Implement patched link/code tagging in all build scripts

build/build-termlist.py

@@ -57,7 +57,7 @@ display_id = ['record_level', 'dc', 'dcterms', 'occurrence', 'organism', 'materi
 # ---------------
 
 # replace URL with link (function used with Audubon Core list of terms build script)
-# Does not correctly handle URLs with close parens ) characters.
+# Does not correctly handle URLs with close parens ) characters, so no longer used.
 #
 def createLinks(text):
     def repl(match):
@@ -69,15 +69,13 @@ def createLinks(text):
     result = re.sub(pattern, repl, text)
     return result
 
-# 2021-08-05 Replace the createLinks() function with functions copied from the QRG build script written by S. Van Hoey
+# 2021-08-06 Replace the createLinks() function with functions copied from the QRG build script written by S. Van Hoey
 def convert_code(text_with_backticks):
     """Takes all back-quoted sections in a text field and converts it to
     the html tagged version of code blocks <code>...</code>
     """
     return re.sub(r'`([^`]*)`', r'<code>\1</code>', text_with_backticks)
 
-# 2021-08-06 Discovered when using this with Audubon Core list of terms build script that it does not
-# correctly handle trailing commas that follow a URL. I don't understand the regex well enough to fix it
 def convert_link(text_with_urls):
     """Takes all links in a text field and converts it to the html tagged
     version of the link
@@ -87,7 +85,7 @@ def convert_link(text_with_urls):
         url = inputstring.group()
         return "<a href=\"{}\">{}</a>".format(url, url)
 
-    regx = "(http[s]?://[\w\d:#@%/;$()~_?\+-;=\\\.&]*)(?<![\)\.])"
+    regx = "(http[s]?://[\w\d:#@%/;$()~_?\+-;=\\\.&]*)(?<![\)\.,])"
     return re.sub(regx, _handle_matched, text_with_urls)
 
 # ---------------

build/build.py

@@ -170,7 +170,7 @@ class DwcDigester(object):
             url = inputstring.group()
             return "<a href=\"{}\">{}</a>".format(url, url)
 
-        regx = "(http[s]?://[\w\d:#@%/;$()~_?\+-;=\\\.&]*)(?<![\)\.])"
+        regx = "(http[s]?://[\w\d:#@%/;$()~_?\+-;=\\\.&]*)(?<![\)\.,])"
         return re.sub(regx, _handle_matched, text_with_urls)
 
     def process_terms(self):

build/doe-cv-build/build-page-simple.ipynb

@@ -65,7 +65,26 @@
     "\n",
     "    pattern = '(https?://[^\\s,;\\)\"]*)'\n",
     "    result = re.sub(pattern, repl, text)\n",
-    "    return result"
+    "    return result\n",
+    "\n",
+    "# 2021-08-06 Replace the createLinks() function with functions copied from the QRG build script written by S. Van Hoey\n",
+    "def convert_code(text_with_backticks):\n",
+    "    \"\"\"Takes all back-quoted sections in a text field and converts it to\n",
+    "    the html tagged version of code blocks <code>...</code>\n",
+    "    \"\"\"\n",
+    "    return re.sub(r'`([^`]*)`', r'<code>\\1</code>', text_with_backticks)\n",
+    "\n",
+    "def convert_link(text_with_urls):\n",
+    "    \"\"\"Takes all links in a text field and converts it to the html tagged\n",
+    "    version of the link\n",
+    "    \"\"\"\n",
+    "    def _handle_matched(inputstring):\n",
+    "        \"\"\"quick hack version of url handling on the current prime versions data\"\"\"\n",
+    "        url = inputstring.group()\n",
+    "        return \"<a href=\\\"{}\\\">{}</a>\".format(url, url)\n",
+    "\n",
+    "    regx = \"(http[s]?://[\\w\\d:#@%/;$()~_?\\+-;=\\\\\\.&]*)(?<![\\)\\.,])\"\n",
+    "    return re.sub(regx, _handle_matched, text_with_urls)\n"
    ]
   },
   {
@@ -300,13 +319,13 @@
     "        if row['usage'] != '':\n",
     "            text += '\\t\\t<tr>\\n'\n",
     "            text += '\\t\\t\\t<td>Usage</td>\\n'\n",
-    "            text += '\\t\\t\\t<td>' + createLinks(row['usage']) + '</td>\\n'\n",
+    "            text += '\\t\\t\\t<td>' + convert_link(convert_code(row['usage'])) + '</td>\\n'\n",
     "            text += '\\t\\t</tr>\\n'\n",
     "\n",
     "        if row['notes'] != '':\n",
     "            text += '\\t\\t<tr>\\n'\n",
     "            text += '\\t\\t\\t<td>Notes</td>\\n'\n",
-    "            text += '\\t\\t\\t<td>' + createLinks(row['notes']) + '</td>\\n'\n",
+    "            text += '\\t\\t\\t<td>' + convert_link(convert_code(row['notes'])) + '</td>\\n'\n",
     "            text += '\\t\\t</tr>\\n'\n",
     "\n",
     "        if (vocab_type == 2 or vocab_type == 3) and row['controlled_value_string'] != '': # controlled vocabulary\n",
@@ -416,7 +435,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.1"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

build/em-cv-build/build-page-simple.ipynb

@@ -65,7 +65,26 @@
     "\n",
     "    pattern = '(https?://[^\\s,;\\)\"]*)'\n",
     "    result = re.sub(pattern, repl, text)\n",
-    "    return result"
+    "    return result\n",
+    "\n",
+    "# 2021-08-06 Replace the createLinks() function with functions copied from the QRG build script written by S. Van Hoey\n",
+    "def convert_code(text_with_backticks):\n",
+    "    \"\"\"Takes all back-quoted sections in a text field and converts it to\n",
+    "    the html tagged version of code blocks <code>...</code>\n",
+    "    \"\"\"\n",
+    "    return re.sub(r'`([^`]*)`', r'<code>\\1</code>', text_with_backticks)\n",
+    "\n",
+    "def convert_link(text_with_urls):\n",
+    "    \"\"\"Takes all links in a text field and converts it to the html tagged\n",
+    "    version of the link\n",
+    "    \"\"\"\n",
+    "    def _handle_matched(inputstring):\n",
+    "        \"\"\"quick hack version of url handling on the current prime versions data\"\"\"\n",
+    "        url = inputstring.group()\n",
+    "        return \"<a href=\\\"{}\\\">{}</a>\".format(url, url)\n",
+    "\n",
+    "    regx = \"(http[s]?://[\\w\\d:#@%/;$()~_?\\+-;=\\\\\\.&]*)(?<![\\)\\.,])\"\n",
+    "    return re.sub(regx, _handle_matched, text_with_urls)\n"
    ]
   },
   {
@@ -300,13 +319,13 @@
     "        if row['usage'] != '':\n",
     "            text += '\\t\\t<tr>\\n'\n",
     "            text += '\\t\\t\\t<td>Usage</td>\\n'\n",
-    "            text += '\\t\\t\\t<td>' + createLinks(row['usage']) + '</td>\\n'\n",
+    "            text += '\\t\\t\\t<td>' + convert_link(convert_code(row['usage'])) + '</td>\\n'\n",
     "            text += '\\t\\t</tr>\\n'\n",
     "\n",
     "        if row['notes'] != '':\n",
     "            text += '\\t\\t<tr>\\n'\n",
     "            text += '\\t\\t\\t<td>Notes</td>\\n'\n",
-    "            text += '\\t\\t\\t<td>' + createLinks(row['notes']) + '</td>\\n'\n",
+    "            text += '\\t\\t\\t<td>' + convert_link(convert_code(row['notes'])) + '</td>\\n'\n",
     "            text += '\\t\\t</tr>\\n'\n",
     "\n",
     "        if (vocab_type == 2 or vocab_type == 3) and row['controlled_value_string'] != '': # controlled vocabulary\n",
@@ -416,7 +435,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.1"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

build/pw-cv-build/build-page-simple.ipynb

@@ -65,7 +65,26 @@
     "\n",
     "    pattern = '(https?://[^\\s,;\\)\"]*)'\n",
     "    result = re.sub(pattern, repl, text)\n",
-    "    return result"
+    "    return result\n",
+    "\n",
+    "# 2021-08-06 Replace the createLinks() function with functions copied from the QRG build script written by S. Van Hoey\n",
+    "def convert_code(text_with_backticks):\n",
+    "    \"\"\"Takes all back-quoted sections in a text field and converts it to\n",
+    "    the html tagged version of code blocks <code>...</code>\n",
+    "    \"\"\"\n",
+    "    return re.sub(r'`([^`]*)`', r'<code>\\1</code>', text_with_backticks)\n",
+    "\n",
+    "def convert_link(text_with_urls):\n",
+    "    \"\"\"Takes all links in a text field and converts it to the html tagged\n",
+    "    version of the link\n",
+    "    \"\"\"\n",
+    "    def _handle_matched(inputstring):\n",
+    "        \"\"\"quick hack version of url handling on the current prime versions data\"\"\"\n",
+    "        url = inputstring.group()\n",
+    "        return \"<a href=\\\"{}\\\">{}</a>\".format(url, url)\n",
+    "\n",
+    "    regx = \"(http[s]?://[\\w\\d:#@%/;$()~_?\\+-;=\\\\\\.&]*)(?<![\\)\\.,])\"\n",
+    "    return re.sub(regx, _handle_matched, text_with_urls)\n"
    ]
   },
   {
@@ -300,13 +319,13 @@
     "        if row['usage'] != '':\n",
     "            text += '\\t\\t<tr>\\n'\n",
     "            text += '\\t\\t\\t<td>Usage</td>\\n'\n",
-    "            text += '\\t\\t\\t<td>' + createLinks(row['usage']) + '</td>\\n'\n",
+    "            text += '\\t\\t\\t<td>' + convert_link(convert_code(row['usage'])) + '</td>\\n'\n",
     "            text += '\\t\\t</tr>\\n'\n",
     "\n",
     "        if row['notes'] != '':\n",
     "            text += '\\t\\t<tr>\\n'\n",
     "            text += '\\t\\t\\t<td>Notes</td>\\n'\n",
-    "            text += '\\t\\t\\t<td>' + createLinks(row['notes']) + '</td>\\n'\n",
+    "            text += '\\t\\t\\t<td>' + convert_link(convert_code(row['notes'])) + '</td>\\n'\n",
     "            text += '\\t\\t</tr>\\n'\n",
     "\n",
     "        if (vocab_type == 2 or vocab_type == 3) and row['controlled_value_string'] != '': # controlled vocabulary\n",
@@ -416,7 +435,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.1"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,