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lib/Bio/Biblio/IO/medlinexml.pm  view on Meta::CPAN

    # Then we have #PCDATA elements without an attribute list.
    # For them I create an entry on @PCDataStack.
    #
    if (exists $PCDATA_NAMES{$e}) {
        push (@PCDataStack, '');

    #
    # And finally, all non-PCDATA elements go to the objectStack
    #
    } elsif (exists $SIMPLE_TREATMENT{$e}) {
        push (@ObjectStack, {});

    } elsif ($e eq 'PersonalNameSubject') {
        push (@ObjectStack, {'type' => 'PersonalName'});

    } elsif ($e eq 'DescriptorName' or
             $e eq 'Descriptor') {
        if (&_eq_hash_elem (\%attrs, 'MajorTopicYN', "Y")) {
            my $peek = $ObjectStack[$#ObjectStack];
            $$peek{'descriptorMajorTopic'} = "Y";
        }

    } elsif ($e eq 'MedlineCitation' ||
             $e eq 'NCBIArticle') {
        my %p = ( 'type' => 'MedlineCitation' );
        $p{'owner'} = $attrs{'Owner'} if $attrs{'Owner'};
        $p{'status'} = $attrs{'Status'} if $attrs{'Status'};
        push (@ObjectStack, \%p);

    } elsif ($e eq 'GrantList') {
        if (&_eq_hash_elem (\%attrs, 'CompleteYN', "N")) {
            my $peek = $ObjectStack[$#ObjectStack];
            $$peek{'grantListComplete'} = "N";
        }

    } elsif ($e eq 'DataBankList') {
        if (&_eq_hash_elem (\%attrs, 'CompleteYN', "N")) {
            my $peek = $ObjectStack[$#ObjectStack];
            $$peek{'dataBankListComplete'} = "N";
        }

    } elsif ($e eq 'AuthorList') {
        if (&_eq_hash_elem (\%attrs, 'CompleteYN', "N")) {
            my $peek = $ObjectStack[$#ObjectStack];
            $$peek{'authorListComplete'} = "N";
        }

    } elsif ($e eq 'OtherAbstract') {
        my %p = ();
        $p{'type'} = $attrs{'Type'} if $attrs{'Type'};
        push (@ObjectStack, \%p);
#       push (@ObjectStack, { 'type' => 'Abstract' });
    }
}


sub handle_end {
    my ($expat, $e) = @_;
    #
    # First I have to deal with those elements which are both PCDATA
    # (and therefore they are on the pcdataStack) and which have an
    # attribute list (therefore they are also known as a separate
    # p-object on the objectStack.
    #
    if ($e eq 'QualifierName' or
        $e eq 'SubHeading') {
        my $p = pop @ObjectStack;   # pSubHeading
        $$p{'subHeading'} = pop @PCDataStack;
        &_add_element ('subHeadings', $p);  # adding to pMeshHeadings
#       &_debug_object_stack ("END", $e);
        return;

    } elsif ($e eq 'GeneralNote') {
        my $p = pop @ObjectStack;  # pGeneralNote
        $$p{'generalNote'} = pop @PCDataStack;
        &_add_element ('generalNotes', $p);  # adding to pMedlineCitation
#       &_debug_object_stack ("END", $e);
        return;

    } elsif ($e eq 'OtherID') {
        my $p = pop @ObjectStack;  # pOtherID
        $$p{'otherID'} = pop @PCDataStack;
        &_add_element ('otherIDs', $p);  # adding to pMedlineCitation
#       &_debug_object_stack ("END", $e);
        return;
    }

    #
    # both object and pcdata stacks elements mixed here together
    # (the element names appear in the order of frequency in the
    # medline data set)
    #

    if (exists $POP_DATA_AND_PEEK_OBJ{$e}) {
        &_data2obj ("\l$e");

    } elsif (exists $POP_OBJ_AND_PEEK_OBJ{$e}) {
        &_obj2obj ("\l$e");

    } elsif (exists $POP_AND_ADD_ELEMENT{$e}) {
        &_add_element ($POP_AND_ADD_ELEMENT{$e}, pop @ObjectStack);

    } elsif (exists $POP_AND_ADD_DATA_ELEMENT{$e}) {
        &_add_element ($POP_AND_ADD_DATA_ELEMENT{$e});

    } elsif ($e eq 'Author' or
             $e eq 'Investigator') {
        my $pAuthor;
        my $p = pop @ObjectStack;  # pPersonalName or pAuthor
        if (&_eq_hash_elem ($p, 'type', 'PersonalName')) {
            $pAuthor = pop @ObjectStack;
            $$pAuthor{'personalName'} = $p;
        } else {
            $pAuthor = $p;
        }
        my $peek = $ObjectStack[$#ObjectStack];   # pMedlineCitation, pArticle or pBook
        if (&_eq_hash_elem ($peek, 'type', 'MedlineCitation')) {
            &_add_element ('investigators', $pAuthor);
        } else {
            &_add_element ('authors', $pAuthor);
        }

    } elsif ($e eq 'MedlineJournalInfo') {
        &_obj2obj ('journalInfo');

    } elsif ($e eq 'PMID') {
        my $peek = $ObjectStack[$#ObjectStack];   # pMedlineCitation, pReference or pDeleteCitation
        if (&_eq_hash_elem ($peek, 'type', 'DeleteCitation')) {
            &_add_element ('PMIDs');
        } else {
            $$peek{'PMID'} = pop @PCDataStack;
        }

    } elsif ($e eq 'MedlineID') {
        my $peek = $ObjectStack[$#ObjectStack];   # pMedlineCitation, pReference or pDeleteCitation
        if (&_eq_hash_elem ($peek, 'type', 'DeleteCitation')) {
            &_add_element ('MedlineIDs');
        } else {
            $$peek{'medlineID'} = pop @PCDataStack;
        }

#    } elsif ($e eq 'OtherAbstract') {
#       my $pAbstract = pop @ObjectStack;
#       my $pOtherAbstract = pop @ObjectStack;
#       $$pOtherAbstract{'abstract'} = $pAbstract
#           &_add_element ('otherAbstracts', $pOtherAbstract);

    } elsif ($e eq 'Affiliation') {
        my $peek = $ObjectStack[$#ObjectStack];