Added a "hivestatus" role that prints the text with the same colour as beekeeper/guiHive

docs/user_manual/conf.py

@@ -21,7 +21,7 @@ import sphinx_rtd_theme
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 sys.path.insert(0, os.path.abspath('.'))
 
-from xhive import hive_setup_if_needed, HiveDiagramDirective
+from xhive import *
 
 hive_setup_if_needed()
 
@@ -355,3 +355,8 @@ epub_exclude_files = ['search.html']
 def setup(app):
     app.add_stylesheet("theme_overrides.css")
     app.add_directive('hive_diagram', HiveDiagramDirective)
+    app.add_role('hivestatus', hivestatus_role)
+    app.add_node(hivestatus,
+        html = (visit_hivestatus_html, depart_hivestatus_html),
+        latex = (visit_hivestatus_latex, depart_hivestatus_latex),
+    )

docs/user_manual/quickstart/quickstart.rst

@@ -135,7 +135,7 @@ Making sense of the beekeeper's output
 
         #. The status of the analysis (typically, "LOADING", "READY", "ALL_CLAIMED", possibly "FAILED"). Analyses that are done are not shown in this table.
 
-        #. A job summary, showing the number of [r]eady, [s]emaphored, [i]n-progress, and [d]one jobs in the analysis
+        #. A job summary, showing the number of [r]eady, [s]emaphored, :hivestatus:`<INPROGRESS> [i]n-progress`, and [d]one jobs in the analysis
 
         #. Average runtime for jobs in the analysis,
 

docs/user_manual/xhive.py

@@ -9,6 +9,8 @@ from docutils import nodes
 from docutils.parsers.rst import directives
 from docutils.parsers.rst import Directive
 
+__all__ = ["HiveDiagramDirective", "hive_setup_if_needed", "hivestatus", "hivestatus_role", "visit_hivestatus_html", "depart_hivestatus_html", "visit_hivestatus_latex", "depart_hivestatus_latex"]
+
 class HiveDiagramDirective(Directive):
 
     # defines the parameter the directive expects
@@ -96,6 +98,7 @@ def generate_diagram(pipeconfig_content, target_image_filename):
     os.remove(json_fh.name)
     os.remove(pipeconfig_fh.name)
 
+hive_colours = {}
 
 def hive_setup_if_needed():
     if os.environ.get("READTHEDOCS", None) == "True":
@@ -108,4 +111,41 @@ def hive_setup_if_needed():
     if True or any(not os.path.exists(os.path.join(doxygen_target, _)) for _ in ["perl", "python3", "java"]):
         mkdoc_path = os.path.join(os.environ["EHIVE_ROOT_DIR"], "scripts", "make_docs.pl")
         subprocess.call([mkdoc_path, "-no_schema_desc"])
+    # eHive's default configuration file
+    default_config_file = os.environ["EHIVE_ROOT_DIR"] + os.path.sep + "hive_config.json"
+    with open(default_config_file, "r") as fc:
+        conf_content = json.load(fc)
+        as_hash = conf_content["Graph"]["Node"]["AnalysisStatus"]
+        for s in as_hash:
+            if isinstance(as_hash[s], dict):
+                hive_colours[s] = as_hash[s]["Colour"]
+        js_hash = conf_content["Graph"]["Node"]["JobStatus"]
+        for s in js_hash:
+            if isinstance(js_hash[s], dict):
+                hive_colours[s] = js_hash[s]["Colour"]
+
+
+class hivestatus(nodes.Element):
+    pass
+
+def hivestatus_role(name, rawtext, text, lineno, inliner, options={}, content=[]):
+    status = text[1:text.index('>')]
+    text = (text[text.index('>')+1:]).strip()
+    hivestatus_node = hivestatus()
+    hivestatus_node.children.append(nodes.Text(text))
+    hivestatus_node['status'] = status
+
+    return [hivestatus_node], []
+
+def visit_hivestatus_html(self, node):
+    self.body.append('<span style="background-color:%s">' % hive_colours[node['status']])
+
+def depart_hivestatus_html(self, node):
+    self.body.append('</span>')
+
+def visit_hivestatus_latex(self, node):
+    self.body.append('\n\\colorbox{%s}{' % hive_colours[node['status']])
+
+def depart_hivestatus_latex(self, node):
+    self.body.append('}')