7e9ec699b6d233213aca70776b2e89a0cc02f976
max
  Wed Nov 29 13:41:32 2023 -0800
first test of a markdown based docs directory, no redmine yet

diff --git docs/staticPage.lua docs/staticPage.lua
new file mode 100644
index 0000000..f236cb7
--- /dev/null
+++ docs/staticPage.lua
@@ -0,0 +1,437 @@
+-- UCSC: Slightly modified to produce html that follows the genome browser
+-- static pages conventions
+--
+--
+-- This is a sample custom writer for pandoc.  It produces output
+-- that is very similar to that of pandoc's HTML writer.
+-- There is one new feature: code blocks marked with class 'dot'
+-- are piped through graphviz and images are included in the HTML
+-- output using 'data:' URLs.
+--
+-- Invoke with: pandoc -t staticPage.lua
+--
+
+-- Character escaping
+local function escape(s, in_attribute)
+  return s:gsub("[<>&\"']",
+    function(x)
+      if x == '<' then
+        return '&lt;'
+      elseif x == '>' then
+        return '&gt;'
+      elseif x == '&' then
+        return '&amp;'
+      elseif x == '"' then
+        return '&quot;'
+      elseif x == "'" then
+        return '&#39;'
+      else
+        return x
+      end
+    end)
+end
+
+-- Helper function to convert an attributes table into
+-- a string that can be put into HTML tags.
+local function attributes(attr)
+  local attr_table = {}
+  for x,y in pairs(attr) do
+    if y and y ~= "" then
+      table.insert(attr_table, ' ' .. x .. '="' .. escape(y,true) .. '"')
+    end
+  end
+  return table.concat(attr_table)
+end
+
+-- Run cmd on a temporary file containing inp and return result.
+local function pipe(cmd, inp)
+  local tmp = os.tmpname()
+  local tmph = io.open(tmp, "w")
+  tmph:write(inp)
+  tmph:close()
+  local outh = io.popen(cmd .. " " .. tmp,"r")
+  local result = outh:read("*all")
+  outh:close()
+  os.remove(tmp)
+  return result
+end
+
+-- Table to store footnotes, so they can be included at the end.
+local notes = {}
+
+-- Table to store headers, so they can be inserted at the end
+local headers = {}
+
+-- flag to see if we have to close a previous div
+local headerOpen = false
+
+-- Blocksep is used to separate block elements.
+function Blocksep()
+  return "\n\n"
+end
+
+-- Print contents of `tbl`, with indentation.
+-- `indent` sets the initial level of indentation.
+function tprint (tbl, indent)
+  if not indent then indent = 0 end
+  for k, v in pairs(tbl) do
+    formatting = string.rep("  ", indent) .. k .. ": "
+    if type(v) == "table" then
+      print(formatting)
+      tprint(v, indent+1)
+    elseif type(v) == 'boolean' then
+      print(formatting .. tostring(v))      
+    else
+      print(formatting .. v)
+    end
+  end
+end
+
+-- remove all special chars from the string and remove all html tags
+function simplifyId(idStr)
+    idStr=idStr:gsub("%b<>", "")
+    idStr = string.lower(string.gsub(idStr, "%s+", "-"))
+    idStr = string.lower(string.gsub(idStr, "[^a-zA-z-]", ""))
+    return idStr
+end
+
+-- This function is called once for the whole document. Parameters:
+-- body is a string, metadata is a table, variables is a table.
+-- This gives you a fragment.  You could use the metadata table to
+-- fill variables in a custom lua template.  Or, pass `--template=...`
+-- to pandoc, and pandoc will add do the template processing as
+-- usual.
+function Doc(body, metadata, variables)
+  local buffer = {}
+  local function add(s)
+    table.insert(buffer, s)
+  end
+
+  -- ucsc changes start
+  
+  -- debugging of meta info:
+  -- print("vars")
+  -- tprint(variables)
+  -- print("meta")
+  -- tprint(metadata)
+
+
+  if metadata["title"] then
+    add("<h1>" .. metadata["title"] .. "</h1>")
+  else
+    add("<h1>No title defined in document, first line must be % mytitle </h1>")
+  end
+
+  add("<h2>Contents</h2>")
+  for i, h in ipairs(headers) do
+    idStr = simplifyId(h)
+    add("<h6><a href='#" .. idStr .. "'>" .. h .. "</a></h6>")
+  end
+  -- ucsc change end
+
+  add(body)
+  if #notes > 0 then
+    add('<ol class="footnotes">')
+    for _,note in pairs(notes) do
+      add(note)
+    end
+    add('</ol>')
+  end
+  return table.concat(buffer,'\n') .. '\n'
+end
+
+-- The functions that follow render corresponding pandoc elements.
+-- s is always a string, attr is always a table of attributes, and
+-- items is always an array of strings (the items in a list).
+-- Comments indicate the types of other variables.
+
+function Str(s)
+  return escape(s)
+end
+
+function Space()
+  return " "
+end
+
+function SoftBreak()
+  return "\n"
+end
+
+function LineBreak()
+  return "<br/>"
+end
+
+function Emph(s)
+  return "<em>" .. s .. "</em>"
+end
+
+function Strong(s)
+  return "<strong>" .. s .. "</strong>"
+end
+
+function Subscript(s)
+  return "<sub>" .. s .. "</sub>"
+end
+
+function Superscript(s)
+  return "<sup>" .. s .. "</sup>"
+end
+
+function SmallCaps(s)
+  return '<span style="font-variant: small-caps;">' .. s .. '</span>'
+end
+
+function Strikeout(s)
+  return '<del>' .. s .. '</del>'
+end
+
+function obfuscate(s)
+   -- obfuscate the email address a la Hiram's encodeEmail.pl 
+   local refs = {}
+   for i = 1, string.len(s) do
+      local ascCode = string.byte(s, i)
+      local ref = "&#" .. tostring(ascCode)
+      table.insert(refs, ref)
+   end
+   return table.concat(refs, "")
+end
+
+function Link(s, src, tit, attr)
+  if string.sub(src, 1, 7)=="mailto:" then
+      src = "mailto:" .. obfuscate(string.sub(src, 7), 7)
+      -- assume that the link label is an email address if it contains an @ character
+      if string.match(s, "%@")~=nil then
+          s = obfuscate(s)
+      end
+  else
+      src = escape(src, true)
+      tit = escape(tit, true)
+      s = escape(s, true)
+  end
+
+
+  return "<a href='" .. src .. "' title='" .. tit .. "'>" .. s .. "</a>"
+
+end
+
+function Image(s, src, tit, attr)
+  return "<img src='" .. escape(src,true) .. "' title='" ..
+         escape(tit,true) .. "'/>"
+end
+
+function RawInline(s)
+  return "<code>" .. escape(s) .. "</code>"
+end
+
+function Code(s, attr)
+  return "<code" .. attributes(attr) .. ">" .. escape(s) .. "</code>"
+end
+
+function InlineMath(s)
+  return "\\(" .. escape(s) .. "\\)"
+end
+
+function DisplayMath(s)
+  return "\\[" .. escape(s) .. "\\]"
+end
+
+function SingleQuoted(s)
+  return "&lsquo;" .. s .. "&rsquo;"
+end
+
+function DoubleQuoted(s)
+  return "&ldquo;" .. s .. "&rdquo;"
+end
+
+function Note(s)
+  local num = #notes + 1
+  -- insert the back reference right before the final closing tag.
+  s = string.gsub(s,
+          '(.*)</', '%1 <a href="#fnref' .. num ..  '">&#8617;</a></')
+  -- add a list item with the note to the note table.
+  table.insert(notes, '<li id="fn' .. num .. '">' .. s .. '</li>')
+  -- return the footnote reference, linked to the note.
+  return '<a id="fnref' .. num .. '" href="#fn' .. num ..
+            '"><sup>' .. num .. '</sup></a>'
+end
+
+function Span(s, attr)
+  return "<span" .. attributes(attr) .. ">" .. s .. "</span>"
+end
+
+function Cite(s, cs)
+  local ids = {}
+  for _,cit in ipairs(cs) do
+    table.insert(ids, cit.citationId)
+  end
+  return "<span class=\"cite\" data-citation-ids=\"" .. table.concat(ids, ",") ..
+    "\">" .. s .. "</span>"
+end
+
+function Plain(s)
+  return s
+end
+
+function Para(s)
+  return "<p>\n" .. s .. "\n</p>"
+end
+
+-- lev is an integer, the header level.
+function Header(lev, s, attr)
+  local lines = { }
+
+  if lev == 1 then
+
+    idStr = simplifyId(s)
+
+    table.insert(headers, s)
+
+    table.insert(lines, "<a name='" .. idStr .. "'></a>")
+    table.insert(lines, "<h2>"  .. s .. "</h2>")
+    headerOpen = true
+
+  else
+    table.insert(lines, "<h" .. lev .. attributes(attr) ..  ">" .. s .. "</h" .. lev .. ">")
+  end
+
+  return table.concat(lines, "\n")
+end
+
+function BlockQuote(s)
+  return "<blockquote>\n" .. s .. "\n</blockquote>"
+end
+
+function HorizontalRule()
+  return "<hr/>"
+end
+
+function CodeBlock(s, attr)
+  -- If code block has class 'dot', pipe the contents through dot
+  -- and base64, and include the base64-encoded png as a data: URL.
+  if attr.class and string.match(' ' .. attr.class .. ' ',' dot ') then
+    local png = pipe("base64", pipe("dot -Tpng", s))
+    return '<img src="data:image/png;base64,' .. png .. '"/>'
+  -- otherwise treat as code (one could pipe through a highlighter)
+  else
+    return "<pre><code" .. attributes(attr) .. ">" .. escape(s) ..
+           "</code></pre>"
+  end
+end
+
+function BulletList(items)
+  local buffer = {}
+  for _, item in pairs(items) do
+    table.insert(buffer, "<li>" .. item .. "</li>")
+  end
+  return "<ul>\n" .. table.concat(buffer, "\n") .. "\n</ul>"
+end
+
+function OrderedList(items)
+  local buffer = {}
+  for _, item in pairs(items) do
+    table.insert(buffer, "<li>" .. item .. "</li>")
+  end
+  return "<ol>\n" .. table.concat(buffer, "\n") .. "\n</ol>"
+end
+
+-- Revisit association list STackValue instance.
+function DefinitionList(items)
+  local buffer = {}
+  for _,item in pairs(items) do
+    for k, v in pairs(item) do
+      table.insert(buffer,"<dt>" .. k .. "</dt>\n<dd>" ..
+                        table.concat(v,"</dd>\n<dd>") .. "</dd>")
+    end
+  end
+  return "<dl>\n" .. table.concat(buffer, "\n") .. "\n</dl>"
+end
+
+-- Convert pandoc alignment to something HTML can use.
+-- align is AlignLeft, AlignRight, AlignCenter, or AlignDefault.
+function html_align(align)
+  if align == 'AlignLeft' then
+    return 'left'
+  elseif align == 'AlignRight' then
+    return 'right'
+  elseif align == 'AlignCenter' then
+    return 'center'
+  else
+    return 'left'
+  end
+end
+
+function CaptionedImage(src, tit, caption)
+   return '<div class="figure">\n<img src="' .. escape(src,true) ..
+      '" title="' .. escape(tit,true) .. '"/>\n' ..
+      '<p class="caption">' .. caption .. '</p>\n</div>'
+end
+
+-- Caption is a string, aligns is an array of strings,
+-- widths is an array of floats, headers is an array of
+-- strings, rows is an array of arrays of strings.
+function Table(caption, aligns, widths, headers, rows)
+  local buffer = {}
+  local function add(s)
+    table.insert(buffer, s)
+  end
+  add("<table>")
+  if caption ~= "" then
+    add("<caption>" .. caption .. "</caption>")
+  end
+  if widths and widths[1] ~= 0 then
+    for _, w in pairs(widths) do
+      add('<col width="' .. string.format("%d%%", w * 100) .. '" />')
+    end
+  end
+  local header_row = {}
+  local empty_header = true
+  for i, h in pairs(headers) do
+    local align = html_align(aligns[i])
+    table.insert(header_row,'<th align="' .. align .. '">' .. h .. '</th>')
+    empty_header = empty_header and h == ""
+  end
+  if empty_header then
+    head = ""
+  else
+    add('<tr class="header">')
+    for _,h in pairs(header_row) do
+      add(h)
+    end
+    add('</tr>')
+  end
+  local class = "even"
+  for _, row in pairs(rows) do
+    class = (class == "even" and "odd") or "even"
+    add('<tr class="' .. class .. '">')
+    for i,c in pairs(row) do
+      add('<td align="' .. html_align(aligns[i]) .. '">' .. c .. '</td>')
+    end
+    add('</tr>')
+  end
+  add('</table')
+  return table.concat(buffer,'\n')
+end
+
+function RawBlock(format, str)
+  if format == "html" then
+    return str
+  else
+    return ''
+  end
+end
+
+function Div(s, attr)
+  return "<div" .. attributes(attr) .. ">\n" .. s .. "</div>"
+end
+
+-- The following code will produce runtime warnings when you haven't defined
+-- all of the functions you need for the custom writer, so it's useful
+-- to include when you're working on a writer.
+local meta = {}
+meta.__index =
+  function(_, key)
+    io.stderr:write(string.format("WARNING: Undefined function '%s'\n",key))
+    return function() return "" end
+  end
+setmetatable(_G, meta)
+