From 0dca905ed5edfe54230efee557ae3a804f7d21d2 Mon Sep 17 00:00:00 2001
From: Robert Langlois <rlanglois@illumina.com>
Date: Thu, 7 Apr 2016 11:02:41 -0700
Subject: [PATCH] Fix for reading legacy run parameters

The filename can have a lowercase r in RunParameters
---
 docs/src/changes.md                      |  2 +-
 interop/logic/summary/error_summary.h    |  2 +-
 interop/model/metric_sets/q_metric_set.h |  7 ----
 interop/model/model_exceptions.h         | 51 ++++++++++++++++++++++++
 interop/model/run_metrics.h              | 16 --------
 src/interop/model/run/parameters.cpp     | 10 ++++-
 6 files changed, 62 insertions(+), 26 deletions(-)
 create mode 100644 interop/model/model_exceptions.h

diff --git a/docs/src/changes.md b/docs/src/changes.md
index 712eb3665..333cbbbe0 100644
--- a/docs/src/changes.md
+++ b/docs/src/changes.md
@@ -10,7 +10,7 @@
 Commit  | Description
 ------- | -----------
         | Update documentation
-        | Added summary tests
+0b22102 | Added summary tests
 13f1fb4 | Added summary logic
 339a914 | Added summary model
 aca0152 | Added run metrics
diff --git a/interop/logic/summary/error_summary.h b/interop/logic/summary/error_summary.h
index dbd7f5f03..3c09e2a7c 100644
--- a/interop/logic/summary/error_summary.h
+++ b/interop/logic/summary/error_summary.h
@@ -166,7 +166,7 @@ void cache_cycle_state_by_lane_read(I beg, I end,
         const read_cycle& read = cycle_to_read[beg->cycle()-1];
         if(read.number == 0) continue;
         INTEROP_ASSERT((read.number-1) < tmp.size());
-        size_t id = static_cast<size_t>(model::metric_base::base_metric::id(beg->lane(), beg->tile()));
+        const size_t id = static_cast<size_t>(model::metric_base::base_metric::id(beg->lane(), beg->tile()));
         tmp[read.number-1][id].update(beg->cycle());
     }
     for(size_t read=0;read<tmp.size();++read)
diff --git a/interop/model/metric_sets/q_metric_set.h b/interop/model/metric_sets/q_metric_set.h
index 872196970..35e34dc8f 100644
--- a/interop/model/metric_sets/q_metric_set.h
+++ b/interop/model/metric_sets/q_metric_set.h
@@ -51,13 +51,6 @@ class q_metrics : public metric_base::metric_set<q_metric>
         size_t histBinCount() const {
             return logic::metric::count_q_metric_bins(*this);
         }
-
-        /** Populate the cumulative distributions
-         */
-        void populateCumulativeDistributions() throw( model::index_out_of_bounds_exception )
-        {
-            logic::metric::populate_cumulative_distribution(*this);
-        }
     };
 }
 }
diff --git a/interop/model/model_exceptions.h b/interop/model/model_exceptions.h
new file mode 100644
index 000000000..76c7d721a
--- /dev/null
+++ b/interop/model/model_exceptions.h
@@ -0,0 +1,51 @@
+/** Exceptions thrown by the model
+ *
+ *  @file
+ *  @date 3/21/16
+ *  @version 1.0
+ *  @copyright GNU Public License.
+ */
+#pragma once
+#include <stdexcept>
+#include "interop/util/exception_specification.h"
+
+#ifdef _MSC_VER
+#pragma warning(disable:4290) // MSVC warns that it ignores the exception specification.
+#endif
+
+namespace illumina {
+namespace interop {
+namespace model {
+
+    /** @defgroup model_exceptions Model Exceptions
+     *
+     * Exceptions that can be thrown if a problem occurs while using the model
+     *
+     * @ingroup interop_exceptions
+     * @{
+     */
+    /** Exception raised if an index goes out of bounds
+     */
+    struct index_out_of_bounds_exception : public std::out_of_range {
+        /** Constructor
+         *
+         *  @param mesg error message
+         */
+        index_out_of_bounds_exception(const std::string &mesg) : std::out_of_range(mesg) { }
+    };
+
+    /** Exception raised if the channel names are invalid
+     */
+    struct invalid_channel_exception : public std::runtime_error {
+        /** Constructor
+         *
+         *  @param mesg error message
+         */
+        invalid_channel_exception(const std::string &mesg) : std::runtime_error(mesg) { }
+    };
+
+    /** @} */
+}
+}
+}
+
diff --git a/interop/model/run_metrics.h b/interop/model/run_metrics.h
index 3f7447d18..8897ba448 100644
--- a/interop/model/run_metrics.h
+++ b/interop/model/run_metrics.h
@@ -66,22 +66,6 @@ class run_metrics
     /** Define tile metric set */
     typedef metric_base::metric_set<tile_metric> tile_metric_set_t;
 
-public:
-    /** Define corrected intensity metric set */
-    typedef metric_base::metric_set<corrected_intensity_metric> corrected_intensity_metric_set_t;
-    /** Define error metric set */
-    typedef metric_base::metric_set<error_metric> error_metric_set_t;
-    /** Define extraction metric set */
-    typedef metric_base::metric_set<extraction_metric> extraction_metric_set_t;
-    /** Define image metric set */
-    typedef metric_base::metric_set<image_metric> image_metric_set_t;
-    /** Define index metric set */
-    typedef metric_base::metric_set<index_metric> index_metric_set_t;
-    /** Define q-metric set */
-    typedef metric_base::metric_set<q_metric> q_metric_set_t;
-    /** Define tile metric set */
-    typedef metric_base::metric_set<tile_metric> tile_metric_set_t;
-
 public:
     /** Constructor
      */
diff --git a/src/interop/model/run/parameters.cpp b/src/interop/model/run/parameters.cpp
index 8025c2e80..62b87ae68 100644
--- a/src/interop/model/run/parameters.cpp
+++ b/src/interop/model/run/parameters.cpp
@@ -127,7 +127,15 @@ void parameters::read(const std::string& run_folder) throw( xml::xml_file_not_fo
                                                             xml::missing_xml_element_exception,
                                                             xml::xml_parse_exception)
 {
-    read_file(io::combine(run_folder, "RunParameters.xml"));
+    try
+    {
+        read_file(io::combine(run_folder, "runParameters.xml"));
+    }
+    catch(const io::file_not_found_exception&)
+    {
+        read_file(io::combine(run_folder, "RunParameters.xml"));
+    }
+
 }