From eee6e9e14fd1d07d2048d8c0472ba34a5b6611f9 Mon Sep 17 00:00:00 2001
From: Olivier Labbe <olivier.labbe@univ-grenoble-alpes.fr>
Date: Wed, 26 Feb 2025 16:16:41 +0100
Subject: [PATCH 1/6] Config MathJax to use TeX in formulas
---
src/ptf/cmds/xml/jats/jats_parser.py | 13 +++++++++++--
src/ptf/cmds/xml_cmds.py | 5 ++++-
src/ptf/static/ptf/css/bs5/base.css | 2 +-
src/ptf/static/ptf/css/bs5/ptf.css | 4 ++--
src/ptf/static/ptf/css/ptf.css | 2 +-
src/ptf/static/ptf/js/mathjax-config.js | 4 ++--
6 files changed, 21 insertions(+), 9 deletions(-)
diff --git a/src/ptf/cmds/xml/jats/jats_parser.py b/src/ptf/cmds/xml/jats/jats_parser.py
index a1c48761..2ce87202 100644
--- a/src/ptf/cmds/xml/jats/jats_parser.py
+++ b/src/ptf/cmds/xml/jats/jats_parser.py
@@ -407,7 +407,7 @@ class JatsBase(XmlParserBase):
img_url = os.path.join(kwargs["base_url"], "png", img_url)
else:
img_url = os.path.join(kwargs["base_url"], "jpg", img_url)
-
+
img_text = '<a href="' + img_url + '" data-lightbox="image-'
img_text += str(len(self.figures)) + '" title="">'
img_text += '<img src="' + img_url + f'" class="{classe}"/>'
@@ -495,7 +495,10 @@ class JatsBase(XmlParserBase):
if label or node.tag == "disp-formula":
html += '<table class="formula"><tr><td class="formula-inner">'
- html += '<span class="mathjax-formula" '
+ if self.formula_with_tex:
+ html += '<span class="mathjax-formula formula-with-tex" '
+ else:
+ html += '<span class="mathjax-formula" '
if formula_id:
html += 'id="' + formula_id + '" '
alt_text = tex_math.replace("\n", "") if node.tag == "disp-formula" else tex_math
@@ -2137,12 +2140,17 @@ class JatsIssue(IssueData, JatsBase):
for child in node:
tag = normalize(child.tag)
+ kwargs = {}
if tag == "article":
+ if self.journal and self.journal.pid in ["CRCHIM"] and int(self.year) > 2024:
+ kwargs["formula_with_tex"] = True
+
article = JatsArticle(
tree=child,
issue=self,
from_folder=self.from_folder,
no_bib=self.no_bib,
+ **kwargs
)
self.warnings.extend(article.warnings)
self.articles.append(article)
@@ -2485,6 +2493,7 @@ class JatsArticle(ArticleData, JatsArticleBase):
self.for_tex_file = kwargs["for_tex_file"] if "for_tex_file" in kwargs else False
self.from_folder = kwargs["from_folder"] if "from_folder" in kwargs else None
self.no_bib = kwargs.get("no_bib", False)
+ self.formula_with_tex = kwargs.get("formula_with_tex", False)
self.parse_tree(kwargs["tree"])
diff --git a/src/ptf/cmds/xml_cmds.py b/src/ptf/cmds/xml_cmds.py
index ad4edf72..339a20ef 100644
--- a/src/ptf/cmds/xml_cmds.py
+++ b/src/ptf/cmds/xml_cmds.py
@@ -784,7 +784,10 @@ class addArticleXmlCmd(addXmlCmd):
self.provider_col = provider_col
def set_article_single_mode(self):
- self.xarticle = jats_parser.JatsArticle(tree=self.tree)
+ kwargs = {}
+ if self.issue and self.issue.my_collection.pid in ["CRCHIM"] and int(self.issue.year) > 2024:
+ kwargs["formula_with_tex"] = True
+ self.xarticle = jats_parser.JatsArticle(tree=self.tree, **kwargs)
self.warnings.extend(self.xarticle.warnings)
# TODO: MaxiDML: allow the creation of an issue on the fly
diff --git a/src/ptf/static/ptf/css/bs5/base.css b/src/ptf/static/ptf/css/bs5/base.css
index 41bcce50..7f0d95ba 100644
--- a/src/ptf/static/ptf/css/bs5/base.css
+++ b/src/ptf/static/ptf/css/bs5/base.css
@@ -128,7 +128,7 @@
/* Not sure if it can break things, add a scrollbar to formulas for tiny screens */
table.formula {
- overflow-x: scroll;
+ overflow-x: auto;
display: block;
margin: 0 auto;
max-width: fit-content;
diff --git a/src/ptf/static/ptf/css/bs5/ptf.css b/src/ptf/static/ptf/css/bs5/ptf.css
index 2ed9f45e..ebcc703a 100644
--- a/src/ptf/static/ptf/css/bs5/ptf.css
+++ b/src/ptf/static/ptf/css/bs5/ptf.css
@@ -844,7 +844,7 @@ body:has(> #lightbox-root.showed) .outline-sm {
display: block;
}
-#summary th, td {
+#summary th, #summary td {
padding: 15px;
}
@@ -1238,4 +1238,4 @@ hr.panel-title-separator {
width: 96%;
padding-top: 10px;
padding-left: 10px;
-}
\ No newline at end of file
+}
diff --git a/src/ptf/static/ptf/css/ptf.css b/src/ptf/static/ptf/css/ptf.css
index d4bfcc18..fb940006 100644
--- a/src/ptf/static/ptf/css/ptf.css
+++ b/src/ptf/static/ptf/css/ptf.css
@@ -873,7 +873,7 @@ ul.cms-breadcrumb {
display: block;
}
-#summary th, td {
+#summary th, #summary td {
padding: 15px;
}
diff --git a/src/ptf/static/ptf/js/mathjax-config.js b/src/ptf/static/ptf/js/mathjax-config.js
index fe6c3471..03e84639 100644
--- a/src/ptf/static/ptf/js/mathjax-config.js
+++ b/src/ptf/static/ptf/js/mathjax-config.js
@@ -1,6 +1,6 @@
function replaceMml() {
console.log("Replacing mml");
- $(".mathjax-formula").each(function () {
+ $(".mathjax-formula.formula-with-tex").each(function () {
var formula = $(this);
var tex = formula.data("tex");
if (tex != "") {
@@ -64,7 +64,7 @@ window.MathJax = {
startup: {
pageReady: function () {
console.log("MathJax pageReady");
- //replaceMml();
+ replaceMml();
//
// Do the usual startup (which does a typeset).
// When that is all done, un-hide the page.
--
GitLab
From d0b2e38f1a12b156231b6892fda2b019fcb4d8e0 Mon Sep 17 00:00:00 2001
From: Olivier Labbe <olivier.labbe@univ-grenoble-alpes.fr>
Date: Wed, 26 Feb 2025 16:30:39 +0100
Subject: [PATCH 2/6] Config MathJax to use TeX in formulas
---
src/ptf/cmds/xml/jats/jats_parser.py | 1 +
1 file changed, 1 insertion(+)
diff --git a/src/ptf/cmds/xml/jats/jats_parser.py b/src/ptf/cmds/xml/jats/jats_parser.py
index 2ce87202..e73035d7 100644
--- a/src/ptf/cmds/xml/jats/jats_parser.py
+++ b/src/ptf/cmds/xml/jats/jats_parser.py
@@ -98,6 +98,7 @@ class JatsBase(XmlParserBase):
self.add_span_around_tex_formula = False
# Used to create a Tex file from an XML value (ie abstract)
self.for_tex_file = False
+ self.formula_with_tex = False
def parse_tree(self, tree):
self.tree = tree
--
GitLab
From 713cd2a90e5d03a7547b616356b87a9a1c501b02 Mon Sep 17 00:00:00 2001
From: Olivier Labbe <olivier.labbe@univ-grenoble-alpes.fr>
Date: Thu, 27 Feb 2025 12:01:09 +0100
Subject: [PATCH 3/6] Config MathJax to use TeX in formulas
---
src/ptf/static/ptf/js/mathjax-config.js | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/src/ptf/static/ptf/js/mathjax-config.js b/src/ptf/static/ptf/js/mathjax-config.js
index 03e84639..b9750fee 100644
--- a/src/ptf/static/ptf/js/mathjax-config.js
+++ b/src/ptf/static/ptf/js/mathjax-config.js
@@ -11,7 +11,7 @@ function replaceMml() {
window.MathJax = {
loader: {
- load: ["[tex]/upgreek", "[tex]/textmacros", "[tex]/noerrors", "[tex]/physics"],
+ load: ["[tex]/upgreek", "[tex]/textmacros", "[tex]/noerrors", "[tex]/physics", "[tex]/textcomp"],
},
tex: {
inlineMath: [
@@ -19,7 +19,7 @@ window.MathJax = {
["\\(", "\\)"],
],
packages: {
- "[+]": ["upgreek", "textmacros", "noerrors", "physics"],
+ "[+]": ["upgreek", "textmacros", "noerrors", "physics", "textcomp"],
},
processEscapes: true, // use \$ to produce a literal dollar sign
processEnvironments: true,
--
GitLab
From f9e5cc9312ac60d777645c548fbd0f0296cc6a06 Mon Sep 17 00:00:00 2001
From: Olivier Labbe <olivier.labbe@univ-grenoble-alpes.fr>
Date: Thu, 27 Feb 2025 17:09:26 +0100
Subject: [PATCH 4/6] mathjax formula with TeX for CRAS 2025
---
src/ptf/cmds/xml/jats/jats_parser.py | 12 ++++++++----
src/ptf/cmds/xml_cmds.py | 10 +++++++---
src/ptf/static/ptf/js/mathjax-config.js | 3 +++
3 files changed, 18 insertions(+), 7 deletions(-)
diff --git a/src/ptf/cmds/xml/jats/jats_parser.py b/src/ptf/cmds/xml/jats/jats_parser.py
index e73035d7..4774c40f 100644
--- a/src/ptf/cmds/xml/jats/jats_parser.py
+++ b/src/ptf/cmds/xml/jats/jats_parser.py
@@ -347,7 +347,6 @@ class JatsBase(XmlParserBase):
=> change the location to "file:/..." for Elsevier JATS (the xarticle has a pii attribute)
"""
href = ""
- style = ""
classe = "article-body-img"
for attrib in node.attrib:
name = normalize(attrib)
@@ -1506,7 +1505,7 @@ class JatsBase(XmlParserBase):
if self.no_bib:
href = "http://www.numdam.org/item/" + os.path.basename(href)
- rel = 'full-text'
+ rel = "full-text"
data = {
"rel": rel,
"mimetype": node_type,
@@ -2143,7 +2142,12 @@ class JatsIssue(IssueData, JatsBase):
kwargs = {}
if tag == "article":
- if self.journal and self.journal.pid in ["CRCHIM"] and int(self.year) > 2024:
+ if (
+ self.journal
+ and self.journal.pid
+ in ["CRMATH", "CRMECA", "CRPHYS", "CRGEOS", "CRCHIM", "CRBIOL"]
+ and int(self.year) > 2024
+ ):
kwargs["formula_with_tex"] = True
article = JatsArticle(
@@ -2151,7 +2155,7 @@ class JatsIssue(IssueData, JatsBase):
issue=self,
from_folder=self.from_folder,
no_bib=self.no_bib,
- **kwargs
+ **kwargs,
)
self.warnings.extend(article.warnings)
self.articles.append(article)
diff --git a/src/ptf/cmds/xml_cmds.py b/src/ptf/cmds/xml_cmds.py
index 339a20ef..5e42dd48 100644
--- a/src/ptf/cmds/xml_cmds.py
+++ b/src/ptf/cmds/xml_cmds.py
@@ -785,7 +785,7 @@ class addArticleXmlCmd(addXmlCmd):
def set_article_single_mode(self):
kwargs = {}
- if self.issue and self.issue.my_collection.pid in ["CRCHIM"] and int(self.issue.year) > 2024:
+ if self.issue and self.issue.is_cr() and int(self.issue.year) > 2024:
kwargs["formula_with_tex"] = True
self.xarticle = jats_parser.JatsArticle(tree=self.tree, **kwargs)
self.warnings.extend(self.xarticle.warnings)
@@ -867,8 +867,12 @@ class addArticleXmlCmd(addXmlCmd):
node = tree.find("body")
self.xarticle.body = xml_utils.get_text_from_node(node)
self.xarticle.body_xml = xml_utils.get_xml_from_text("body", self.xarticle.body)
- elif not self.xarticle.body_xml and self.xarticle.body_html: # Triggered when an article is accepted in editor and submitted to trammel.
- self.xarticle.body_xml = xml_utils.get_xml_from_text("body", xml_utils.remove_html(self.xarticle.body_html))
+ elif (
+ not self.xarticle.body_xml and self.xarticle.body_html
+ ): # Triggered when an article is accepted in editor and submitted to trammel.
+ self.xarticle.body_xml = xml_utils.get_xml_from_text(
+ "body", xml_utils.remove_html(self.xarticle.body_html)
+ )
def internal_do(self):
super().internal_do()
diff --git a/src/ptf/static/ptf/js/mathjax-config.js b/src/ptf/static/ptf/js/mathjax-config.js
index b9750fee..df5384be 100644
--- a/src/ptf/static/ptf/js/mathjax-config.js
+++ b/src/ptf/static/ptf/js/mathjax-config.js
@@ -21,6 +21,7 @@ window.MathJax = {
packages: {
"[+]": ["upgreek", "textmacros", "noerrors", "physics", "textcomp"],
},
+ textmacros: {packages: {'[+]': ['textcomp']}},
processEscapes: true, // use \$ to produce a literal dollar sign
processEnvironments: true,
macros: {
@@ -43,6 +44,8 @@ window.MathJax = {
bb: "\\mathbb ",
dbar: "\\overline\\partial",
protect: "",
+ rmDelta: "\\Delta",
+ hyphen: "\\text{-}",
},
noundefined: {
color: "red",
--
GitLab
From 51f1b47bc9aefea652149746f6cd3a3154a78e58 Mon Sep 17 00:00:00 2001
From: Olivier Labbe <olivier.labbe@univ-grenoble-alpes.fr>
Date: Fri, 28 Feb 2025 09:21:48 +0100
Subject: [PATCH 5/6] Config MathJax to use TeX in formulas
---
src/ptf/cmds/xml/jats/jats_parser.py | 13 ++++++-------
src/ptf/cmds/xml_cmds.py | 9 +++++++--
2 files changed, 13 insertions(+), 9 deletions(-)
diff --git a/src/ptf/cmds/xml/jats/jats_parser.py b/src/ptf/cmds/xml/jats/jats_parser.py
index 4774c40f..db0058f0 100644
--- a/src/ptf/cmds/xml/jats/jats_parser.py
+++ b/src/ptf/cmds/xml/jats/jats_parser.py
@@ -2142,13 +2142,12 @@ class JatsIssue(IssueData, JatsBase):
kwargs = {}
if tag == "article":
- if (
- self.journal
- and self.journal.pid
- in ["CRMATH", "CRMECA", "CRPHYS", "CRGEOS", "CRCHIM", "CRBIOL"]
- and int(self.year) > 2024
- ):
- kwargs["formula_with_tex"] = True
+ try:
+ year = int(self.year)
+ if year > 2024:
+ kwargs["formula_with_tex"] = True
+ except ValueError:
+ pass
article = JatsArticle(
tree=child,
diff --git a/src/ptf/cmds/xml_cmds.py b/src/ptf/cmds/xml_cmds.py
index 554a367a..90591872 100644
--- a/src/ptf/cmds/xml_cmds.py
+++ b/src/ptf/cmds/xml_cmds.py
@@ -847,8 +847,13 @@ class addArticleXmlCmd(addXmlCmd):
def set_article_single_mode(self):
kwargs = {}
- if self.issue and self.issue.is_cr() and int(self.issue.year) > 2024:
- kwargs["formula_with_tex"] = True
+ if self.issue:
+ try:
+ year = int(self.issue.year)
+ if year > 2024:
+ kwargs["formula_with_tex"] = True
+ except ValueError:
+ pass
self.xarticle = jats_parser.JatsArticle(tree=self.tree, **kwargs)
self.warnings.extend(self.xarticle.warnings)
--
GitLab
From 6cb51fc6c394024b00fdb80248816494ad9cc7d8 Mon Sep 17 00:00:00 2001
From: Olivier Labbe <olivier.labbe@univ-grenoble-alpes.fr>
Date: Tue, 11 Mar 2025 17:13:06 +0100
Subject: [PATCH 6/6] display tex directly
---
src/ptf/cmds/xml/jats/jats_parser.py | 7 ++++---
src/ptf/static/ptf/js/mathjax-config.js | 2 +-
2 files changed, 5 insertions(+), 4 deletions(-)
diff --git a/src/ptf/cmds/xml/jats/jats_parser.py b/src/ptf/cmds/xml/jats/jats_parser.py
index 9d993a3e..b24b0f72 100644
--- a/src/ptf/cmds/xml/jats/jats_parser.py
+++ b/src/ptf/cmds/xml/jats/jats_parser.py
@@ -502,10 +502,11 @@ class JatsBase(XmlParserBase):
if formula_id:
html += 'id="' + formula_id + '" '
alt_text = tex_math.replace("\n", "") if node.tag == "disp-formula" else tex_math
- if math_text:
- html += f'data-tex="{alt_text}">{math_text}</span>'
+
+ if self.formula_with_tex or not math_text:
+ html += f'data-tex="{alt_text}">{escape(tex_math)}</span>'
else:
- html += f'data-tex="{alt_text}">{tex_math}</span>'
+ html += f'data-tex="{alt_text}">{math_text}</span>'
if label or node.tag == "disp-formula":
html += '</td><td class="formula-label">'
diff --git a/src/ptf/static/ptf/js/mathjax-config.js b/src/ptf/static/ptf/js/mathjax-config.js
index df5384be..445b8722 100644
--- a/src/ptf/static/ptf/js/mathjax-config.js
+++ b/src/ptf/static/ptf/js/mathjax-config.js
@@ -67,7 +67,7 @@ window.MathJax = {
startup: {
pageReady: function () {
console.log("MathJax pageReady");
- replaceMml();
+ // replaceMml();
//
// Do the usual startup (which does a typeset).
// When that is all done, un-hide the page.
--
GitLab