|
|
(list 'ob-ein--initiate-session (ein:url url-or-port path))
|
||
|
|
(ein:notebook-url notebook)
|
||
|
|
:type "DELETE"))
|
||
|
|
(cl-loop repeat 8
|
||
|
|
for extant = (file-exists-p path)
|
||
|
|
until (not extant)
|
||
|
|
do (sleep-for 0 500)
|
||
|
|
finally do (if extant
|
||
|
|
(ein:display-warning (format "cannot del %s" path))
|
||
|
|
(ob-ein--initiate-session session kernelspec callback))))
|
||
|
|
(notebook (funcall callback notebook))
|
||
|
|
((string= (url-host parsed-url) ein:url-localhost)
|
||
|
|
(ein:process-refresh-processes)
|
||
|
|
(ein:aif (ein:process-url-match nbpath)
|
||
|
|
(ein:notebooklist-login (ein:process-url-or-port it) callback-login)
|
||
|
|
(ein:jupyter-server-start
|
||
|
|
(executable-find (or (ein:eval-if-bound 'ein:jupyter-default-server-command)
|
||
|
|
"jupyter"))
|
||
|
|
(read-directory-name "Notebook directory: " default-directory)
|
||
|
|
nil
|
||
|
|
callback-login
|
||
|
|
(let* ((port (url-port parsed-url))
|
||
|
|
(avoid (url-scheme-get-property (url-type parsed-url) 'default-port)))
|
||
|
|
(cond ((= port avoid) nil)
|
||
|
|
(t (url-port parsed-url)))))))
|
||
|
|
(t (ein:notebooklist-login url-or-port callback-login)))))
|
||
|
|
|
||
|
|
(defun ob-ein--edit-ctrl-c-ctrl-c ()
|
||
|
|
"C-c C-c mapping in ein:connect-mode-map."
|
||
|
|
(interactive)
|
||
|
|
(if (not (org-src-edit-buffer-p))
|
||
|
|
(ein:connect-run-buffer)
|
||
|
|
(org-edit-src-save)
|
||
|
|
(when (boundp 'org-src--beg-marker)
|
||
|
|
(let* ((beg org-src--beg-marker)
|
||
|
|
(buf (marker-buffer beg)))
|
||
|
|
(with-current-buffer buf
|
||
|
|
(save-excursion
|
||
|
|
(goto-char beg)
|
||
|
|
(org-ctrl-c-ctrl-c)))))))
|
||
|
|
|
||
|
|
(defcustom ob-ein-babel-edit-polymode-ignore nil
|
||
|
|
"When false override default python mode key mapping for `\C-c\C-c' while inside a babel edit buffer.
|
||
|
|
Instead the binding will be to `ob-ein--edit-ctrl-c-ctrl-c', which will execute the code block being edited."
|
||
|
|
:group 'ein
|
||
|
|
:type '(boolean))
|
||
|
|
|
||
|
|
(defun org-babel-edit-prep:ein (babel-info)
|
||
|
|
(if (and ein:polymode (not ob-ein-babel-edit-polymode-ignore))
|
||
|
|
(progn
|
||
|
|
(use-local-map (copy-keymap python-mode-map))
|
||
|
|
(local-set-key "\C-c\C-c" 'ob-ein--edit-ctrl-c-ctrl-c))
|
||
|
|
(let* ((buffer (current-buffer))
|
||
|
|
(processed-parameters (nth 2 babel-info))
|
||
|
|
(session (or (ein:aand (cdr (assoc :session processed-parameters))
|
||
|
|
(unless (string= "none" it)
|
||
|
|
(format "%s" it)))
|
||
|
|
ein:url-localhost))
|
||
|
|
(lang (car babel-info))
|
||
|
|
(kernelspec (or (cdr (assoc :kernelspec processed-parameters))
|
||
|
|
(ein:aif (cdr (assoc lang org-src-lang-modes))
|
||
|
|
(cons 'language (format "%s" it))
|
||
|
|
(error "ob-ein--execute-body: %s not among %s"
|
||
|
|
lang (mapcar #'car org-src-lang-modes))))))
|
||
|
|
(ob-ein--initiate-session
|
||
|
|
session
|
||
|
|
kernelspec
|
||
|
|
(lambda (notebook)
|
||
|
|
(ein:connect-buffer-to-notebook notebook buffer t)
|
||
|
|
(define-key ein:connect-mode-map "\C-c\C-c" 'ob-ein--edit-ctrl-c-ctrl-c))
|
||
|
|
babel-info))))
|
||
|
|
|
||
|
|
(defun org-babel-edit-prep:ein-python (babel-info)
|
||
|
|
(org-babel-edit-prep:ein babel-info))
|
||
|
|
|
||
|
|
(cl-loop for (lang . mode) in ob-ein-languages
|
||
|
|
do (ob-ein--babelize-lang lang mode))
|
||
|
|
|
||
|
|
;;;###autoload
|
||
|
|
(if (featurep 'org)
|
||
|
|
(let* ((orig (get 'org-babel-load-languages 'custom-type))
|
||
|
|
(orig-cdr (cdr orig))
|
||
|
|
(choices (plist-get orig-cdr :key-type)))
|
||
|
|
(push '(const :tag "Ein" ein) (nthcdr 1 choices))
|
||
|
|
(put 'org-babel-load-languages 'custom-type
|
||
|
|
(cons (car orig) (plist-put orig-cdr :key-type choices)))))
|
||
|
|
|
||
|
|
(provide 'ob-ein)
|