Fix headers bug

src/dgenies/lib/functions.py

@@ -283,3 +283,12 @@ class Functions:
     def query_fasta_file_exists(res_dir):
         fasta_file = os.path.join(res_dir, ".query")
         return os.path.exists(fasta_file) and os.path.isfile(fasta_file)
+
+    @staticmethod
+    def replace_headers(text):
+        headers = re.findall("<h\d id=\"[^\"]+\">", text)
+        for header in headers:
+            id_header = re.search("id=\"([^\"]+)\"", header).group(1)
+            text = text.replace(header, "<span class=\"anchor\" id=\"%s\"></span>%s" %
+                                (id_header, re.sub(r"id=\"[^\"]+\"", "class=\"section\"", header)))
+        return text

src/dgenies/md/doc_run.md

@@ -49,7 +49,7 @@ Files must be in fasta format. We recommend using gzipped files to preserve band
 
 Allowed extensions: fa, fasta, fna, fa.gz, fasta.gz, fna.gz
 
-Max file size: ###size### (###size_unc### once uncompressed, ###size_ava### in all-vs-all mode)
+Max file size: {{size}} ({{size_unc}} once uncompressed, {{size_ava}} in all-vs-all mode)
 
 {% set puce=puce+1 %}
 
@@ -59,7 +59,7 @@ Optional field
 
 Works like the target fasta. If not given, target file will be mapped to itself, in all-vs-all mode.
 
-Max file size: ###size### (###size_unc### once uncompressed)
+Max file size: {{size}} ({{size_unc}} once uncompressed)
 
 {% set puce=puce+1 %}
 

src/dgenies/static/css/dgenies.css

@@ -4,6 +4,13 @@ body {
     padding-top: 50px;
 }
 
+.anchor{
+  display: block;
+  height: 50px; /*same height as header*/
+  margin-top: -50px; /*same height as header*/
+  visibility: hidden;
+}
+
 #main-error {
     display: none;
     width: 100%;

src/dgenies/templates/documentation.html

@@ -63,7 +63,7 @@
     {% endif %}
 
     <div id="body">
-        {{ content }}
+        {{ content | safe }}
     </div>
 
 {% endblock %}
\ No newline at end of file

src/dgenies/views.py

@@ -325,12 +325,6 @@ def get_file(file, gzip=False):  # pragma: no cover
 def documentation_run():
     latest = Latest()
     version = latest.latest
-    with open(os.path.join(app_folder, "md", "doc_run.md"), "r",  encoding='utf-8') as install_instr:
-        content = install_instr.read()
-    env = Environment()
-    template = env.from_string(content)
-    content = template.render(mode=MODE, version=version)
-    md = Markdown(extensions=[TocExtension(baselevel=1)])
     max_upload_file_size = config_reader.max_upload_file_size
     if max_upload_file_size == -1:
         max_upload_file_size = "no limit"
@@ -346,9 +340,14 @@ def documentation_run():
         max_upload_size_ava = "no limit"
     else:
         max_upload_size_ava = Functions.get_readable_size(max_upload_size_ava, 0)
-    content = Markup(md.convert(content)).replace("###size###", max_upload_file_size)\
-                                         .replace("###size_unc###", max_upload_size)\
-                                         .replace("###size_ava###", max_upload_size_ava)
+    with open(os.path.join(app_folder, "md", "doc_run.md"), "r",  encoding='utf-8') as install_instr:
+        content = install_instr.read()
+    env = Environment()
+    template = env.from_string(content)
+    content = template.render(mode=MODE, version=version, size=max_upload_file_size, size_unc=max_upload_size,
+                              size_ava=max_upload_size_ava)
+    md = Markdown(extensions=[TocExtension(baselevel=1)])
+    content = Functions.replace_headers(str(Markup(md.convert(content))))
     toc = Markup(md.toc)
     return render_template("documentation.html", menu="documentation", content=content, toc=toc)
 
@@ -359,7 +358,7 @@ def documentation_result():
               encoding='utf-8') as install_instr:
         content = install_instr.read()
     md = Markdown(extensions=[TocExtension(baselevel=1)])
-    content = Markup(md.convert(content))
+    content = Functions.replace_headers(str(Markup(md.convert(content))))
     toc = Markup(md.toc)
     return render_template("documentation.html", menu="documentation", content=content, toc=toc)
 
@@ -370,7 +369,7 @@ def documentation_formats():
               encoding='utf-8') as install_instr:
         content = install_instr.read()
     md = Markdown(extensions=[TocExtension(baselevel=1), TableExtension()])
-    content = Markup(md.convert(content))
+    content = Functions.replace_headers(str(Markup(md.convert(content))))
     toc = Markup(md.toc)
     return render_template("documentation.html", menu="documentation", content=content, toc=toc)
 
@@ -381,7 +380,7 @@ def documentation_dotplot():
               encoding='utf-8') as install_instr:
         content = install_instr.read()
     md = Markdown(extensions=[TocExtension(baselevel=1)])
-    content = Markup(md.convert(content))
+    content = Functions.replace_headers(str(Markup(md.convert(content))))
     toc = Markup(md.toc)
     return render_template("documentation.html", menu="documentation", content=content, toc=toc)
 
@@ -396,7 +395,7 @@ def install():
     template = env.from_string(content)
     content = template.render(version=latest.latest, win32=latest.win32)
     md = Markdown(extensions=[TocExtension(baselevel=1)])
-    content = Markup(md.convert(content))
+    content = Functions.replace_headers(str(Markup(md.convert(content))))
     toc = Markup(md.toc)
     return render_template("documentation.html", menu="install", content=content, toc=toc)