test_parser.rb in scout-gear-10.7.0

- old
+ new

@@ -113,11 +113,26 @@
     content.rewind
     tsv = TSV.parse(content, :head => 3)
     assert_equal 3, tsv.keys.length
   end
 
+  def test_parse_tsv_grep
+    content =<<-EOF
+#: :sep=" "#:type=:double
+#Key ValueA ValueB
+k a|A b|B
+k1 a|A b|B
+k2 a|A b|B
+k3 a|A b|B
+k4 a|A b|B
+    EOF
+    content = StringIO.new content
 
+    tsv = TSV.parse(content, :tsv_grep => ["k3","k4"])
+    assert_equal %w(k3 k4), tsv.keys.sort
+  end
+
   def test_parse_fields
     content =<<-EOF
 #: :sep=" "#:type=:double
 #Key ValueA ValueB
 k a|A b|B
@@ -243,8 +258,63 @@
     TmpFile.with_file do |db|
       content.rewind
       data = ScoutCabinet.open db, true, "HDB"
       TSV.parse content, sep: " ", header_hash: '', data: data, cast: :to_i, type: :list, serializer: :float_array
       assert_equal [1.0, 2.0], data["k"]
+    end
+  end
+
+  def test_merge
+    content =<<-EOF
+#: :type=:double
+#PMID:Sentence number:TF:TG	Transcription Factor (Associated Gene Name)	Target Gene (Associated Gene Name)	Sign	Negation	PMID
+24265317:3:NR1H3:FASN	NR1H3	FASN			24265317
+17522048:0:NR1H3:FASN	NR1H3	FASN	+		17522048
+19903962:0:NR1H3:FASN	NR1H3	FASN			19903962
+19903962:7:NR1H3:FASN	NR1H3	FASN			19903962
+22183856:4:NR1H3:FASN	NR1H3	FASN			22183856
+22641099:4:NR1H3:FASN	NR1H3	FASN	+		22641099
+23499676:8:NR1H3:FASN	NR1H3	FASN	+		23499676
+11790787:5:NR1H3:FASN	NR1H3	FASN			11790787
+11790787:7:NR1H3:FASN	NR1H3	FASN	+		11790787
+11790787:9:NR1H3:FASN	NR1H3	FASN	+		11790787
+11790787:11:NR1H3:FASN	NR1H3	FASN			11790787
+17522048:1:NR1H3:FASN	NR1H3	FASN	+		17522048
+17522048:3:NR1H3:FASN	NR1H3	FASN			17522048
+22160584:1:NR1H3:FASN	NR1H3	FASN			22160584
+22160584:5:NR1H3:FASN	NR1H3	FASN	+		22160584
+22160584:8:NR1H3:FASN	NR1H3	FASN	+		22160584
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(filename, key_field: "Transcription Factor (Associated Gene Name)", fields: ["Target Gene (Associated Gene Name)", "Sign", "PMID"], merge: true, one2one: true, type: :double)
+      assert_equal 16, tsv["NR1H3"]["Sign"].length
+    end
+  end
+
+  def test_load_stream
+    content =<<-EOF
+#Key    ValueA    ValueB
+k    a|A    b|B
+k1    a|A    b|B
+k2    a|A    b|B
+k3    a|A    b|B
+k4    a|A    b|B
+    EOF
+    content = StringIO.new content.gsub('    ', "\t")
+
+    TmpFile.with_file do |tmp_logfile|
+      old_logfile = Log.logfile
+      Log.logfile(tmp_logfile)
+      TmpFile.with_file do |persistence|
+        data = ScoutCabinet.open persistence, true
+        tsv = Log.with_severity(0) do
+          TSV.parse(content, data: data)
+        end
+        assert_equal %w(b B), tsv["k"]["ValueB"]
+        assert_equal %w(a A), tsv["k4"]["ValueA"]
+      end
+      Log.logfile(old_logfile)
+      assert Open.read(tmp_logfile).include?("directly into")
     end
   end
 end