def __init__(
self,
path,
job,
caption,
env,
category,
workflow,
wildcards_overwrite=None,
mode_embedded=True,
aux_files=None,
name_overwrite=None,
labels=None,
):
self.labels = labels
self.name_overwrite = name_overwrite
self.mode_embedded = mode_embedded
self.path = path
self.target = os.path.basename(path)
self.size = os.path.getsize(self.path)
self.size_mb = f"{self.size / 1e6:.2g} MB"
logger.info(f"Adding {self.name} ({self.size_mb}).")
self.raw_caption = caption
self.mime, _ = mime_from_file(self.path)
self.workflow = workflow
h = hashlib.sha256()
h.update(path.encode())
self.id = h.hexdigest()
self.job = job
self._wildcards = (job.wildcards if wildcards_overwrite is None else
wildcards_overwrite)
self.wildcards = logging.format_wildcards(self._wildcards)
self.params = (logging.format_dict(job.params).replace("\n",
r"\n").replace(
'"', r"\""))
self.category = category
self.aux_files = aux_files or []
self.data_uri = self._data_uri()
def __init__(self, path, job, caption, env, category):
self.path = path
self.target = os.path.basename(path)
self.size = os.path.getsize(self.path)
logger.info("Adding {} ({:.2g} MB).".format(self.name, self.size / 1e6))
self.raw_caption = caption
self.mime, _ = mime_from_file(self.path)
self.id = uuid.uuid4()
self.job = job
self.wildcards = logging.format_wildcards(job.wildcards)
self.params = logging.format_dict(job.params)
self.png_uri = None
self.category = category
if self.is_img:
convert = shutil.which("convert")
if convert is not None:
try:
# 2048 aims at a reasonable balance between what displays
# can show in a png-preview image and what renders quick
# into a small enough png
max_width = "2048"
max_height = "2048"
# '>' means only larger images scaled down to within max-dimensions
max_spec = max_width + "x" + max_height + ">"
png = sp.check_output(
["convert", "-resize", max_spec, self.path, "png:-"],
stderr=sp.PIPE,
)
uri = data_uri(
png, os.path.basename(self.path) + ".png", mime="image/png"
)
self.png_uri = uri
except sp.CalledProcessError as e:
logger.warning(
"Failed to convert image to png with "
"imagemagick convert: {}".format(e.stderr)
)
else:
logger.warning(
"Command convert not in $PATH. Install "
"imagemagick in order to have embedded "
"images and pdfs in the report."
)
if self.is_table:
if self.size > 1e6:
logger.warning(
"Table {} >1MB. Rendering as generic file.".format(self.path)
)
else:
with open(self.path) as table:
dialect = None
for prefix in range(10, 17):
try:
table.seek(0)
dialect = csv.Sniffer().sniff(table.read(prefix))
break
except csv.Error:
pass
except UnicodeDecodeError:
# table is not readable as UTF-8
break
if dialect is None:
logger.warning(
"Failed to infer CSV/TSV dialect from table {}. "
"Rendering as generic file.".format(self.path)
)
else:
table.seek(0)
reader = csv.reader(table, dialect)
columns = next(reader)
table = map(lambda row: list(map(num_if_possible, row)), reader)
template = env.get_template("table.html")
html = template.render(
columns=columns, table=table, name=self.name
).encode()
self.mime = "text/html"
self.path = os.path.basename(self.path) + ".html"
self.data_uri = data_uri(html, self.path, mime=self.mime)
return
# fallback
self.data_uri = data_uri_from_file(path)
def __init__(
self,
path,
job,
caption,
env,
category,
wildcards_overwrite=None,
mode_embedded=True,
):
self.mode_embedded = mode_embedded
self.path = path
self.target = os.path.basename(path)
self.size = os.path.getsize(self.path)
logger.info("Adding {} ({:.2g} MB).".format(self.name,
self.size / 1e6))
self.raw_caption = caption
self.mime, _ = mime_from_file(self.path)
h = hashlib.sha256()
h.update(path.encode())
self.id = h.hexdigest()
self.job = job
self._wildcards = (job.wildcards if wildcards_overwrite is None else
wildcards_overwrite)
self.wildcards = logging.format_wildcards(self._wildcards)
self.params = (logging.format_dict(job.params).replace("\n",
r"\n").replace(
'"', r"\""))
self.category = category
self.table_content = None
if self.is_table:
if self.size > 1e6:
logger.warning(
"Table {} >1MB. Rendering as generic file.".format(
self.path))
else:
with open(self.path) as table:
dialect = None
for prefix in range(10, 17):
try:
table.seek(0)
dialect = csv.Sniffer().sniff(table.read(prefix))
break
except csv.Error:
pass
except UnicodeDecodeError:
# table is not readable as UTF-8
break
if dialect is None:
logger.warning(
"Failed to infer CSV/TSV dialect from table {}. "
"Rendering as generic file.".format(self.path))
else:
table.seek(0)
reader = csv.reader(table, dialect)
columns = next(reader)
table = map(
lambda row: list(map(num_if_possible, row)),
reader)
template = env.get_template("table.html")
html = template.render(columns=columns,
table=table,
name=self.name).encode()
self.table_content = html
self.mime = "text/html"
self.path = os.path.basename(self.path) + ".html"
self.data_uri = self._data_uri()
self.png_uri = self._png_uri()
