def urlquote(s, safe=''):
"""Quote all reserved characters according to RFC3986 unless told otherwise.
The urllib.urlquote has a weird default which excludes '/' from
quoting even though it is a reserved character. We would never
want this when encoding elements in Deriva REST API URLs, so
this wrapper changes the default to have no declared safe
characters.
"""
return _urlquote(s.encode('utf-8'), safe=safe)
def urlquote(url, safe='/', **kwargs):
safe += '~'
return _urlquote(url, safe=safe, **kwargs)
def as_xml(self, seqno, sample_id, indent_level=1, print_xml=False):
"""
Build an XML string representation of this AcquisitionActivity (for
use in instances of the NexusLIMS schema)
Parameters
----------
seqno : int
An integer number representing what number activity this is in a
sequence of activities.
sample_id : str
A unique identifier pointing to a sample identifier. No checks
are done on this value; it is merely reproduced in the XML output
indent_level : int
(Default is 1) the level of indentation to use in exporting. If
0, no lines will be indented. A value of 1 should be appropriate
for most cases as used in the Nexus schema
print_xml : bool
Whether to print the XML output to the console or not (Default:
False)
Returns
-------
activity_xml : str
A string representing this AcquisitionActivity (note: is not a
properly-formed complete XML document since it does not have a
header or namespace definitions)
"""
aqAc_xml = ''
INDENT = ' ' * indent_level
line_ending = '\n'
aqAc_xml += f'{INDENT}<acquisitionActivity seqno="{seqno}">{line_ending}'
aqAc_xml += f'{INDENT*2}<startTime>{self.start.isoformat()}' \
f'</startTime>{line_ending}'
aqAc_xml += f'{INDENT*2}<sampleID>{sample_id}</sampleID>{line_ending}'
aqAc_xml += f'{INDENT*2}<setup>{line_ending}'
for pk, pv in sorted(self.setup_params.items(),
key=lambda i: i[0].lower()):
# metadata values to skip in XML output
if pk in ['warnings', 'DatasetType']:
pass
else:
if isinstance(pv, str) and any(c in pv for c in '<&'):
pv = escape(pv)
# for setup parameters, a key in the first dataset's warning
# list is the same as in all of them
pk_warning = pk in self.warnings[0]
aqAc_xml += f'{INDENT*3}<param name="{pk}"' + \
(' warning="true">' if pk_warning else '>') + \
f'{pv}</param>{line_ending}'
aqAc_xml += f'{INDENT*2}</setup>{line_ending}'
for f, m, um, w in zip(self.files, self.meta, self.unique_meta,
self.warnings):
# escape any bad characters in the filename
if isinstance(f, str) and any(c in f for c in '<&'):
f = escape(f)
# build path to thumbnail
rel_fname = f.replace(_os.environ["mmfnexus_path"], '')
rel_thumb_name = f'{rel_fname}.thumb.png'
# encode for safe URLs
rel_fname = _urlquote(rel_fname)
rel_thumb_name = _urlquote(rel_thumb_name)
# f is string; um is a dictionary, w is a list
aqAc_xml += f'{INDENT*2}<dataset ' \
f'type="{m["DatasetType"]}" ' \
f'role="Experimental">{line_ending}'
aqAc_xml += f'{INDENT*3}<name>{_os.path.basename(f)}' \
f'</name>{line_ending}'
aqAc_xml += f'{INDENT*3}<location>{rel_fname}' \
f'</location>{line_ending}'
aqAc_xml += f'{INDENT*3}<preview>{rel_thumb_name}' \
f'</preview>{line_ending}'
for meta_k, meta_v in sorted(um.items(),
key=lambda i: i[0].lower()):
if meta_k in ['warnings', 'DatasetType']:
pass
else:
if isinstance(meta_v, str) and \
any(c in meta_v for c in '<&'):
meta_v = escape(meta_v)
meta_k_warning = meta_k in w
aqAc_xml += f'{INDENT*3}<meta name="{meta_k}"' + \
(' warning="true">' if
meta_k_warning else '>') + \
f'{meta_v}</meta>{line_ending}'
aqAc_xml += f'{INDENT*2}</dataset>{line_ending}'
aqAc_xml += f'{INDENT}</acquisitionActivity>{line_ending}'
if print_xml:
print(aqAc_xml)
return aqAc_xml
# under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
# CONDITIONS OF ANY KIND, either express or implied. See the License for the
# specific language governing permissions and limitations under the License.
from urllib.parse import quote_plus as _urlquote
from . import _utils
from .base import *
DATABASE_URI = 'postgres://{username}:{password}@{host}:{port}/{database}'.format(
host=_utils.VCAP.SERVICES['pz-postgres.credentials.hostname'],
port=_utils.VCAP.SERVICES['pz-postgres.credentials.port'],
database=_utils.VCAP.SERVICES['pz-postgres.credentials.database'],
username=_utils.VCAP.SERVICES['pz-postgres.credentials.username'],
password=_urlquote(_utils.VCAP.SERVICES['pz-postgres.credentials.password']),
)
SECRET_KEY = os.urandom(32).hex()
CATALOG_SCHEME = 'https'
CATALOG_HOST = os.getenv('CATALOG_HOST')
PIAZZA_SCHEME = 'https'
PIAZZA_HOST = os.getenv('PIAZZA_HOST')
PIAZZA_API_KEY = os.getenv('PIAZZA_API_KEY')
GEOSERVER_SCHEME = 'http'
GEOSERVER_HOST = _utils.VCAP.SERVICES['pz-geoserver-efs.credentials.hostname']
GEOSERVER_USERNAME = _utils.VCAP.SERVICES['pz-geoserver-efs.credentials.username']
GEOSERVER_PASSWORD = _utils.VCAP.SERVICES['pz-geoserver-efs.credentials.password']