def addHeaders(headers, request, response):
HEADS = [
'COUNT-SOURCES', 'COUNT-ATOMS', 'COUNT-MOLECULES', 'COUNT-SPECIES',
'COUNT-STATES', 'COUNT-COLLISIONS', 'COUNT-RADIATIVE',
'COUNT-NONRADIATIVE', 'TRUNCATED', 'APPROX-SIZE'
]
headers = CaselessDict(headers)
headlist_asString = ''
for h in HEADS:
if headers.has_key(h):
response['VAMDC-' + h] = '%s' % headers[h]
headlist_asString += 'VAMDC-' + h + ', '
response['Access-Control-Allow-Origin'] = '*'
response['Access-Control-Expose-Headers'] = headlist_asString[:-2]
lastmod = headers.get('LAST-MODIFIED')
if not lastmod and hasattr(settings, 'LAST_MODIFIED'):
lastmod = settings.LAST_MODIFIED
if isinstance(lastmod, datetime.date):
response['Last-Modified'] = getFormatLastModified(lastmod)
elif isinstance(lastmod, str):
response['Last-Modified'] = lastmod
else:
pass
return response
def addHeaders(headers, response):
HEADS = [
'COUNT-SOURCES', 'COUNT-ATOMS', 'COUNT-MOLECULES', 'COUNT-SPECIES',
'COUNT-STATES', 'COUNT-COLLISIONS', 'COUNT-RADIATIVE',
'COUNT-NONRADIATIVE', 'TRUNCATED', 'APPROX-SIZE'
]
headers = CaselessDict(headers)
for h in HEADS:
if headers.has_key(h):
response['VAMDC-' + h] = '%s' % headers[h]
lastmod = headers.get('LAST-MODIFIED')
if not lastmod and hasattr(settings, 'LAST_MODIFIED'):
lastmod = settings.LAST_MODIFIED
if isinstance(lastmod, datetime.date):
response['Last-Modified'] = getFormatLastModified(lastmod)
elif isinstance(lastmod, str):
response['Last-Modified'] = lastmod
else:
pass
return response
def __init__(self, request):
self.HTTPmethod = request.method
self.isvalid = True
self.errormsg = ''
try:
self.request = CaselessDict(dict(request.GET or request.POST))
except Exception, e:
self.isvalid = False
self.errormsg = 'Could not read argument dict: %s' % e
log.error(self.errormsg)
def __init__(self, data):
try:
data = CaselessDict(dict(data))
self.lang = lower(data['LANG'])
self.query = data['QUERY']
self.format = lower(data['FORMAT'])
self.isvalid = True
except Exception, e:
self.isvalid = False
LOG(str(e))
def BibTeX2XML(bibtexstring, key=None):
"""
Derives an XSAMS source element from the given BibTeX and returns the XML text.
The ID of the Source is set in the form B(node)-(key) where (node) is replaced
by the ID string for this node and (key) is replaced by the unique key for this
Source. If the key argument is given, this value is used for the key; otherwise,
a key is generated from the BibTeX content.
"""
e = getEntryFromString(bibtexstring)
if key:
xml = u'<Source sourceID="B%s-%s">\n<Authors>\n' % (NODEID, key)
else:
xml = u'<Source sourceID="B%s-%s">\n<Authors>\n' % (NODEID, e.key)
for a in e.persons['author']:
name = a.first() + a.middle() + a.last() + a.lineage()
name = map(strip, name)
name = map(strip, name, ['{}'] * len(name))
xml += '<Author><Name>%s</Name></Author>' % ' '.join(name)
xml += '\n</Authors>'
category = TYPE2CATEGORY.get(e.type)
f = CaselessDict(e.fields)
url = f.get('bdsk-url-1')
title = f.get('title', "").strip().strip('{}')
sourcename = f.get('journal', 'unknown')
doi = f.get('doi', "")
year = f.get('year', "")
volume = f.get('volume', "")
pages = f.get('pages', "")
p1, p2 = '', ''
pages = re.findall(r'[0-9][0-9]*', pages)
if pages:
p1 = pages[0]
if len(pages) > 1:
p2 = pages[-1]
xml += """<Title>%s</Title>
<Category>%s</Category>
<Year>%s</Year>
<SourceName>%s</SourceName>
<Volume>%s</Volume>
<PageBegin>%s</PageBegin>
<PageEnd>%s</PageEnd>
<UniformResourceIdentifier>%s</UniformResourceIdentifier>
<DigitalObjectIdentifier>%s</DigitalObjectIdentifier>
""" % (title, category, year or 2222, sourcename, volume, p1, p2, url, doi)
xml += '<BibTeX>%s</BibTeX></Source>' % quoteattr(bibtexstring)[1:-1]
return xml
def BibTeX2XML(bibtexstring):
e = getEntryFromString(bibtexstring)
xml = u'<Source sourceID="B%s-%s">\n<Authors>\n' % (NODEID, e.key)
for a in e.persons['author']:
name = a.first() + a.middle() + a.last() + a.lineage()
name = map(strip, name)
name = map(strip, name, ['{}'] * len(name))
xml += '<Author><Name>%s</Name></Author>' % ' '.join(name)
xml += '\n</Authors>'
category = TYPE2CATEGORY.get(e.type)
f = CaselessDict(e.fields)
url = f.get('bdsk-url-1')
title = f.get('title').strip().strip('{}')
sourcename = f.get('journal', 'unknown')
doi = f.get('doi')
year = f.get('year')
volume = f.get('volume')
pages = f.get('pages')
if pages:
if '-' in pages:
p1, p2 = pages.split('-')
else:
p1, p2 = pages, ''
else:
p1, p2 = '', ''
xml += """<Title>%s</Title>
<Category>%s</Category>
<Year>%s</Year>
<SourceName>%s</SourceName>
<Volume>%s</Volume>
<PageBegin>%s</PageBegin>
<PageEnd>%s</PageEnd>
<UniformResourceIdentifier>%s</UniformResourceIdentifier>
<DigitalObjectIdentifier>%s</DigitalObjectIdentifier>
""" % (title, category, year or 2222, sourcename, volume, p1, p2, url, doi)
xml += '<BibTeX>%s</BibTeX></Source>' % quoteattr(bibtexstring)[1:-1]
return xml
oracleSqlComment = "--" + restOfLine
selectStmt.ignore(oracleSqlComment)
return selectStmt
SQL = setupSQLparser()
############ SQL PARSER FINISHED; SOME HELPER THINGS BELOW
from django.db.models import Q, F
from django.conf import settings
from importlib import import_module
DICTS = import_module(settings.NODEPKG + '.dictionaries')
from caselessdict import CaselessDict
RESTRICTABLES = CaselessDict(DICTS.RESTRICTABLES)
from types import TupleType, FunctionType
from django.db.models.query_utils import Q as QType
from string import strip
import logging
log = logging.getLogger('vamdc.tap.sql')
# Q-objects for always True / False
QTrue = Q(pk=F('pk'))
QFalse = ~QTrue
OPTRANS= { # transfer SQL operators to django-style
'<': '__lt',
'>': '__gt',
'=': '__exact',
def getEntryFromString(s):
parser = bibtex.Parser()
try:
parser.parse_stream(StringIO(s))
key, entry = parser.data.entries.items()[0]
except:
bib = parser.parse_stream(StringIO(DUMMY))
key, entry = parser.data.entries.items()[0]
return entry
TYPE2CATEGORY=CaselessDict({\
'article':'journal',
'book':'book',
'techreport':'report',
'misc':'private communication',
'inproceedings':'proceedings',
})
def BibTeX2XML(bibtexstring):
e = getEntryFromString(bibtexstring)
xml = u'<Source sourceID="B%s-%s">\n<Authors>\n' % (NODEID, e.key)
for a in e.persons['author']:
name = a.first() + a.middle() + a.last() + a.lineage()
name = map(strip, name)
name = map(strip, name, ['{}'] * len(name))
xml += '<Author><Name>%s</Name></Author>' % ' '.join(name)
xml += '\n</Authors>'
from django.utils.unittest import TestCase
except ImportError:
from django.test import TestCase
try:
from django.utils import unittest
except ImportError:
import unittest
from django.test.client import Client
from django.utils.importlib import import_module
from vamdctap import generators, views
# node-specific
from django.conf import settings
from caselessdict import CaselessDict
DICTS = import_module(settings.NODEPKG + ".dictionaries")
RETURNABLES = CaselessDict(DICTS.RETURNABLES)
try:
NODEID = RETURNABLES['NodeID']
except:
NODEID = RETURNABLES["TempNodeID"]
from nodes.ExampleNode.node import queryfunc
if not hasattr(settings, "EXAMPLENODE") or not settings.EXAMPLENODE:
print "Error: The NodeSoftware unit tests must be run from nodes/ExampleNode."
sys.exit()
#------------------------------------------------------------
# Testing of sending TAP queries and their response
#------------------------------------------------------------
#
def getEntryFromString(s):
parser = bibtex.Parser()
try:
parser.parse_stream(StringIO(s))
key, entry = parser.data.entries.items()[0]
except Exception:
parser.parse_stream(StringIO(DUMMY))
key, entry = parser.data.entries.items()[0]
return entry
TYPE2CATEGORY=CaselessDict({\
'article':'journal',
'book':'book',
'techreport':'report',
'misc':'private communication',
'inproceedings':'proceedings',
'phdthesis':'thesis',
'unpublished':'private communication'
})
def BibTeX2XML(bibtexstring, key=None):
"""
Derives an XSAMS source element from the given BibTeX and returns the XML text.
The ID of the Source is set in the form B(node)-(key) where (node) is replaced
by the ID string for this node and (key) is replaced by the unique key for this
Source. If the key argument is given, this value is used for the key; otherwise,
a key is generated from the BibTeX content.
"""
e = getEntryFromString(bibtexstring)
from importlib import import_module
from django.utils.http import http_date
if settings.LOG_CENTRALLY:
try:
import requests as librequests
except:
log.critical(
'settings.LOG_CENTRALLY is set but requests package is missing!')
QUERYFUNC = import_module(settings.NODEPKG + '.queryfunc')
DICTS = import_module(settings.NODEPKG + '.dictionaries')
# import helper modules that reside in the same directory
from caselessdict import CaselessDict
NODEID = CaselessDict(DICTS.RETURNABLES)['NodeID']
from generators import *
from sqlparse import SQL
REQUESTABLES = map(lower, [\
'AtomStates',
'Atoms',
'Collisions',
'Environments',
'Functions',
'Methods',
'MoleculeBasisStates',
'MoleculeQuantumNumbers',
'MoleculeStates',
'Molecules',
'NonRadiativeTransitions',