rbbt-text 1.4.0 → 1.5.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 58f2fb21eee7ac37ca30a771609f6b0c394a2b646690fbcd59b0d623261e0522
+  metadata.gz: 2a1a38b7a9c9f9fe0ce8fd7b8fd19a3ca39f483e8ccaaa1412af023262181fd8
+  data.tar.gz: ddec2f95b5c6fe9a69e67cf79a29c3ef2d9c37301e442d8664c7bbff1298a365
 SHA512:
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+  metadata.gz: b554f4db313a65e0b682e2fd4456aaf9d1b4a489ca025ad3dc89cf71df772d97807b8b2ec62e3753eb62cf93bd88d7d0555c7ca5f9d76bd52a6c6d5fd56b313d
+  data.tar.gz: c419af9eb52723c0a761ddc025aadad99cebd1891cbd178aff466d509b84fdf76f449dfa62ba574a0b9dbeb0c519a4341b53375f18c09e52d19fd912cf5c1188

data/lib/rbbt/segment.rb

@@ -167,15 +167,29 @@ module Segment
       offset = text.index part
       next if offset.nil?
       Segment.setup(part, pre_offset + offset, docid)
-      pre_offset += offset + part.segment_length - 1
-      text = text[(offset + part.segment_length - 1)..-1]
+      pre_offset += offset + part.segment_length
+      text = text[(offset + part.segment_length)..-1]
+    end
+  end
+
+  def self.relocate(segment, original, target, pad = 20)
+    if segment != target[segment.range]
+      start_pad = [pad, segment.offset].min
+      end_pad = [pad, original.length - segment.end].min
+      start = segment.offset - start_pad
+      eend = segment.end + end_pad
+
+      context = original[start..eend].gsub(/\s/,' ')
+      target = target.gsub(/\s/, ' ')
+      i = target.index context
+      raise "Context not found in original text" if i.nil?
+      segment.offset = i + start_pad
     end
   end
 
   def self.index(*args)
     Segment::RangeIndex.index(*args)
   end
-
 end
 
 require 'rbbt/segment/range_index'

data/test/rbbt/test_segment.rb

@@ -134,6 +134,39 @@ Atypical teratoid/rhabdoid tumors (AT/RTs) are highly aggressive brain tumors of
     assert_equal parts.first.docid, text.docid
   end
 
+  def test_align_parts
+    text =<<-EOF
+aabbccdd
+    EOF
+
+    parts = %w(aa bb cc dd)
+    Segment.align(text, parts)
+
+    parts.each do |p|
+      assert_equal p, text[p.range]
+    end
+  end
+
+
+  def test_relocate
+    original =<<-EOF
+This sentences contains
+a mention to gene TP53
+This is a followup sentence
+    EOF
+
+    target = <<-EOF
+    This sentence is added before
+This sentences contains a mention to gene TP53
+This is a followup sentence
+    EOF
+
+    segment = Segment.setup("TP53")
+    Segment.align(original, [segment])
+    Segment.relocate(segment, original, target)
+    assert_equal segment, target[segment.range]
+  end
+
   def test_segment_index
     text = "This sentence mentions the TP53 gene and the CDK5R1 protein"
     Document.setup(text, "TEST", "test_doc1", nil)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-text
 version: !ruby/object:Gem::Version
-  version: 1.4.0
+  version: 1.5.1
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-12-21 00:00:00.000000000 Z
+date: 2024-02-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util