def extract_more_verses(text, ref, point, outline):
"""
-text: string of verse numbers without book or chapter, e.g. '3, 7, 10-14, 16'.
-ref: Reference immediately preceding this string of verse numbers.
-point: outline point the verses are under.
-outline: outline list from extract().
Helper function for extract() -- creates References for verses and adds them to outline.
Creates References for verses and adds them to outline.
"""
# gets list of tuples: (verse, end_verse,)
# e.g. '3, 7, 10-14, 16' --> [(3, None,), (7, None,), (10, 14,), (16, None,)]
verses = re.findall(re.compile(r'(?P<verse>\d{1,3})(?:-(?P<end_verse>\d{1,3}))?'), text)
for verse in verses:
more_verses_ref = Reference(outline_point=point,
book=ref.book,
verse=int(verse[0]))
more_verses_ref.end_verse = int(verse[1]) if verse[1] else None
if ref.end_chapter is not None:
more_verses_ref.chapter = ref.end_chapter
else:
more_verses_ref.chapter = ref.chapter
if more_verses_ref.end_verse is not None:
more_verses_ref.end_chapter = more_verses_ref.chapter
more_verses_ref.save()
outline[-1][1].append(more_verses_ref)
return
def save_references(request):
"""
SGD_features.tab format looks like this:
0) Primary SGDID (mandatory)
1) Feature type (mandatory)
2) Feature qualifier (optional)
3) Feature name (optional)
4) Standard gene name (optional)
5) Alias (optional, multiples separated by |)
6) Parent feature name (optional)
7) Secondary SGDID (optional, multiples separated by |)
8) Chromosome (optional)
9) Start_coordinate (optional)
10) Stop_coordinate (optional)
11) Strand (optional)
12) Genetic position (optional)
13) Coordinate version (optional)
14) Sequence version (optional)
15) Description (optional)
"""
featuresFile = request.FILES['features_file']
features = [x.split('\t') for x in featuresFile.read().splitlines()]
for line in features:
reference = Reference()
reference.sgdid = line[0]
reference.feature_type = line[1]
if line[2]:
reference.qualifier = line[2]
if line[3]:
reference.feature_name = line[3]
if line[4]:
reference.standard_name = line[4]
if line[5]:
reference.aliases = line[5]
if line[6]:
reference.parent_name = line[6]
if line[7]:
reference.secondary_sgdid = line[7]
if line[15]:
reference.description = line[15]
reference.createdDate = datetime.datetime.now()
reference.modifiedDate = datetime.datetime.now()
reference.save()
return HttpResponseRedirect('/strains/')
def extract(text):
"""
Extract from a block of text a list of 2-tuples
containing an outline point and a list of normalized, tupled verse references under that outline point.
"""
outline = []
point = OutlinePoint(level=0, string='Scripture Reading:')
point.save()
outline.append((point, [],))
for r in re.finditer(scripture_re, text):
try:
# find Roman numerals / outline points
is_bullet = False
for i in range(1,5):
if r.group(i):
point = OutlinePoint(level=i, string=r.group(i))
point.save()
outline.append((point, [],))
is_bullet = True
if is_bullet == False:
ref = Reference(outline_point=point)
outline[-1][1].append(ref)
if r.group('book'): # reference contains book name
ref.book = get_book(r.group('book'))[1]
ref.chapter = int(r.group('chapter')) if r.group('chapter') else None
ref.verse = int(r.group('verse')) if r.group('verse') else None
ref.end_chapter = int(r.group('end_chapter')) if r.group('end_chapter') else None
ref.end_verse = int(r.group('end_verse')) if r.group('end_verse') else None
if ((ref.end_verse is not None) and (ref.end_chapter is None)):
ref.end_chapter = ref.chapter
ref.save()
if r.group('more_verses'):
extract_more_verses(r.group('more_verses'), ref, point, outline)
else: # get book from previous reference
if len(outline[-1][1]) > 1:
ref.book = outline[-1][1][-2].book
else: # if this is the first reference under an outline point
ref.book = outline[-2][1][-1].book
if r.group('headless_chapter'): # reference has no book
ref.chapter = int(r.group('headless_chapter'))
ref.verse = int(r.group('headless_verse')) if r.group('headless_verse') else None
ref.end_chapter = int(r.group('headless_end_chapter')) if r.group('headless_end_chapter') else None
ref.end_verse = int(r.group('headless_end_verse')) if r.group('headless_end_verse') else None
if ((ref.end_verse is not None) and (ref.end_chapter is None)):
ref.end_chapter = ref.chapter
ref.save()
if r.group('more_headless_verses'):
extract_more_verses(r.group('more_headless_verses'), ref, point, outline)
else:
if r.group('lonely_verse'):
if len(outline[-1][1]) > 1:
ref.chapter = outline[-1][1][-2].chapter
else: # this is the first reference under an outline point
ref.chapter = outline[-2][1][-1].chapter
ref.verse = int(r.group('lonely_verse'))
ref.end_verse = int(r.group('lonely_end_verse')) if r.group('lonely_end_verse') else None
if ((ref.end_verse is not None) and (ref.end_chapter is None)):
ref.end_chapter = ref.chapter
ref.save()
if r.group('more_lonely_verses'):
extract_more_verses(r.group('more_lonely_verses'), ref, point, outline)
except InvalidReferenceException:
pass
return outline
def post(self, request):
param = QueryDict(request.body)
uuid = param.get('uuid')
title = param.get('title')
time = param.get('time')
origin = param.get('origin')
_authors = param.getlist('authors')
link = param.get('link')
_tags = param.getlist('tags')
content = param.get('content')
refer_to = param.getlist('reference')
score = param.get('score')
try:
year, month = time.split('-')
year, month = int(year), int(month)
publish_time = datetime.date(year, month, 1)
except Exception as e:
logger.error(traceback.format_exc(e))
return JsonResponse({'msg': '提供的日期{}有误'.format(time)}, status=500)
for _tag in _tags:
try:
_tag = int(_tag)
_ = ResearchTag.objects.get(research_tag_id=_tag)
except Exception as e:
logger.error(traceback.format_exc(e))
return JsonResponse({'msg': '错误的标签{}'.format(_tag)},
status=500)
tags = ResearchTag.objects.filter(
research_tag_id__in=[int(_t) for _t in _tags])
author_ids = []
for _author in _authors:
if _author.isdigit():
author_ids.append(int(_author))
elif Author.objects.filter(name=_author).exists():
a = Author.objects.get(name=_author).author_id
author_ids.append(a)
else:
a = Author(name=_author)
a.save()
author_ids.append(a.author_id)
authors = Author.objects.filter(author_id__in=author_ids)
try:
score = int(score)
except Exception as e:
logger.error(traceback.format_exc(e))
return JsonResponse({'msg': '错误的评分分数格式'}, status=500)
if not Paper.objects.filter(paper_uuid=uuid).exists():
# 新建的场合
try:
comment = PaperComment(content=content)
comment.save()
paper = Paper(paper_uuid=uuid,
title=title,
publish_origin=origin,
publish_time=publish_time,
author=authors,
link=link,
tag=tags,
comment=comment,
self_score=score)
paper.save()
redis.set(self.LATEST_KEY, str(uuid_gen.uuid4()))
except Exception as e:
logger.error(traceback.format_exc(e))
return JsonResponse({'msg': '保存失败'}, status=500)
else:
return JsonResponse({
'next':
reverse('paperdb.detail',
kwargs={'paper_uuid': paper.paper_uuid})
})
try:
# 编辑的场合
paper = Paper.objects.get(paper_uuid=uuid)
except Exception as e:
logger.error(traceback.format_exc(e))
return JsonResponse({'msg': '错误的uuid/未找到相关论文记录'}, status=404)
else:
paper.title = title
paper.publish_time = publish_time
paper.publish_origin = origin
paper.author = authors
paper.link = paper.link
paper.tag = tags
paper.self_score = score
try:
paper.save()
except Exception as e:
logger.error(traceback.format_exc(e))
return JsonResponse({'msg': '保存失败'}, status=500)
if paper.comment is None:
if content != '':
comment = PaperComment(content=content)
comment.save()
paper.comment = comment
paper.save()
elif content != paper.comment.content.replace(
'\r\n', '\n'): # traditional下的换行符出入
paper.comment.content = content
paper.comment.save()
for refer_to_paper in Paper.objects.filter(paper_uuid__in=refer_to):
if not Reference.objects.filter(
reference_src=paper,
reference_trg=refer_to_paper).exists():
reference = Reference(reference_src=paper,
reference_trg=refer_to_paper)
reference.save()
return JsonResponse({
'next':
reverse('paperdb.detail', kwargs={'paper_uuid': paper.paper_uuid})
})
