def param_role(role, rawtext, text, lineno, inliner,
options={}, content=[]):
'''inserts a member variable of a tracker class in the text.'''
parts = text.split(".")
if len(parts) < 2:
msg = inliner.reporter.error(
':param: should be in class.value format '
': "%s" is invalid.' % text, line=lineno)
prb = inliner.problematic(rawtext, rawtext, msg)
return [prb], [msg]
class_name, parameter_name = ".".join(parts[:-1]), parts[-1]
try:
code, tracker, tracker_path = Utils.makeTracker(class_name)
except AttributeError:
tracker = None
if not tracker:
msg = inliner.reporter.error(
':param: can not find class '
'"%s".' % class_name, line=lineno)
prb = inliner.problematic(rawtext, rawtext, msg)
return [prb], [msg]
try:
value = getattr(tracker, parameter_name)
except AttributeError:
msg = inliner.reporter.error(
':param: can not find variable %s in '
': "%s" is invalid -tracker=%s.' %
(parameter_name, class_name, str(tracker)), line=lineno)
prb = inliner.problematic(rawtext, rawtext, msg)
return [prb], [msg]
linked_codename = writeCode(class_name, code, inliner)
node = nodes.reference(rawtext,
utils.unescape(str(value)),
refuri=linked_codename,
**options)
return [node], []
def value_role(role, rawtext, text, lineno, inliner,
options={}, content=[]):
'''insert a single value from a tracker into text.'''
class_name = text
try:
code, tracker, tracker_path = Utils.makeTracker(class_name)
except (AttributeError, ImportError):
tracker = None
if not tracker:
msg = inliner.reporter.error(
':value: can not find class '
'"%s".' % class_name, line=lineno)
prb = inliner.problematic(rawtext, rawtext, msg)
return [prb], [msg]
# Python 2/3
try:
value = str(tracker())
except TypeError as msg:
print("python 3 problem: %s: tracker=%s" % (msg, str(tracker())))
linked_codename = writeCode(class_name, code, inliner)
# Base URL mainly used by inliner.rfc_reference, so this is correct:
# ref = inliner.document.settings.rfc_base_url + inliner.rfc_url % value
# in example, but deprecated
# set_classes(options)
# node = nodes.literal(rawtext,
# utils.unescape(str(value)),
# **options)
node = nodes.reference(rawtext,
utils.unescape(str(value)),
refuri=linked_codename,
**options)
return [node], []
def main(argv=None, **kwargs):
'''main function for test.py.
Long-form of command line arguments can also be supplied as kwargs.
If argv is not None, command line parsing will be performed.
'''
parser = optparse.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option("-t", "--tracker", dest="tracker", type="string",
help="tracker to use [default=%default]")
parser.add_option("-p", "--page", dest="page", type="string",
help="render an rst page [default=%default]")
parser.add_option("-a", "--tracks", dest="tracks", type="string",
help="tracks to use [default=%default]")
parser.add_option("-m", "--transformer", dest="transformers",
type="string", action="append",
help="add transformation [default=%default]")
parser.add_option("-s", "--slices", dest="slices", type="string",
help="slices to use [default=%default]")
parser.add_option("-r", "--renderer", dest="renderer", type="string",
help="renderer to use [default=%default]")
parser.add_option("-w", "--path", "--trackerdir",
dest="trackerdir", type="string",
help="path to trackers [default=%default]")
parser.add_option("-f", "--force", dest="force", action="store_true",
help="force recomputation of data by deleting cached "
"results [default=%default]")
parser.add_option("-o", "--option", dest="options", type="string",
action="append",
help="renderer options - supply as key=value pairs "
"(without spaces). [default=%default]")
parser.add_option("-l", "--language", dest="language", type="choice",
choices=("rst", "notebook"),
help="output language for snippet. Use ``rst`` "
"to create a snippet to paste "
"into a cgatreport document. Use ``notebook`` to "
"create a snippet to paste "
"into an ipython notebook [default=%default]")
parser.add_option("--no-print", dest="do_print", action="store_false",
help="do not print an rst text element to create "
"the displayed plots [default=%default].")
parser.add_option("--no-show", dest="do_show", action="store_false",
help="do not show a plot [default=%default].")
parser.add_option("--layout", dest="layout", type="string",
help="output rst with layout [default=%default].")
parser.add_option("-i", "--start-interpreter", dest="start_interpreter",
action="store_true",
help="do not render, but start python interpreter "
"[default=%default].")
parser.add_option("-I", "--ii", "--start-ipython", dest="start_ipython",
action="store_true",
help="do not render, start ipython interpreter "
"[default=%default].")
parser.add_option(
"--workdir", dest="workdir", type="string",
help="working directory - change to this directory "
"before executing "
"[default=%default]")
parser.add_option(
"--hardcopy", dest="hardcopy", type="string",
help="output images of plots. The parameter should "
"contain one or more %s "
"The suffix determines the type of plot. "
"[default=%default].")
parser.set_defaults(
loglevel=1,
tracker=None,
transformers=[],
tracks=None,
slices=None,
options=[],
renderer="table",
do_show=True,
do_print=True,
force=False,
trackerdir=TRACKERDIR,
caption="add caption here",
start_interpreter=False,
start_ipython=False,
language="rst",
workdir=None,
layout=None,
dpi=100)
if argv is None and len(kwargs) == 0:
argv = sys.argv
if argv:
(options, args) = parser.parse_args(argv)
if len(args) == 2:
options.tracker, options.renderer = args
else:
(options, args) = parser.parse_args([])
######################################################
# set keyword arguments as options
for keyword, value in kwargs.items():
if hasattr(options, keyword):
setattr(options, keyword, value)
del kwargs[keyword]
# change some kwarguments
if options.transformers:
for keyword, value in kwargs.items():
if keyword.startswith("tf"):
kwargs["tf-{}".format(keyword[2:])] = value
if options.workdir is not None:
savedir = os.getcwd()
os.chdir(options.workdir)
Utils.getParameters(sorted(glob.glob("*.ini")))
else:
savedir = None
######################################################
# configure options
options.trackerdir = os.path.abspath(
os.path.expanduser(options.trackerdir))
if os.path.exists(options.trackerdir):
sys.path.insert(0, options.trackerdir)
else:
L.warn("directory %s does not exist" % options.trackerdir)
######################################################
# test plugins
for x in options.options:
if "=" in x:
data = x.split("=")
key, val = [y.strip() for y in (data[0], "=".join(data[1:]))]
else:
key, val = x.strip(), None
kwargs[key] = val
if options.tracks:
kwargs["tracks"] = options.tracks
if options.slices:
kwargs["slices"] = options.slices
kwargs = Utils.updateOptions(kwargs)
option_map = getOptionMap()
renderer_options = Utils.selectAndDeleteOptions(
kwargs, option_map["render"])
transformer_options = Utils.selectAndDeleteOptions(
kwargs, option_map["transform"])
display_options = Utils.selectAndDeleteOptions(
kwargs, option_map["display"])
######################################################
# decide whether to render or not
if options.renderer == "none" or options.start_interpreter or \
options.start_ipython or options.language == "notebook":
renderer = None
else:
renderer = Utils.getRenderer(options.renderer, renderer_options)
transformers = Utils.getTransformers(
options.transformers, transformer_options)
exclude = set(("Tracker",
"TrackerSQL",
"returnLabeledData",
"returnMultipleColumnData",
"returnMultipleColumns",
"returnSingleColumn",
"returnSingleColumnData",
"SQLError",
"MultipleColumns",
"MultipleColumnData",
"LabeledData",
"DataSimple",
"Data"))
######################################################
# build from tracker
if options.tracker:
if "." in options.tracker:
parts = options.tracker.split(".")
tracker_modulename = ".".join(parts[:-1])
tracker_name = parts[-1]
else:
tracker_modulename = None
tracker_name = options.tracker
try:
_code, tracker, tracker_path = Utils.makeTracker(
options.tracker, (), kwargs)
except ImportError:
# try to find class in module
trackers = []
for filename in glob.glob(
os.path.join(options.trackerdir, "*.py")):
modulename = os.path.basename(filename)
trackers.extend(
[x for x in getTrackers(modulename)
if x[0] not in exclude])
for name, tracker_class, modulename, is_derived in trackers:
if name == tracker_name:
if tracker_modulename is not None:
if modulename == tracker_modulename:
break
else:
tracker_modulename = modulename
break
else:
available_trackers = set([x[0] for x in trackers if x[3]])
print(
"unknown tracker '%s': possible trackers are\n %s" %
(options.tracker, "\n ".join(sorted(available_trackers))))
print(
"(the list above does not contain functions).")
sys.exit(1)
# instantiate functors
if is_derived:
tracker = tracker_class(**kwargs)
# but not functions
else:
tracker = tracker_class
# remove everything related to that tracker for a clean slate
if options.force:
removed = CGATReport.clean.removeTracker(tracker_name)
print("removed all data for tracker %s: %i files" %
(tracker_name, len(removed)))
dispatcher = Dispatcher(tracker, renderer, transformers)
if renderer is None:
# dispatcher.parseArguments(**kwargs)
# result = dispatcher.collect()
# result = dispatcher.transform()
result = dispatcher(**kwargs)
options.do_print = options.language == "notebook"
options.do_show = False
options.hardcopy = False
else:
# needs to be resolved between renderer and dispatcher options
result = dispatcher(**kwargs)
if options.do_print:
sys.stdout.write(".. ---- TEMPLATE START --------\n\n")
if options.language == "rst":
writeRST(sys.stdout,
options,
kwargs,
renderer_options,
transformer_options,
display_options,
tracker_modulename,
tracker_name)
elif options.language == "notebook":
writeNotebook(sys.stdout,
options,
kwargs,
renderer_options,
transformer_options,
display_options,
tracker_modulename,
tracker_name)
sys.stdout.write("\n.. ---- TEMPLATE END ----------\n")
sys.stdout.write("\n.. ---- OUTPUT-----------------\n")
if result and renderer is not None:
if options.layout is not None:
lines = Utils.layoutBlocks(result, layout=options.layout)
print "\n".join(lines)
else:
for r in result:
if r.title:
print ("")
print ("title: %s" % r.title)
print ("")
for s in r:
print(str(s))
if options.hardcopy:
fig_managers = _pylab_helpers.Gcf.get_all_fig_managers()
# create all the images
for figman in fig_managers:
# create all images
figid = figman.num
outfile = re.sub("%s", str(figid), options.hardcopy)
figman.canvas.figure.savefig(outfile, dpi=options.dpi)
if result and options.do_show:
if options.renderer.startswith("r-"):
for rr in result:
for r in rr:
if hasattr(r, 'rggplot'):
from rpy2.robjects import r as R
import rpy2.rinterface
try:
R.plot(r.rggplot)
except rpy2.rinterface.RRuntimeError, msg:
if re.search("object.*not found", str(msg)):
print '%s: available columns in dataframe=%s' % \
(msg,
R('''colnames(rframe)'''))
print("press Ctrl-c to stop")
while 1:
pass
elif len(_pylab_helpers.Gcf.get_all_fig_managers()) > 0:
plt.show()
else:
for rr in result:
for r in rr:
if hasattr(r, 'xls'):
tmpfile, outpath = tempfile.mkstemp(
dir='.', suffix='.xlsx')
os.close(tmpfile)
print ('saving xlsx to %s' % outpath)
r.xls.save(outpath)
elif hasattr(r, 'bokeh'):
import bokeh.plotting as bk
bk.show()
def run(arguments,
options,
lineno,
content,
state_machine=None,
document=None,
srcdir=None,
builddir=None):
"""process:report: directive.
*srdir* - top level directory of rst documents
*builddir* - build directory
"""
tag = "%s:%i" % (str(document), lineno)
logging.debug("report_directive.run: profile: started: rst: %s" % tag)
# sort out the paths
# reference is used for time-stamping
tracker_name = directives.uri(arguments[0])
(basedir, fname, basename, ext, outdir,
codename, notebookname) = Utils.build_paths(tracker_name)
# get the directory of the rst file
# state_machine.document.attributes['source'])
rstdir, rstfile = os.path.split(document)
# root of document tree
if srcdir is None:
srcdir = setup.srcdir
# build directory
if builddir is None:
builddir = setup.builddir
# remove symbolic links
srcdir, builddir, rstdir = [
os.path.realpath(x) for x in (srcdir, builddir, rstdir)]
# there are three directories:
# builddir = directory where document is built in
# (usually _build/html or similar)
# rstdir = directory where rst sources are located
# srcdir = directory from which the build process is started
# path to root relative to rst
rst2srcdir = os.path.join(os.path.relpath(srcdir, start=rstdir), outdir)
# path to root relative to rst
rst2builddir = os.path.join(
os.path.relpath(builddir, start=rstdir), outdir)
# path relative to source (for images)
root2builddir = os.path.join(
os.path.relpath(builddir, start=srcdir), outdir)
logging.debug(
"report_directive.run: arguments=%s, options=%s, lineno=%s, "
"content=%s, document=%s" %
(str(arguments),
str(options),
str(lineno),
str(content),
str(document)))
logging.debug(
"report_directive.run: plotdir=%s, basename=%s, ext=%s, "
"fname=%s, rstdir=%s, srcdir=%s, builddir=%s" %
(tracker_name, basename, ext, fname, rstdir, srcdir, builddir))
logging.debug(
"report_directive.run: tracker_name=%s, basedir=%s, "
"rst2src=%s, root2build=%s, outdir=%s, codename=%s" %
(tracker_name, basedir, rst2srcdir, rst2builddir, outdir, codename))
# try to create. If several processes try to create it,
# testing with `if` will not work.
try:
os.makedirs(outdir)
except OSError as msg:
pass
if not os.path.exists(outdir):
raise OSError("could not create directory %s: %s" % (outdir, msg))
########################################################
# collect options
# replace placedholders
try:
options = Utils.updateOptions(options)
except ValueError as msg:
logging.warn("failure while updating options: %s" % msg)
logging.debug("report_directive.run: options=%s" % (str(options),))
transformer_names = []
renderer_name = None
# get layout option
layout = options.get("layout", "column")
option_map = Component.getOptionMap()
renderer_options = Utils.selectAndDeleteOptions(
options, option_map["render"])
transformer_options = Utils.selectAndDeleteOptions(
options, option_map["transform"])
dispatcher_options = Utils.selectAndDeleteOptions(
options, option_map["dispatch"])
tracker_options = Utils.selectAndDeleteOptions(
options, option_map["tracker"])
display_options = Utils.selectAndDeleteOptions(
options, option_map["display"])
logging.debug("report_directive.run: renderer options: %s" %
str(renderer_options))
logging.debug("report_directive.run: transformer options: %s" %
str(transformer_options))
logging.debug("report_directive.run: dispatcher options: %s" %
str(dispatcher_options))
logging.debug("report_directive.run: tracker options: %s" %
str(tracker_options))
logging.debug("report_directive.run: display options: %s" %
str(display_options))
if "transform" in display_options:
transformer_names = display_options["transform"].split(",")
del display_options["transform"]
if "render" in display_options:
renderer_name = display_options["render"]
del display_options["render"]
########################################################
# check for missing files
if renderer_name is not None:
options_key = str(renderer_options) +\
str(transformer_options) +\
str(dispatcher_options) +\
str(tracker_options) +\
str(transformer_names)
options_hash = hashlib.md5(options_key.encode()).hexdigest()
template_name = Utils.quote_filename(
Config.SEPARATOR.join((tracker_name, renderer_name,
options_hash)))
filename_text = os.path.join(outdir, "%s.txt" % (template_name))
notebookname += options_hash
logging.debug("report_directive.run: options_hash=%s" % options_hash)
###########################################################
# check for existing files
# update strategy does not use file stamps, but checks
# for presence/absence of text element and if all figures
# mentioned in the text element are present
###########################################################
queries = [re.compile("%s(%s\S+.%s)" %
(root2builddir, outdir, suffix))
for suffix in ("png", "pdf", "svg")]
logging.debug("report_directive.run: checking for changed files.")
# check if text element exists
if os.path.exists(filename_text):
lines = [x[:-1] for x in open(filename_text, "r").readlines()]
filenames = []
# check if all figures are present
for line in lines:
for query in queries:
x = query.search(line)
if x:
filenames.extend(list(x.groups()))
logging.debug(
"report_directive.run: %s: checking for %s" %
(tag, str(filenames)))
for filename in filenames:
if not os.path.exists(filename):
logging.info(
"report_directive.run: %s: redo: %s missing" %
(tag, filename))
break
else:
logging.info(
"report_directive.run: %s: noredo: all files are present" %
tag)
# all is present - save text and return
if lines and state_machine:
state_machine.insert_input(
lines, state_machine.input_lines.source(0))
return []
else:
logging.debug(
"report_directive.run: %s: no check performed: %s missing" %
(tag, str(filename_text)))
else:
template_name = ""
filename_text = None
##########################################################
# Initialize collectors
collectors = []
for collector in list(Component.getPlugins("collect").values()):
collectors.append(collector())
##########################################################
# instantiate tracker, dispatcher, renderer and transformers
# and collect output
###########################################################
try:
########################################################
# find the tracker
logging.debug(
"report_directive.run: collecting tracker %s with options %s " %
(tracker_name, tracker_options))
code, tracker, tracker_path = Utils.makeTracker(
tracker_name, (), tracker_options)
if not tracker:
logging.error(
"report_directive.run: no tracker - no output from %s " %
str(document))
raise ValueError("tracker `%s` not found" % tracker_name)
logging.debug(
"report_directive.run: collected tracker %s" % tracker_name)
tracker_id = Cache.tracker2key(tracker)
########################################################
# determine the transformer
logging.debug("report_directive.run: creating transformers")
transformers = Utils.getTransformers(
transformer_names, transformer_options)
########################################################
# determine the renderer
logging.debug("report_directive.run: creating renderer.")
if renderer_name is None:
logging.error(
"report_directive.run: no renderer - no output from %s" %
str(document))
raise ValueError("the report directive requires a renderer")
renderer = Utils.getRenderer(renderer_name, renderer_options)
try:
renderer.set_paths(rstdir, srcdir, builddir)
renderer.set_display_options(display_options)
except AttributeError:
# User renderers will not have these methods
pass
########################################################
# create and call dispatcher
logging.debug("report_directive.run: creating dispatcher")
dispatcher = Dispatcher.Dispatcher(tracker,
renderer,
transformers)
# add the tracker options
dispatcher_options.update(tracker_options)
blocks = dispatcher(**dispatcher_options)
if blocks is None:
blocks = ResultBlocks(ResultBlocks(
Utils.buildWarning(
"NoData",
"tracker %s returned no Data" % str(tracker))))
code = None
tracker_id = None
except:
logging.warn(
"report_directive.run: exception caught at %s:%i - see document" %
(str(document), lineno))
blocks = ResultBlocks(ResultBlocks(
Utils.buildException("invocation")))
code = None
tracker_id = None
logging.debug(
"report_directive.run: profile: started: collecting: %s" % tag)
########################################################
# write code output
linked_codename = re.sub("\\\\", "/", os.path.join(rst2srcdir, codename))
if code and basedir != outdir:
with open(os.path.join(outdir, codename), "w") as outfile:
for line in code:
outfile.write(line)
########################################################
# write notebook snippet
linked_notebookname = re.sub(
"\\\\", "/", os.path.join(rst2srcdir, notebookname))
if basedir != outdir and tracker_id is not None:
with open(os.path.join(outdir, notebookname), "w") as outfile:
Utils.writeNoteBookEntry(outfile,
renderer=renderer_name,
tracker=tracker_name,
transformers=transformer_names,
tracker_path=tracker_path,
options=renderer_options.items() +
tracker_options.items() +
transformer_options.items())
###########################################################
# collect images
###########################################################
map_figure2text = {}
links = {'code_url': linked_codename,
'notebook_url': linked_notebookname}
try:
for collector in collectors:
map_figure2text.update(collector.collect(
blocks,
template_name,
outdir,
rstdir,
builddir,
srcdir,
content,
display_options,
tracker_id,
links=links))
except:
logging.warn("report_directive.run: exception caught while "
"collecting with %s at %s:%i - see document" %
(collector, str(document), lineno))
blocks = ResultBlocks(ResultBlocks(
Utils.buildException("collection")))
code = None
tracker_id = None
###########################################################
# replace place holders or add text
###########################################################
# add default for text-only output
urls = Utils.asList(Utils.PARAMS["report_urls"])
code_url, nb_url = "", ""
if "code" in urls:
code_url = "`code <%(code_url)s>`__" % links
if "notebook" in urls:
nb_url = '`nb <%(notebook_url)s>`__' % links
map_figure2text["default-prefix"] = TEMPLATE_TEXT % locals()
map_figure2text["default-suffix"] = ""
blocks.updatePlaceholders(map_figure2text)
# render the output taking into account the layout
lines = Utils.layoutBlocks(blocks, layout)
lines.append("")
# add caption
lines.extend(['::', ''])
if content:
lines.extend([' %s' % row.strip() for row in content])
lines.append("")
lines.append("")
# output rst text for this renderer
if filename_text:
outfile = open(filename_text, "w")
outfile.write("\n".join(lines))
outfile.close()
if CGATREPORT_DEBUG:
for x, l in enumerate(lines):
print("%5i %s" % (x, l))
if len(lines) and state_machine:
state_machine.insert_input(
lines, state_machine.input_lines.source(0))
logging.debug(
"report_directive.run: profile: finished: collecting: %s" % tag)
logging.debug(
"report_directive.run: profile: finished: rst: %s:%i" %
(str(document), lineno))
return []
