From 28e32478ba6e2850f29950d783118cc875e7d3fa Mon Sep 17 00:00:00 2001
From: Diane Trout <diane@ghic.org>
Date: Thu, 5 Dec 2013 16:02:51 -0800
Subject: [PATCH] After implementing proper tests get a working implementation
 of runfolder name from IPAR tree.

My first couple tries didn't work hopefully this one will work
---
 htsworkflow/pipelines/ipar.py                 |    9 +-
 .../pipelines/test/test_alignment_free.py     |   32 +
 .../testdata/run_C23KDACXX_2013-05-11.xml     | 1653 +++++++++++++++++
 3 files changed, 1692 insertions(+), 2 deletions(-)
 create mode 100644 htsworkflow/pipelines/test/test_alignment_free.py
 create mode 100644 htsworkflow/pipelines/test/testdata/run_C23KDACXX_2013-05-11.xml

diff --git a/htsworkflow/pipelines/ipar.py b/htsworkflow/pipelines/ipar.py
index fd49b78..c2cc6a3 100644
--- a/htsworkflow/pipelines/ipar.py
+++ b/htsworkflow/pipelines/ipar.py
@@ -79,8 +79,13 @@ class IPAR(object):
         """Return runfolder name"""
         if self.tree is None:
             raise ValueError("Can't query an empty run")
-        runfolder = self.tree.xpath('RunParameters/Runfolder')
-        return runfolder
+        runfolder = self.tree.xpath('RunParameters/RunFolder')
+        if len(runfolder) == 0:
+            return None
+        elif len(runfolder) > 1:
+            raise RuntimeError("RunXml parse error looking for RunFolder")
+        else:
+            return runfolder[0].text
     runfolder_name = property(_get_runfolder_name)
     
     def _get_software(self):
diff --git a/htsworkflow/pipelines/test/test_alignment_free.py b/htsworkflow/pipelines/test/test_alignment_free.py
new file mode 100644
index 0000000..700000b
--- /dev/null
+++ b/htsworkflow/pipelines/test/test_alignment_free.py
@@ -0,0 +1,32 @@
+#!/usr/bin/env python
+
+from datetime import datetime, date
+import os
+import tempfile
+import shutil
+from unittest2 import TestCase
+
+from htsworkflow.pipelines.test.simulate_runfolder import TESTDATA_DIR
+
+from htsworkflow.pipelines import eland
+from htsworkflow.pipelines import ipar
+from htsworkflow.pipelines import bustard
+from htsworkflow.pipelines import gerald
+from htsworkflow.pipelines import runfolder
+
+class AlignmentFreeRunfolderTests(TestCase):
+    def test_loading(self):
+        run_xml = os.path.join(TESTDATA_DIR, 'run_C23KDACXX_2013-05-11.xml')
+        run = runfolder.load_pipeline_run_xml(run_xml)
+        self.assertEqual(run.runfolder_name, '130508_SN787_0146_BC23KDACXX')
+
+def suite():
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(AlignmentFreeRunfolderTests))
+    return suite
+
+
+if __name__ == "__main__":
+    from unittest2 import main
+    main(defaultTest="suite")
diff --git a/htsworkflow/pipelines/test/testdata/run_C23KDACXX_2013-05-11.xml b/htsworkflow/pipelines/test/testdata/run_C23KDACXX_2013-05-11.xml
new file mode 100644
index 0000000..4f5ce85
--- /dev/null
+++ b/htsworkflow/pipelines/test/testdata/run_C23KDACXX_2013-05-11.xml
@@ -0,0 +1,1653 @@
+<PipelineRun>
+  <FlowcellID>C23KDACXX</FlowcellID>
+  <IPAR version="1">
+    <timestamp>1368271031</timestamp>
+    <Run Name="Intensities">
+      <Cycles First="1" Last="58" Number="58"/>
+      <ImageParameters>
+        <AutoOffsetFlag>0</AutoOffsetFlag>
+        <AutoSizeFlag>0</AutoSizeFlag>
+        <Fwhm>0</Fwhm>
+        <RemappingDistance>0</RemappingDistance>
+        <Threshold>0</Threshold>
+      </ImageParameters>
+      <RunParameters>
+        <AutoCycleFlag>0</AutoCycleFlag>
+        <BasecallFlag>0</BasecallFlag>
+        <Deblocked>0</Deblocked>
+        <DebugFlag>0</DebugFlag>
+        <FirstRunOnlyFlag>0</FirstRunOnlyFlag>
+        <ImagingReads Index="1">
+          <FirstCycle>1</FirstCycle>
+          <LastCycle>50</LastCycle>
+          <RunFolder>130508_SN787_0146_BC23KDACXX</RunFolder>
+        </ImagingReads>
+        <ImagingReads Index="2">
+          <FirstCycle>51</FirstCycle>
+          <LastCycle>58</LastCycle>
+          <RunFolder>130508_SN787_0146_BC23KDACXX</RunFolder>
+        </ImagingReads>
+        <Instrument>HWI-ST0787</Instrument>
+        <IterativeMatrixFlag>0</IterativeMatrixFlag>
+        <MakeFlag>0</MakeFlag>
+        <MaxCycle>0</MaxCycle>
+        <MinCycle>0</MinCycle>
+        <Reads Index="1">
+          <FirstCycle>1</FirstCycle>
+          <LastCycle>50</LastCycle>
+          <RunFolder>130508_SN787_0146_BC23KDACXX</RunFolder>
+        </Reads>
+        <Reads Index="2">
+          <FirstCycle>51</FirstCycle>
+          <LastCycle>58</LastCycle>
+          <RunFolder>130508_SN787_0146_BC23KDACXX</RunFolder>
+        </Reads>
+        <RunFolder>130508_SN787_0146_BC23KDACXX</RunFolder>
+        <RunFolderDate>130508</RunFolderDate>
+        <RunFolderId>0146</RunFolderId>
+        <RunFlowcellId>C23KDACXX</RunFlowcellId>
+        <Barcode>
+          <Cycle Use="true">51</Cycle>
+          <Cycle Use="true">52</Cycle>
+          <Cycle Use="true">53</Cycle>
+          <Cycle Use="true">54</Cycle>
+          <Cycle Use="true">55</Cycle>
+          <Cycle Use="true">56</Cycle>
+          <Cycle Use="true">57</Cycle>
+          <Cycle Use="true">58</Cycle>
+        </Barcode>
+        <QTableVersion>V6</QTableVersion>
+      </RunParameters>
+      <Software Name="RTA" Version="1.13.48.0"/>
+      <TileSelection>
+        <Lane Index="1">
+          <Sample>s</Sample>
+          <Tile>1103</Tile>
+          <Tile>1104</Tile>
+          <Tile>1101</Tile>
+          <Tile>1102</Tile>
+          <Tile>1108</Tile>
+          <Tile>1105</Tile>
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+    </BaseCallAnalysis>
+  </Bustard>
+</PipelineRun>
-- 
2.30.2