def dashboard_asf_jira_links(project_key, project_id, components=None):
try:
from urllib.parse import quote_plus as url_escape
except ImportError:
from urllib import quote_plus as url_escape
links = []
all_issues_jql = "project = {}".format(project_key)
open_issues_jql = all_issues_jql + " and resolution is null"
if components is not None:
components = ", ".join(["\"{}\"".format(x) for x in components])
constraint = " and component in ({})".format(components)
open_issues_jql += constraint
all_issues_jql += constraint
summary_url = "https://issues.apache.org/jira/projects/{}".format(project_key)
open_issues_url = "https://issues.apache.org/jira/issues/?jql={}".format(url_escape(open_issues_jql))
all_issues_url = "https://issues.apache.org/jira/issues/?jql={}".format(url_escape(all_issues_jql))
create_issue_url = "https://issues.apache.org/jira/secure/CreateIssue!default.jspa?pid={}".format(project_id)
links.append("<a href=\"{}\">Summary</a>".format(summary_url))
links.append("<a href=\"{}\">Open issues</a>".format(open_issues_url))
links.append("<a href=\"{}\">All issues</a>".format(all_issues_url))
links.append("<a href=\"{}\">Create issue</a>".format(create_issue_url))
return " • ".join(links)
def _json_for_name(name: str, kind: str):
# check the name
name = name.replace('.json', '')
def match_in_index(name, index, kind):
return [(obj['organism'], obj[kind + '_name'])
for obj in index[kind + 's']
if obj[kind + '_name'] == name]
try:
index = server_index()
except URLError:
raise Exception('Could not connect to the Escher server')
match = match_in_index(name, server_index(), kind)
if len(match) == 0:
raise Exception(f'Could not find the {kind} {name} on the server')
org, name = match[0]
url = (
get_url(kind + '_download') +
'/'.join([url_escape(x) for x in [org, name + '.json']])
)
print('Downloading %s from %s' % (kind.title(), url))
try:
download = urlopen(url)
except URLError:
raise ValueError('No %s found in at %s' % (kind, url))
data = _decode_response(download)
return data
def _json_for_name(name: str, kind: str):
# check the name
name = name.replace('.json', '')
def match_in_index(name, index, kind):
return [(obj['organism'], obj[kind + '_name'])
for obj in index[kind + 's'] if obj[kind + '_name'] == name]
try:
index = server_index()
except URLError:
raise Exception('Could not connect to the Escher server')
match = match_in_index(name, server_index(), kind)
if len(match) == 0:
raise Exception(f'Could not find the {kind} {name} on the server')
org, name = match[0]
url = (get_url(kind + '_download') +
'/'.join([url_escape(x) for x in [org, name + '.json']]))
print('Downloading %s from %s' % (kind.title(), url))
try:
download = urlopen(url)
except URLError:
raise ValueError('No %s found in at %s' % (kind, url))
data = _decode_response(download)
return data
def _listobjs(self, objs, name):
if objs:
yield "<p>{} {}(s):</p>".format(len(objs), name)
yield "<ul>"
for o in sorted(objs, key=attrgetter("name")):
title = html_escape(o.name)
url = html_escape("{}/{}".format(self.url, url_escape(o.name)))
yield '<li><a href="{}">{}</a></li>'.format(url, title)
yield "</ul><br/>"
def add_anchor(match):
uuid = match.group(1)
if uuid not in tokens:
return match.group(0)
original = match.group(0)
entry_type = tokens[uuid][0]
entry_name = url_escape(tokens[uuid][1])
anchor_name = f"//apple_ref/cpp/{entry_type}/{entry_name}"
return f"{original}<a name=\"{anchor_name}\" class=\"dashAnchor\"></a>"
def links(self):
if self.is_dir:
for f in self._files:
yield dict(
rel="enclosure",
href="{}/{}".format(self.url, url_escape(f.name)),
length=str(f.stat().st_size),
type=get_mimetype(f.name),
)
else:
yield dict(
rel="enclosure",
href=self.url,
length=str(self.size),
type=get_mimetype(self.url),
)
def populate_config(self):
config = self.config
for s in self.CONFIG_SPECIALS:
config[s] = {}
for opt, val in self.parser.items(u'global'):
if opt in self.CONFIG_SPECIALS:
raise ValueError('"%s" is an invalid ' '[global] option' % opt)
config[opt] = val
config['tls_verify_client'] = self.parser.getboolean(
'global', 'tls_verify_client', fallback=False)
config['debug'] = self.parser.getboolean('global',
'debug',
fallback=False)
config['makedirs'] = self.parser.getboolean('global',
'makedirs',
fallback=False)
if self.args.debug:
config['debug'] = self.args.debug
config['auditlog'] = os.path.abspath(config.get('auditlog'))
config['umask'] = int(config.get('umask', '027'), 8)
url = config.get('server_url')
sock = config.get('server_socket')
if url and sock:
raise ValueError(
"'server_url' and 'server_socket' are mutually exclusive.")
if not url and not sock:
# no option but, use default socket path
socketdir = self.parser.get(u'DEFAULT', u'socketdir')
name = self.args.instance if self.args.instance else 'custodia'
sock = os.path.join(socketdir, name + '.sock')
if sock:
server_socket = os.path.abspath(sock)
config['server_url'] = 'http+unix://{}/'.format(
url_escape(server_socket, ''))
def __init__(self, base_url, start_path, rel_path):
self.title = os.path.basename(rel_path)
self.url = "{}/{}".format(base_url, url_escape(rel_path))
self.path = os.path.join(start_path, rel_path)
self.is_dir = os.path.isdir(self.path)
stat = os.stat(self.path)
self._files, self._dirs = [], []
if self.is_dir:
self.size = None
for x in os.scandir(self.path):
if x.is_file():
self._files.append(x)
elif x.is_dir():
self._dirs.append(x)
else:
self.size = stat.st_size
self.date = datetime.utcfromtimestamp(
stat.st_mtime).replace(tzinfo=timezone.utc)
def tack_on_reports(self):
""" Copy every file into the data_dir and bung in a link to it here.
"""
links = OrderedDict()
# Go through the already-sorted list of samples.
for s_name in self.samples_list:
links[s_name] = "<span class='alt_col_link'>"
# Cycle through the reports. Presumably there are one or two.
reps = sorted([r for r in self.html_reports if r.sample == s_name],
key=lambda r: r.read)
for n, rep in enumerate(reps):
# This is a little funky but seems most legible...
rep_label = "{}_{}".format(
rep.sample, rep.read) if len(reps) > 1 else rep.sample
link_label = rep_label if n == 0 else "..._{}".format(rep.read)
fname = os.path.basename(rep.file)
shutil.copy(rep.file, os.path.join(config.data_dir, fname))
file_relpath = os.path.join(config.data_dir_name, fname)
links[
s_name] += "<a href='{f}' title='{rl} FastQC Report'>{ll}</a> ".format(
f=url_escape(file_relpath),
rl=html_escape(rep_label),
ll=html_escape(link_label))
links[s_name] += "</span>"
#Output in sorted order.
if not links:
links['error'] = "No FastQC HTML plots were found."
return "<div>" + " ".join(links[k] for k in sorted(links)) + "</div>"