parsers: create an NLM parser #209
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Signed-off-by: Szymon Łopaciuk <[email protected]>
Signed-off-by: Szymon Łopaciuk <[email protected]>
ghost
assigned 
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| Args: | ||
| nlm_records (Union[string, scrapy.selector.Selector]): records | ||
| source (Optional[string]): source passed to `__init__` |
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please document return value
hepcrawl/parsers/nlm.py
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| day = node.xpath('./Day/text()').extract_first() | ||
| month = node.xpath('./Month/text()').extract_first() | ||
| year = node.xpath('./Year/text()').extract_first() | ||
| return PartialDate( |
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It's better to use PartialDate.from_parts, which handles empty values and non-numeric months just fine:
In [1]: from inspire_utils.date import PartialDate
In [2]: PartialDate.from_parts(2017, 'Jan')
Out[2]: PartialDate(year=2017, month=1, day=None)
hepcrawl/parsers/nlm.py
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| pub_type = self.root.xpath('./PublicationType/text()').extract_first() | ||
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| if 'Conference' in pub_type or pub_type == 'Congresses': | ||
| return 'proceedings' |
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I think this is conference paper rather than proceedings, but would need to look at some examples.
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I got an example IOP update from @david-caro with a few records, but unfortunately none of them actually have the <PublicationType> set. Maybe when we get access, there will be more records, or maybe IOP don't use the field at all... Meanwhile I found a few in this at NLM, so I think that means you are right?
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Looks like it. But I would not be surprised if IOP put its own values there anyway, that have nothing to do with those in the spec.
| authors = self.root.xpath('./AuthorList/Author') | ||
| authors_in_collaborations = self.root.xpath( | ||
| './GroupList/Group' | ||
| '[GroupName/text()=../../AuthorList/Author/CollectiveName/text()]' |
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what's the purpose of this?
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<CollectiveName> inside the <Author> acts as sort of a pointer to the <Group> of the same name, where the actual people of the group are listed, like here: https://www.ncbi.nlm.nih.gov/books/NBK3828/#publisherhelp.Can_Collaborator_Names_be. So this gets all the people from groups referenced in <Authors>. Though maybe it is too strict, now that I think about it, I don't think there is a use case for an "unreferenced" group?
| return self.root.xpath('./Journal/Volume/text()').extract_first() | ||
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| @property | ||
| def material(self): |
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PublicationType may also contain Published Erratum, which maps to erratum. Don't know how this relates to the NLM field you are reading here. Maybe you should link to https://www.ncbi.nlm.nih.gov/books/NBK3828/#publisherhelp.Object_O, here or close to the NLM_OBJECT_TYPE_TO_HEP_MAP definition.
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| NLM_OBJECT_TYPE_TO_HEP_MAP = { | ||
| 'Erratum': 'erratum', | ||
| 'Reprint': 'reprint', |
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'Republished': 'reprint' also
Signed-off-by: Szymon Łopaciuk <[email protected]>
Signed-off-by: Szymon Łopaciuk <[email protected]>
Check in PublicationType for `Published Erratum` too, if `<Object>` check didn't return any matches. Add references to NLM docs. Signed-off-by: Szymon Łopaciuk <[email protected]>
Signed-off-by: Szymon Łopaciuk <[email protected]>
Signed-off-by: Szymon Łopaciuk <[email protected]>
Signed-off-by: Szymon Łopaciuk <[email protected]>
Signed-off-by: Szymon Łopaciuk <[email protected]>
Signed-off-by: Szymon Łopaciuk <[email protected]>
Description
This is an implementation of a parser for the NLM format, it takes a very similar approach to the JATS parser which we already have, using LiteratureBuilder to build HEP records.
Related Issue
This is a step towards refreshing the IOP spider (#205)
Motivation and Context
IOP uses NLM format to publish their citation records. Currently the IOP spider uses web-scraping, however we will move to using OAI-PMH and this instead.
Checklist:
RFCand look for it).