def run(self):
node = graphviz()
dotted = self.arguments[0].split()[0]
# Get the workflow for ``dotted``.
try:
workflow = Workflow(dotted)
except WorkflowException as err:
return [node.document.reporter.warning(
err.args[0], line=self.lineno)]
node['code'] = workflow.generate_dot(self.name)
node['options'] = {}
if 'graphviz_dot' in self.options:
node['options']['graphviz_dot'] = self.options['graphviz_dot']
if 'alt' in self.options:
node['alt'] = self.options['alt']
if 'inline' in self.options:
node['inline'] = True
caption = self.options.get('caption')
if caption:
node = figure_wrapper(self, node, caption)
return [node]
def make_field(self, directive):
# treat content like docfields.Field
value = directive.options.get(self.name)
if value:
name = nodes.field_name('', self.label)
para = nodes.paragraph(rawsource=value)
bases = value.split(',')
# graph attributes
code = ['rankdir=LR;']
code += ['size="8.0, 12.0";']
t = directive.arguments[0]
# node attributes
node_attrs = ', '.join([
'shape="box"', 'fontsize="10"', 'height="0.25"',
'fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans"',
'style="setlinewidth(0.5) filled"', 'fillcolor="khaki3:khaki1"'
])
code += ['%s [%s, label="%s"];' % (t, node_attrs, t)]
code += [
'%s [%s, label="%s"];' % (b, node_attrs, b) for b in bases
]
code += ['%s -> %s;' % (t, b) for b in bases]
node = graphviz.graphviz()
node['code'] = 'digraph I {\n%s\n}\n' % '\n'.join(code)
node['options'] = {}
body = nodes.field_body('', node)
return nodes.field('', name, body)
def process_doctree(self, doctree, docname):
for graph_node in doctree.traverse(traceable_graph):
# Determine graph's starting traceables.
start_tags = graph_node["traceable-tags"]
start_traceables = self.get_start_traceables(start_tags,
graph_node)
if not start_traceables:
self.env.warn_node("Traceables: no valid tags for graph,"
" so skipping graph", node)
continue
# Determine relationships to include in graph.
input = graph_node.get("traceable-relationships")
relationship_length_pairs = self.parse_relationships(input)
# Construct input for graph.
graph_input = self.construct_graph_input(start_traceables,
relationship_length_pairs)
# Generate diagram input and create output node.
graphviz_node = graphviz.graphviz()
graphviz_node["code"] = self.generate_dot(graph_input)
graphviz_node["options"] = []
graphviz_node["inline"] = False
# caption = "Relationship diagram for {0}".format(traceable.tag)
# figure_node = graphviz.figure_wrapper(self, graphviz_node,
# caption)
graph_node.replace_self(graphviz_node)
def process_doctree(self, doctree, docname):
for graph_node in doctree.traverse(traceable_graph):
# Determine graph's starting traceables.
start_tags = graph_node["traceables-tags"]
start_traceables = self.get_start_traceables(start_tags,
graph_node)
if not start_traceables:
message = ("Traceables: no valid tags for graph,"
" so skipping graph")
self.env.warn_node(message, graph_node)
msg = nodes.system_message(message=message,
level=2, type="ERROR",
source=graph_node["source"],
line=graph_node["line"])
graph_node.replace_self(msg)
continue
# Determine relationships to include in graph.
input = graph_node.get("traceables-relationships")
relationship_length_pairs = self.parse_relationships(input)
# Construct input for graph.
graph_input = self.construct_graph_input(start_traceables,
relationship_length_pairs)
# Generate diagram input and create output node.
graphviz_node = graphviz.graphviz()
graphviz_node["code"] = self.generate_dot(graph_input)
graphviz_node["options"] = {}
caption = graph_node.get("traceables-caption", "Traceables graph")
graphviz_node["alt"] = caption
graph_node.replace_self(graphviz_node)
def process_doctree(self, doctree, docname):
for graph_node in doctree.traverse(traceable_graph):
# Determine graph's starting traceables.
start_tags = graph_node["traceables-tags"]
start_traceables = self.get_start_traceables(
start_tags, graph_node)
if not start_traceables:
message = ("Traceables: no valid tags for graph,"
" so skipping graph")
self.node_warning(self.env, message, graph_node)
msg = nodes.system_message(message=message,
level=2,
type="ERROR",
source=graph_node["source"],
line=graph_node["line"])
graph_node.replace_self(msg)
continue
# Determine relationships to include in graph.
input = graph_node.get("traceables-relationships")
relationship_length_pairs = self.parse_relationships(input)
# Construct input for graph.
graph_input = self.construct_graph_input(
start_traceables, relationship_length_pairs)
# Generate diagram input and create output node.
graphviz_node = graphviz.graphviz()
graphviz_node["code"] = self.generate_dot(graph_input)
graphviz_node["options"] = {}
caption = graph_node.get("traceables-caption", "Traceables graph")
graphviz_node["alt"] = caption
graph_node.replace_self(graphviz_node)
def run(self):
name = self.arguments[0]
command = directives.choice(self.arguments[1], allowed_commands)
if command == 'init':
# Create a temporary file to hold the database
db_fh = tempfile.NamedTemporaryFile(delete=False)
ehive_db_urls[name] = 'sqlite:///' + db_fh.name
command_array = [
'init_pipeline.pl', self.arguments[2], '-pipeline_url',
ehive_db_urls[name]
]
for tweak in self.options.get('tweaks', '').split():
command_array.extend(['-tweak', tweak])
else:
db = ehive_db_urls[name]
if command == 'run_job':
command_array = [
'runWorker.pl', '-url', db, '-job_id', self.arguments[2]
]
elif command == 'sync':
command_array = ['beekeeper.pl', '-url', db, '-sync']
if self.options.has_key('analyses_pattern'):
command_array.extend([
'-analyses_pattern', self.options['analyses_pattern']
])
elif command == 'analysis_diagram':
default_config_file = os.environ[
"EHIVE_ROOT_DIR"] + os.path.sep + "hive_config.json"
command_array = [
'generate_graph.pl', '-url', db, '-output', '/dev/stdout',
'-format', 'dot', '-config_file', default_config_file
]
elif command == 'job_diagram':
default_config_file = os.environ[
"EHIVE_ROOT_DIR"] + os.path.sep + "hive_config.json"
command_array = [
'visualize_jobs.pl', '-url', db, '-output', '/dev/stdout',
'-format', 'dot', '-config_file', default_config_file
]
command_array.extend(
self.options.get('vj_options', '').split())
command_array[0] = os.path.join(os.environ["EHIVE_ROOT_DIR"],
'scripts', command_array[0])
dotcontent = subprocess.check_output(command_array, stderr=sys.stderr)
if command.endswith('diagram'):
# We reuse the graphviz node (from the graphviz extension) as it deals better with image formats vs builders
graphviz_node = graphviz()
graphviz_node['code'] = dotcontent
graphviz_node['options'] = {}
return [graphviz_node]
else:
return []
def run(self):
dotcode = self.dotcode()
if not dotcode.strip():
return [self.state_machine.reporter.warning(
'Ignoring "graphviz" directive without content.',
line=self.lineno)]
node = graphviz()
node['code'] = dotcode
node['options'] = []
return [node]
def run(self):
p = parser.Parser()
graph = Root(p.parse('\n'.join(self.content) + '\n'))
node = graphviz()
node['code'] = '\n'.join(graph.as_digraph())
node['options'] = []
if 'alt' in self.options:
node['alt'] = self.options['alt']
if 'caption' in self.options:
node['caption'] = self.options['caption']
node['inline'] = 'inline' in self.options
return [node]
def run(self):
# The PipeConfig sample is shown in a literal block
content = '\n'.join(self.content)
code_block_node = nodes.literal_block(text=content)
# We reuse the graphviz node (from the graphviz extension) as it deals better with image formats vs builders
graphviz_node = graphviz()
graphviz_node['code'] = generate_dot_diagram(content)
graphviz_node['options'] = {}
table = [[[code_block_node], [graphviz_node]]]
table_node = self.build_table_from_list(table, [50,50], 0, 0)
return [table_node]
def run(self):
# The PipeConfig sample is shown in a literal block
content = '\n'.join(self.content)
code_block_node = nodes.literal_block(text=content)
# We reuse the graphviz node (from the graphviz extension) as it deals better with image formats vs builders
graphviz_node = graphviz()
graphviz_node['code'] = generate_dot_diagram(content)
graphviz_node['options'] = {}
table = [[[code_block_node], [graphviz_node]]]
table_node = self.build_table_from_list(table, 'auto', [50,50], 0, 0)
return [table_node]
def run(self):
name = self.arguments[0]
command = directives.choice(self.arguments[1], allowed_commands)
if command == 'init':
# Create a temporary file to hold the database
db_fh = tempfile.NamedTemporaryFile(delete = False)
ehive_db_urls[name] = 'sqlite:///' + db_fh.name
command_array = ['init_pipeline.pl', self.arguments[2], '-pipeline_url', ehive_db_urls[name]]
for tweak in self.options.get('tweaks', '').split():
command_array.extend(['-tweak', tweak])
else:
db = ehive_db_urls[name]
if command == 'run_job':
command_array = ['runWorker.pl', '-url', db, '-job_id', self.arguments[2]]
elif command == 'sync':
command_array = ['beekeeper.pl', '-url', db, '-sync']
if self.options.has_key('analyses_pattern'):
command_array.extend(['-analyses_pattern', self.options['analyses_pattern']])
elif command == 'analysis_diagram':
default_config_file = os.environ["EHIVE_ROOT_DIR"] + os.path.sep + "hive_config.json"
command_array = ['generate_graph.pl', '-url', db, '-output', '/dev/stdout', '-format', 'dot', '-config_file', default_config_file]
elif command == 'job_diagram':
default_config_file = os.environ["EHIVE_ROOT_DIR"] + os.path.sep + "hive_config.json"
command_array = ['visualize_jobs.pl', '-url', db, '-output', '/dev/stdout', '-format', 'dot', '-config_file', default_config_file]
command_array.extend(self.options.get('vj_options', '').split())
command_array[0] = os.path.join(os.environ["EHIVE_ROOT_DIR"], 'scripts', command_array[0])
dotcontent = subprocess.check_output(command_array, stderr=sys.stderr)
if command.endswith('diagram'):
# We reuse the graphviz node (from the graphviz extension) as it deals better with image formats vs builders
graphviz_node = graphviz()
graphviz_node['code'] = dotcontent
graphviz_node['options'] = {}
return [graphviz_node]
else:
return []
def run(self):
module = self.arguments[0]
# Generate dot:
save_dir = os.getcwd()
tmp_dir = tempfile.mkdtemp()
os.chdir(tmp_dir)
basename = 'foo'
cmd = ['pyreverse', '-p', basename]
classes = self.options.get('classes', [])
for c in classes:
raise NotImplementedError('classes option')
cmd.extend(['-c', c])
cmd.append(module)
subprocess.check_call(cmd)
with open('classes_{}.dot'.format(basename)) as f:
dotcode = f.read()
os.chdir(save_dir)
# create graphviz node:
node = graphviz()
node['code'] = dotcode
node['options'] = {}
return [node]
def run(self):
package_diagram_node = graphviz()
package_diagram_node[
'code'] = 'digraph {A->FAKE->DOT->DIAGRAM}' # TODO replace hardcoded dot code
package_diagram_node['options'] = {}
return [package_diagram_node]
def run(self):
func_name = self.content[0]
base_name = func_name.split(".")[0]
if len(func_name.split(".")) == 1:
func_name = None
base_path = __import__(base_name).__path__[0]
direction = "vertical"
if "direction" in self.options:
direction = self.options["direction"]
dotcode = create_callgraph(
filenames=f"{base_path}/**/*.py",
function=func_name,
namespace=base_name,
format="dot",
grouped="no-groups" not in self.options,
draw_uses="no-uses" not in self.options,
draw_defines="no-defines" not in self.options,
nested_groups="nested-groups" in self.options,
colored="no-colors" not in self.options,
annotated="annotated" in self.options,
rankdir={
"horizontal": "LR",
"vertical": "TB"
}[direction],
)
node = graphviz()
# insert link targets into groups: first insert link, then reformat link
if "toctree" in self.options:
path = self.options["toctree"].strip("/")
# create raw link
dotcode = re.sub(
r'([\w\d]+)(\s.+), (style="filled")',
r'\1\2, href="../' + path + r'/\1.html", target="_blank", \3',
dotcode,
)
def create_link(dot_name):
raw_link = re.sub(r"__(\w)", r".\1", dot_name)
# determine if name this is a class by checking if its first letter is capital
# (heuristic but should work almost always)
splits = raw_link.rsplit(".", 2)
if len(splits) > 1 and splits[-2][0].capitalize(
) == splits[-2][0]:
# is class
link = ".".join(splits[:-1]) + ".html#" + raw_link + '"'
else:
link = raw_link + '.html"'
return link
dotcode = re.sub(
r'(href="../' + path + r'/)(\w+)(\.html")',
lambda m: m.groups()[0] + create_link(m.groups()[1]),
dotcode,
)
node["code"] = dotcode
node["options"] = {"docname": self.env.docname}
if "graphviz_dot" in self.options:
node["options"]["graphviz_dot"] = self.options["graphviz_dot"]
if "layout" in self.options:
node["options"]["graphviz_dot"] = self.options["layout"]
if "alt" in self.options:
node["alt"] = self.options["alt"]
if "align" in self.options:
node["align"] = self.options["align"]
if "class" in self.options:
classes = self.options["class"]
else:
classes = []
if "zoomable" in self.options:
if len(classes) == 0:
classes = ["zoomable-callgraph"]
else:
classes.append("zoomable-callgraph")
if len(classes) > 0:
node["classes"] = classes
if "caption" not in self.options:
self.add_name(node)
return [node]
else:
figure = figure_wrapper(self, node, self.options["caption"])
self.add_name(figure)
return [figure]
def run(self):
package_diagram_node = graphviz()
package_diagram_node['code'] = 'digraph {A->FAKE->DOT->DIAGRAM}' # TODO replace hardcoded dot code
package_diagram_node['options'] = {}
return [package_diagram_node]
