def __call__(self, dataframe, path):
result = ResultBlocks()
texts = []
if self.head or self.tail:
if self.head:
texts.append(str(dataframe.head(self.head)))
if self.tail:
texts.append(str(dataframe.tail(self.tail)))
elif self.summary:
texts.append(str(dataframe.describe()))
else:
texts.append(str(dataframe))
# add indentation
texts = ['\n'.join([' %s' % y for y in x.split('\n')])
for x in texts]
formatted = '''
::
%s
''' % '\n ...\n'.join(texts)
result.append(ResultBlock(formatted,
title=path2str(path)))
return result
def __call__(self, track, slice=None):
edir = EXPORTDIR
method = "utr_extension"
blocks = ResultBlocks()
filepath = "%(edir)s/%(method)s/%(track)s.readextension_%(region)s_%(direction)s.%(slice)s.png"
block = \
'''
.. figure:: %(filename)s
:height: 300
'''
# append spaces for file extension
block = "\n".join([x + " " * 200 for x in block.split("\n")])
for region, direction in itertools.product(("downstream", "upstream"),
("sense", "antisense", "anysense")):
filename = filepath % locals()
if os.path.exists(filename):
blocks.append(ResultBlock(text=block % locals(),
title="%(track)s %(region)s %(direction)s" % locals()))
# else:
# blocks.append( ResultBlock( "",
# title = "%(track)s %(region)s %(direction)s" % locals() ) )
return odict((("rst", "\n".join(Utils.layoutBlocks(blocks, layout="columns-3"))),))
def __call__(self, track, slice=None):
edir = EXPORTDIR
method = "utr_extension"
blocks = ResultBlocks()
filepath = "%(edir)s/%(method)s/%(track)s.readextension_%(region)s_%(direction)s.%(slice)s.png"
block = \
'''
.. figure:: %(filename)s
:height: 300
'''
# append spaces for file extension
block = "\n".join([x + " " * 200 for x in block.split("\n")])
for region, direction in itertools.product(
("downstream", "upstream"), ("sense", "antisense", "anysense")):
filename = filepath % locals()
if os.path.exists(filename):
blocks.append(
ResultBlock(text=block % locals(),
title="%(track)s %(region)s %(direction)s" %
locals()))
# else:
# blocks.append( ResultBlock( "",
# title = "%(track)s %(region)s %(direction)s" % locals() ) )
return odict(
(("rst", "\n".join(Utils.layoutBlocks(blocks,
layout="columns-3"))), ))
def __call__(self, track, slice=None):
# note there are spaces behind the %(image)s directive to accomodate
# for path substitution
block = '''
.. figure:: %(image)s
:height: 300
'''
blocks = ResultBlocks()
tracks = sorted([x.asFile() for x in TRACKS])
for track in tracks:
files = glob.glob(
os.path.join(EXPORTDIR, "fastqc", "%s*_fastqc" % track))
for x, fn in enumerate(sorted(files)):
y = x + 1
image = os.path.abspath(
os.path.join(fn, "Images", "%s.png" % slice))
if not os.path.exists(image):
continue
blocks.append(
ResultBlock(text=block % locals(),
title=os.path.basename(fn)))
return odict(
(("rst", "\n".join(Utils.layoutBlocks(blocks,
layout="columns-2"))), ))
def __call__(self, track, slice=None):
# note there are spaces behind the %(image)s directive to accomodate
# for path substitution
block = '''
.. figure:: %(image)s
:height: 300
'''
blocks = ResultBlocks()
tracks = sorted([x.asFile() for x in TRACKS])
for track in tracks:
files = glob.glob(
os.path.join(EXPORTDIR, "fastqc", "%s*_fastqc" % track))
for x, fn in enumerate(sorted(files)):
y = x + 1
image = os.path.abspath(
os.path.join(fn, "Images", "%s.png" % slice))
if not os.path.exists(image):
continue
blocks.append(ResultBlock(text=block % locals(),
title=os.path.basename(fn)))
return odict((("rst", "\n".join(Utils.layoutBlocks(
blocks,
layout="columns-2"))),))
def render(self, data):
# initiate output structure
results = ResultBlocks(title='debug')
try:
results.append(ResultBlock(json.dumps(
data, indent=4), title=''))
except TypeError:
results.append(ResultBlock(str(data), title=''))
return results
def __call__(self, dataframe, path):
results = ResultBlocks()
if dataframe is None:
return results
title = path2str(path)
row_headers = dataframe.index
col_headers = dataframe.columns
results.append(self.asSpreadSheet(dataframe, row_headers,
col_headers, title))
return results
def __call__(self, track, slice=None):
blocks = ResultBlocks()
block = '''
.. figure:: %(image)s
:height: 300
'''
for image in glob.glob(os.path.join(IMAGEDIR, "*.png")):
blocks.append(ResultBlock(text=block % locals(),
title="image"))
return odict((("rst", "\n".join(Utils.layoutBlocks(blocks, layout="columns-2"))),))
def render(self, dataframe, path):
blocks = ResultBlocks()
options = self.get_slideshow_options()
lines = [self.prefix % options]
for title, row in dataframe.iterrows():
row = row[row.notnull()]
values = row.tolist()
headers = list(row.index)
dataseries = dict(zip(headers, values))
try:
# return value is a series
filename = dataseries['filename']
except KeyError:
self.warn(
"no 'filename' key in path %s" % (path2str(path)))
return blocks
try:
# return value is a series
name = dataseries['name']
except KeyError:
self.warn(
"no 'name' key in path %s" % (path2str(path)))
return blocks
description, title = os.path.split(name)
lines.extend(self.add_image(filename, title, description))
lines.append("""</div>""")
lines.append(self.skin % options)
lines.append("""</div>""")
lines = "\n".join(lines).split("\n")
lines = [".. only::html\n"] +\
[" .. raw:: html\n"] +\
[" " + x for x in lines]
lines = "\n".join(lines)
blocks.append(ResultBlock(text=lines,
title=path2str(path)))
return blocks
def render(self, data):
# initiate output structure
results = ResultBlocks(title='user')
labels = DataTree.getPaths(data)
# iterate over all items at leaf
for path, branch in DataTree.getNodes(data, len(labels) - 2):
for key in Utils.TrackerKeywords:
if key in branch:
# add a result block
results.append(ResultBlock(branch[key],
title=path2str(path)))
return results
def render(self, work, path):
"""render the data.
"""
results = ResultBlocks(title=path)
matrix, rows, columns = self.buildMatrix(work)
title = path2str(path)
if len(rows) == 0:
return ResultBlocks(ResultBlock("", title=title))
# do not output large matrices as rst files
# separate and force need to be mixed in.
if self.separate or (not self.force and
(len(rows) > self.max_rows or
len(columns) > self.max_cols)):
return ResultBlocks(self.asFile(pandas.DataFrame(matrix,
index=rows,
columns=columns),
rows,
columns,
title),
title=path)
lines = []
lines.append(".. csv-table:: %s" % title)
lines.append(' :header: "track","%s" ' % '","'.join(columns))
lines.append('')
for row in range(len(rows)):
lines.append(
' "%s","%s"' %
(rows[row], '","'.join(
[self.toString(x) for x in matrix[row]])))
lines.append("")
if path is None:
subtitle = ""
else:
subtitle = path2str(path)
results.append(ResultBlock("\n".join(lines), title=subtitle))
return results
def endPlot(self, plots, legends, path):
"""close plots.
"""
result = ResultBlocks()
title = path2str(path)
for plot in plots:
figid = plot._id
lines = []
lines.append("")
lines.append("#$bkh %s$#" % figid)
lines.append("")
r = ResultBlock("\n".join(lines), title=title)
r.bokeh = plot
result.append(r)
return result
def __call__(self, dataframe, path):
results = ResultBlocks()
if dataframe is None:
return results
title = path2str(path)
row_headers = dataframe.index
col_headers = dataframe.columns
# do not output large matrices as rst files
if self.separate or (not self.force and
(len(row_headers) > self.max_rows or
len(col_headers) > self.max_cols)):
if self.large == "xls":
results.append(self.asSpreadSheet(dataframe, row_headers,
col_headers, title))
else:
results.append(self.asFile(dataframe, row_headers,
col_headers, title))
results.append(self.asRST(dataframe, row_headers, col_headers, title))
return results
def __call__(self, dataframe, path):
results = ResultBlocks()
if dataframe is None:
return results
title = path2str(path)
lines = []
lines.append(".. glossary::")
lines.append("")
for x, row in enumerate(dataframe.iterrows()):
header, data = row
txt = "\n ".join([x.strip() for x in str(data).split("\n")])
lines.append(' %s\n %s\n' % (path2str(header), txt))
lines.append("")
results.append(ResultBlock("\n".join(lines), title=title))
return results
def __call__(self, dataframe, path):
# modify table (adding/removing columns) according to user options
# matrix, row_headers, col_headers = \
# self.modifyTable(matrix, row_headers, col_headers)
dataframe = self.modifyTable(dataframe)
title = path2str(path)
results = ResultBlocks()
row_headers = dataframe.index
col_headers = dataframe.columns
# as of sphinx 1.3.1, tables with more than 100 columns cause an
# error:
# Exception occurred:
# File "/ifs/apps/apps/python-2.7.9/lib/python2.7/site-packages/docutils/writers/html4css1/__init__.py", line 642, in write_colspecs
# colwidth = int(node['colwidth'] * 100.0 / width + 0.5)
# ZeroDivisionError: float division by zero
#
# Thus, for table with more than 100 columns, force will be
# disabled and max_cols set to a low value in order to make
# sure the table is not displayed inline
if len(col_headers) >= 90:
self.force = False
self.max_cols = 10
# do not output large matrices as rst files
if self.separate or (not self.force and
(len(row_headers) > self.max_rows or
len(col_headers) > self.max_cols)):
if self.large == "xls":
results.append(self.asSpreadSheet(dataframe, row_headers,
col_headers, title))
else:
results.append(self.asFile(dataframe, row_headers,
col_headers, title))
if self.preview:
raise NotImplementedError('preview not implemented')
row_headers = row_headers[:self.max_rows]
col_headers = col_headers[:self.max_cols]
# matrix = [x[:self.max_cols] for x in
# matrix[:self.max_rows]]
else:
return results
results.append(self.asCSV(dataframe, row_headers, col_headers, title))
return results
def __call__(self, dataframe, path):
# modify table (adding/removing columns) according to user options
# matrix, row_headers, col_headers = \
# self.modifyTable(matrix, row_headers, col_headers)
dataframe = self.modifyTable(dataframe)
title = path2str(path)
results = ResultBlocks()
row_headers = dataframe.index
col_headers = dataframe.columns
# do not output large matrices as rst files
if self.separate or (not self.force and
(len(row_headers) > self.max_rows or
len(col_headers) > self.max_cols)):
if self.large == "xls":
results.append(self.asSpreadSheet(dataframe, row_headers,
col_headers, title))
else:
results.append(self.asFile(dataframe, row_headers,
col_headers, title))
if self.preview:
raise NotImplementedError('preview not implemented')
row_headers = row_headers[:self.max_rows]
col_headers = col_headers[:self.max_cols]
# matrix = [x[:self.max_cols] for x in
# matrix[:self.max_rows]]
else:
return results
results.append(self.asCSV(dataframe, row_headers, col_headers, title))
return results
def __call__(self, *args, **kwargs):
try:
self.parseArguments(*args, **kwargs)
except:
self.error("%s: exception in parsing" % self)
return ResultBlocks(ResultBlocks(Utils.buildException("parsing")))
# collect no data if tracker is the empty tracker
# and go straight to rendering
try:
if self.tracker.getTracks() == ["empty"]:
# is instance does not work because of module mapping
# type(Tracker.Empty) == CGATReport.Tracker.Empty
# type(self.tracker) == Tracker.Empty
# if isinstance(self.tracker, Tracker.Empty):
result = self.renderer()
return ResultBlocks(result)
except AttributeError:
# for function trackers
pass
self.debug("profile: started: tracker: %s" % (self.tracker))
# collecting data
try:
self.collect()
except:
self.error("%s: exception in collection" % self)
return ResultBlocks(ResultBlocks(
Utils.buildException("collection")))
finally:
self.debug("profile: finished: tracker: %s" % (self.tracker))
if self.tree is None or len(self.tree) == 0:
self.info("%s: no data - processing complete" % self.tracker)
return None
data_paths = DataTree.getPaths(self.tree)
self.debug("%s: after collection: %i data_paths: %s" %
(self, len(data_paths), str(data_paths)))
# special Renderers - do not process data further but render
# directly. Note that no transformations will be applied.
if isinstance(self.renderer, Renderer.User):
results = ResultBlocks(title="main")
results.append(self.renderer(self.tree))
return results
elif isinstance(self.renderer, Renderer.Debug):
results = ResultBlocks(title="main")
results.append(self.renderer(self.tree))
return results
# merge all data to hierarchical indexed dataframe
self.data = DataTree.asDataFrame(self.tree)
self.debug("dataframe memory usage: total=%i,data=%i,index=%i,col=%i" %
(self.data.values.nbytes +
self.data.index.nbytes +
self.data.columns.nbytes,
self.data.values.nbytes,
self.data.index.nbytes,
self.data.columns.nbytes))
# if tracks are set by tracker, call tracker with dataframe
if self.indexFromTracker:
self.tracker.setIndex(self.data)
# transform data
try:
self.transform()
except:
self.error("%s: exception in transformation" % self)
return ResultBlocks(ResultBlocks(
Utils.buildException("transformation")))
# data_paths = DataTree.getPaths(self.data)
# self.debug("%s: after transformation: %i data_paths: %s" %
# (self, len(data_paths), str(data_paths)))
# restrict
try:
self.filterPaths(self.restrict_paths, mode="restrict")
except:
self.error("%s: exception in restrict" % self)
return ResultBlocks(ResultBlocks(
Utils.buildException("restrict")))
# data_paths = DataTree.getPaths(self.data)
# self.debug("%s: after restrict: %i data_paths: %s" %
# (self, len(data_paths), str(data_paths)))
# exclude
try:
self.filterPaths(self.exclude_paths, mode="exclude")
except:
self.error("%s: exception in exclude" % self)
return ResultBlocks(ResultBlocks(Utils.buildException("exclude")))
# data_paths = DataTree.getPaths(self.data)
# self.debug("%s: after exclude: %i data_paths: %s" %
# (self, len(data_paths), str(data_paths)))
# No pruning - maybe enable later as a user option
self.pruned = []
# try:
# self.prune()
# except:
# self.error("%s: exception in pruning" % self)
# return ResultBlocks(ResultBlocks(Utils.buildException("pruning")))
# data_paths = DataTree.getPaths(self.data)
# self.debug("%s: after pruning: %i data_paths: %s" %
# (self, len(data_paths), str(data_paths)))
try:
self.group()
except:
self.error("%s: exception in grouping" % self)
return ResultBlocks(ResultBlocks(Utils.buildException("grouping")))
# data_paths = DataTree.getPaths(self.data)
# self.debug("%s: after grouping: %i data_paths: %s" %
# (self, len(data_paths), str(data_paths)))
if self.renderer is not None:
self.debug("profile: started: renderer: %s" % (self.renderer))
try:
result = self.render()
except:
self.error("%s: exception in rendering" % self)
return ResultBlocks(ResultBlocks(
Utils.buildException("rendering")))
finally:
self.debug("profile: finished: renderer: %s" % (self.renderer))
else:
result = ResultBlocks(title="")
return result
def render(self):
'''supply the:class:`Renderer.Renderer` with the data to render.
The data supplied will depend on the ``groupby`` option.
returns a ResultBlocks data structure.
'''
self.debug("%s: rendering data started for %i items" %
(self,
len(self.data)))
# initiate output structure
results = ResultBlocks(title="")
dataframe = self.data
# dataframe.write_csv("test.csv")
if dataframe is None:
self.warn("%s: no data after conversion" % self)
raise ValueError("no data for renderer")
# special patch: set column names to pruned levels
# if there are no column names
if len(dataframe.columns) == len(self.pruned):
if list(dataframe.columns) == list(range(len(dataframe.columns))):
dataframe.columns = [x[1] for x in self.pruned]
nlevels = Utils.getDataFrameLevels(dataframe)
self.debug("%s: rendering data started. "
"levels=%i, group_level=%s" %
(self, nlevels,
str(self.group_level)))
if self.group_level < 0:
# no grouping for renderers that will accept
# a dataframe with any level of indices and no explicit
# grouping has been asked for.
results.append(self.renderer(dataframe, path=()))
else:
level = Utils.getGroupLevels(
dataframe,
max_level=self.group_level+1)
self.debug("%s: grouping by levels: %s" %
(self, str(level)))
for key, work in dataframe.groupby(level=level):
try:
results.append(self.renderer(work,
path=key))
except:
self.error("%s: exception in rendering" % self)
results.append(
ResultBlocks(Utils.buildException("rendering")))
if len(results) == 0:
self.warn("renderer returned no data.")
raise ValueError("renderer returned no data.")
self.debug("%s: rendering data finished with %i blocks" %
(self.tracker, len(results)))
return results
def layoutBlocks(blocks, layout="column"):
"""layout blocks of rst text.
layout can be one of "column", "row", or "grid".
The layout uses an rst table to arrange elements.
"""
lines = []
if len(blocks) == 0:
return lines
# flatten blocks
bb = ResultBlocks()
for b in blocks:
if b.title:
b.updateTitle(b.title, "prefix")
try:
bb.extend(b)
except TypeError:
bb.append(b)
blocks = bb
# check if postambles are identical across all blocks
postambles = set([b.postamble for b in blocks])
if len(postambles) == 1:
blocks.clearPostamble()
postamble = postambles.pop()
else:
postamble = None
if layout == "column":
for block in blocks:
if block.title:
lines.extend(block.title.split("\n"))
lines.append("")
else:
warn("report_directive.layoutBlocks: missing title")
lines.extend(block.text.split("\n"))
lines.extend(block.postamble.split("\n"))
lines.append("")
if postamble:
lines.extend(postamble.split("\n"))
lines.append("")
return lines
elif layout in ("row", "grid"):
if layout == "row":
ncols = len(blocks)
elif layout == "grid":
ncols = int(math.ceil(math.sqrt(len(blocks))))
elif layout.startswith("column"):
ncols = min(len(blocks), int(layout.split("-")[1]))
# TODO: think about appropriate fix for empty data
if ncols == 0:
ncols = 1
return lines
else:
raise ValueError("unknown layout %s " % layout)
if ncols == 0:
warn("no columns")
return lines
# compute column widths
widths = [x.getWidth() for x in blocks]
text_heights = [x.getTextHeight() for x in blocks]
title_heights = [x.getTitleHeight() for x in blocks]
columnwidths = []
for x in range(ncols):
columnwidths.append(max([widths[y] for y in
range(x, len(blocks), ncols)]))
separator = "+%s+" % "+".join(["-" * x for x in columnwidths])
# add empty blocks
if len(blocks) % ncols:
blocks.extend([ResultBlock("", "")] * (ncols - len(blocks) % ncols))
for nblock in range(0, len(blocks), ncols):
# add text
lines.append(separator)
max_height = max(text_heights[nblock:nblock + ncols])
new_blocks = ResultBlocks()
for xx in range(nblock, min(nblock + ncols, len(blocks))):
txt, col = blocks[xx].text.split("\n"), xx % ncols
txt = blocks[xx].text.split("\n") + \
blocks[xx].postamble.split("\n")
col = xx % ncols
max_width = columnwidths[col]
# add missig lines
txt.extend([""] * (max_height - len(txt)))
# extend lines
txt = [x + " " * (max_width - len(x)) for x in txt]
new_blocks.append(txt)
for l in zip(*new_blocks):
lines.append("|%s|" % "|".join(l))
# add subtitles
max_height = max(title_heights[nblock:nblock + ncols])
if max_height > 0:
new_blocks = ResultBlocks()
lines.append(separator)
for xx in range(nblock, min(nblock + ncols, len(blocks))):
txt, col = blocks[xx].title.split("\n"), xx % ncols
max_width = columnwidths[col]
# add missig lines
txt.extend([""] * (max_height - len(txt)))
# extend lines
txt = [x + " " * (max_width - len(x)) for x in txt]
new_blocks.append(txt)
for l in zip(*new_blocks):
lines.append("|%s|" % "|".join(l))
lines.append(separator)
if postamble:
lines.append(postamble)
lines.append("")
return lines
