Fixing Exportation for sequence segment data (#532)

bertrandboudaud · web-flow · commit 8aa76a7f5758 · 2022-04-11T23:02:43.000+02:00
* Load data for all sequence segments

* When exporting data from sequenceSegmentHandler, export from all segments

* Use empty path for folder selection dialog as it does not work on MacOS (and having a default folder name is useless)

* Fixed: FeatureFilter and QC have only one copy per sequence.

* * Fixed: StoreFeatureRSDFilters, StoreFeatureRSDQCs, StoreFeatureBackgroundFilters and StoreFeatureBackgroundQCs have only one copy per sequence.
diff --git a/src/examples/source/SmartPeakGUI.cpp b/src/examples/source/SmartPeakGUI.cpp
@@ -523,22 +523,22 @@ int main(int argc, char** argv)
             {std::make_shared<StoreValidationData>(), true},
             // {std::make_shared<StoreStandardsConcentrations>(), true}, // not implemented
             {std::make_shared<StoreQuantitationMethods>(true), false},
-            {std::make_shared<StoreFeatureFilters>(FeatureFiltersUtilsMode::EFeatureFiltersModeComponent, true), true},
-            {std::make_shared<StoreFeatureFilters>(FeatureFiltersUtilsMode::EFeatureFiltersModeGroup, true), true},
-            {std::make_shared<StoreFeatureQCs>(FeatureFiltersUtilsMode::EFeatureFiltersModeComponent, true), true},
-            {std::make_shared<StoreFeatureQCs>(FeatureFiltersUtilsMode::EFeatureFiltersModeGroup, true), true},
-            {std::make_shared<StoreFeatureRSDFilters>(FeatureFiltersUtilsMode::EFeatureFiltersModeComponent, true), true},
-            {std::make_shared<StoreFeatureRSDFilters>(FeatureFiltersUtilsMode::EFeatureFiltersModeGroup, true), true},
-            {std::make_shared<StoreFeatureRSDQCs>(FeatureFiltersUtilsMode::EFeatureFiltersModeComponent, true), true},
-            {std::make_shared<StoreFeatureRSDQCs>(FeatureFiltersUtilsMode::EFeatureFiltersModeGroup, true), true},
-            {std::make_shared<StoreFeatureBackgroundFilters>(FeatureFiltersUtilsMode::EFeatureFiltersModeComponent, true), true},
-            {std::make_shared<StoreFeatureBackgroundFilters>(FeatureFiltersUtilsMode::EFeatureFiltersModeGroup, true), true},
-            {std::make_shared<StoreFeatureBackgroundQCs>(FeatureFiltersUtilsMode::EFeatureFiltersModeComponent, true), true},
-            {std::make_shared<StoreFeatureBackgroundQCs>(FeatureFiltersUtilsMode::EFeatureFiltersModeGroup, true), true},
-            {std::make_shared<StoreFeatureRSDEstimations>(FeatureFiltersUtilsMode::EFeatureFiltersModeComponent, true), true},
-            {std::make_shared<StoreFeatureRSDEstimations>(FeatureFiltersUtilsMode::EFeatureFiltersModeGroup, true), true},
-            {std::make_shared<StoreFeatureBackgroundEstimations>(FeatureFiltersUtilsMode::EFeatureFiltersModeComponent, true), true},
-            {std::make_shared<StoreFeatureBackgroundEstimations>(FeatureFiltersUtilsMode::EFeatureFiltersModeGroup, true), true}
+            {std::make_shared<StoreFeatureFilters>(FeatureFiltersUtilsMode::EFeatureFiltersModeComponent, true), true},           // have only one copy per sequence.
+            {std::make_shared<StoreFeatureFilters>(FeatureFiltersUtilsMode::EFeatureFiltersModeGroup, true), true},               // have only one copy per sequence.
+            {std::make_shared<StoreFeatureQCs>(FeatureFiltersUtilsMode::EFeatureFiltersModeComponent, true), true},               // have only one copy per sequence.
+            {std::make_shared<StoreFeatureQCs>(FeatureFiltersUtilsMode::EFeatureFiltersModeGroup, true), true},                   // have only one copy per sequence.
+            {std::make_shared<StoreFeatureRSDFilters>(FeatureFiltersUtilsMode::EFeatureFiltersModeComponent, false), true},       // have only one copy per sequence.
+            {std::make_shared<StoreFeatureRSDFilters>(FeatureFiltersUtilsMode::EFeatureFiltersModeGroup, true), true},            // have only one copy per sequence.
+            {std::make_shared<StoreFeatureRSDQCs>(FeatureFiltersUtilsMode::EFeatureFiltersModeComponent, true), true},            // have only one copy per sequence.
+            {std::make_shared<StoreFeatureRSDQCs>(FeatureFiltersUtilsMode::EFeatureFiltersModeGroup, true), true},                // have only one copy per sequence.
+            {std::make_shared<StoreFeatureBackgroundFilters>(FeatureFiltersUtilsMode::EFeatureFiltersModeComponent, true), true}, // have only one copy per sequence.
+            {std::make_shared<StoreFeatureBackgroundFilters>(FeatureFiltersUtilsMode::EFeatureFiltersModeGroup, true), true},     // have only one copy per sequence.
+            {std::make_shared<StoreFeatureBackgroundQCs>(FeatureFiltersUtilsMode::EFeatureFiltersModeComponent, true), true},     // have only one copy per sequence.
+            {std::make_shared<StoreFeatureBackgroundQCs>(FeatureFiltersUtilsMode::EFeatureFiltersModeGroup, true), true},         // have only one copy per sequence.
+            {std::make_shared<StoreFeatureRSDEstimations>(FeatureFiltersUtilsMode::EFeatureFiltersModeComponent, true), false},
+            {std::make_shared<StoreFeatureRSDEstimations>(FeatureFiltersUtilsMode::EFeatureFiltersModeGroup, true), false},
+            {std::make_shared<StoreFeatureBackgroundEstimations>(FeatureFiltersUtilsMode::EFeatureFiltersModeComponent, true), false},
+            {std::make_shared<StoreFeatureBackgroundEstimations>(FeatureFiltersUtilsMode::EFeatureFiltersModeGroup, true), false}
           };
           for (const auto& [export_processor, export_as_file] : export_processors)
           {
diff --git a/src/smartpeak/include/SmartPeak/core/SequenceSegmentProcessors/StoreFeatureBackgroundFilters.h b/src/smartpeak/include/SmartPeak/core/SequenceSegmentProcessors/StoreFeatureBackgroundFilters.h
@@ -56,7 +56,7 @@ namespace SmartPeak
     /* IFilePickerHandler */
     virtual void getFilenames(Filenames& filenames) const override;
 
-    /* IProcessorDescription */
+    /* IFilePickerHandler */
     bool onFilePicked(const std::filesystem::path& filename, ApplicationHandler* application_handler) override;
   };
 
diff --git a/src/smartpeak/include/SmartPeak/core/SequenceSegmentProcessors/StoreFeatureFilters.h b/src/smartpeak/include/SmartPeak/core/SequenceSegmentProcessors/StoreFeatureFilters.h
@@ -56,7 +56,7 @@ namespace SmartPeak
     /* IFilenamesHandler */
     virtual void getFilenames(Filenames& filenames) const override;
 
-    /* IProcessorDescription */
+    /* IFilePickerHandler */
     bool onFilePicked(const std::filesystem::path& filename, ApplicationHandler* application_handler) override;
   };
 
diff --git a/src/smartpeak/include/SmartPeak/core/SequenceSegmentProcessors/StoreFeatureQCs.h b/src/smartpeak/include/SmartPeak/core/SequenceSegmentProcessors/StoreFeatureQCs.h
@@ -56,7 +56,7 @@ namespace SmartPeak
     /* IFilenamesHandler */
     virtual void getFilenames(Filenames& filenames) const override;
 
-    /* IProcessorDescription */
+    /* IFilePickerHandler */
     bool onFilePicked(const std::filesystem::path& filename, ApplicationHandler* application_handler) override;
   };
 
diff --git a/src/smartpeak/include/SmartPeak/core/SequenceSegmentProcessors/StoreFeatureRSDFilters.h b/src/smartpeak/include/SmartPeak/core/SequenceSegmentProcessors/StoreFeatureRSDFilters.h
@@ -55,7 +55,7 @@ namespace SmartPeak
     /* IFilenamesHandler */
     virtual void getFilenames(Filenames& filenames) const override;
 
-    /* IProcessorDescription */
+    /* IFilePickerHandler */
     bool onFilePicked(const std::filesystem::path& filename, ApplicationHandler* application_handler) override;
   };
 
diff --git a/src/smartpeak/include/SmartPeak/core/SequenceSegmentProcessors/StoreFeatureRSDQCs.h b/src/smartpeak/include/SmartPeak/core/SequenceSegmentProcessors/StoreFeatureRSDQCs.h
@@ -56,7 +56,7 @@ namespace SmartPeak
     /* IFilenamesHandler */
     virtual void getFilenames(Filenames& filenames) const override;
 
-    /* IProcessorDescription */
+    /* IFilePickerHandler */
     virtual bool onFilePicked(const std::filesystem::path& filename, ApplicationHandler* application_handler) override;
   };
 
diff --git a/src/smartpeak/include/SmartPeak/core/SequenceSegmentProcessors/StoreQuantitationMethods.h b/src/smartpeak/include/SmartPeak/core/SequenceSegmentProcessors/StoreQuantitationMethods.h
@@ -56,9 +56,7 @@ namespace SmartPeak
     /* IFilenamesHandler */
     virtual void getFilenames(Filenames& filenames) const override;
 
-    /**
-    IFilePickerHandler
-    */
+    /* IFilePickerHandler */
     bool onFilePicked(const std::filesystem::path& filename, ApplicationHandler* application_handler) override;
   };
 
diff --git a/src/smartpeak/source/core/ApplicationProcessors/LoadSession.cpp b/src/smartpeak/source/core/ApplicationProcessors/LoadSession.cpp
@@ -121,17 +121,19 @@ namespace SmartPeak
         {
           if (!application_handler_.sequenceHandler_.getSequenceSegments().empty())
           {
-            SequenceSegmentHandler& sequenceSegmentHandler = application_handler_.sequenceHandler_.getSequenceSegments().at(0);
-            sequence_segment_processor->sequence_segment_observable_ = &application_handler_.sequenceHandler_;
-            try
-            {
-              sequence_segment_processor->process(sequenceSegmentHandler, SequenceHandler(), {}, *filenames_);
-            }
-            catch (const std::exception& e)
+            for (auto& sequenceSegmentHandler : application_handler_.sequenceHandler_.getSequenceSegments())
             {
-              LOGE << e.what();
-              notifyApplicationProcessorError(e.what());
-              return false;
+              sequence_segment_processor->sequence_segment_observable_ = &application_handler_.sequenceHandler_;
+              try
+              {
+                sequence_segment_processor->process(sequenceSegmentHandler, SequenceHandler(), {}, *filenames_);
+              }
+              catch (const std::exception& e)
+              {
+                LOGE << e.what();
+                notifyApplicationProcessorError(e.what());
+                return false;
+              }
             }
           }
           else
diff --git a/src/smartpeak/source/core/SequenceSegmentProcessors/StoreFeatureBackgroundEstimations.cpp b/src/smartpeak/source/core/SequenceSegmentProcessors/StoreFeatureBackgroundEstimations.cpp
@@ -47,21 +47,16 @@ namespace SmartPeak
     return { };
   }
 
-  bool StoreFeatureBackgroundEstimations::onFilePicked(const std::filesystem::path& filename, ApplicationHandler* application_handler)
+  bool StoreFeatureBackgroundEstimations::onFilePicked(const std::filesystem::path& directory, ApplicationHandler* application_handler)
   {
     Filenames filenames;
-    if (!FeatureFiltersUtils::onFilePicked(
-      filename,
-      application_handler,
-      filenames,
-      "featureBackgroundEstimationComponents",
-      "featureBackgroundEstimationComponentGroups",
-      feature_filter_mode_))
+    filenames.setTagValue(Filenames::Tag::FEATURES_OUTPUT_PATH, directory.generic_string());
+    static_filenames_ = false;
+    for (auto& sequence_segment : application_handler->sequenceHandler_.getSequenceSegments())
     {
-      return false;
+      filenames.setTagValue(Filenames::Tag::OUTPUT_SEQUENCE_SEGMENT_NAME, sequence_segment.getSequenceSegmentName());
+      process(sequence_segment, application_handler->sequenceHandler_, {}, filenames);
     }
-    sequence_segment_observable_ = &application_handler->sequenceHandler_;
-    process(application_handler->sequenceHandler_.getSequenceSegments()[0], SequenceHandler(), {}, filenames);
     return true;
   }
 
diff --git a/src/smartpeak/source/core/SequenceSegmentProcessors/StoreFeatureFilters.cpp b/src/smartpeak/source/core/SequenceSegmentProcessors/StoreFeatureFilters.cpp
@@ -71,6 +71,7 @@ namespace SmartPeak
       return false;
     }
     sequence_segment_observable_ = &application_handler->sequenceHandler_;
+    // have only one copy per sequence, so just take the 1st one
     process(application_handler->sequenceHandler_.getSequenceSegments()[0], SequenceHandler(), {}, filenames);
     return true;
   }
diff --git a/src/smartpeak/source/core/SequenceSegmentProcessors/StoreFeatureQCs.cpp b/src/smartpeak/source/core/SequenceSegmentProcessors/StoreFeatureQCs.cpp
@@ -71,6 +71,7 @@ namespace SmartPeak
       return false;
     }
     sequence_segment_observable_ = &application_handler->sequenceHandler_;
+    // have only one copy per sequence, so just take the 1st one
     process(application_handler->sequenceHandler_.getSequenceSegments()[0], SequenceHandler(), {}, filenames);
     return true;
   }
diff --git a/src/smartpeak/source/core/SequenceSegmentProcessors/StoreFeatureRSDEstimations.cpp b/src/smartpeak/source/core/SequenceSegmentProcessors/StoreFeatureRSDEstimations.cpp
@@ -47,21 +47,16 @@ namespace SmartPeak
     return { };
   }
 
-  bool StoreFeatureRSDEstimations::onFilePicked(const std::filesystem::path& filename, ApplicationHandler* application_handler)
+  bool StoreFeatureRSDEstimations::onFilePicked(const std::filesystem::path& directory, ApplicationHandler* application_handler)
   {
     Filenames filenames;
-    if (!FeatureFiltersUtils::onFilePicked(
-      filename,
-      application_handler,
-      filenames,
-      "featureRSDEstimationComponents",
-      "featureRSDEstimationComponentGroups",
-      feature_filter_mode_))
+    filenames.setTagValue(Filenames::Tag::FEATURES_OUTPUT_PATH, directory.generic_string());
+    static_filenames_ = false;
+    for (auto& sequence_segment : application_handler->sequenceHandler_.getSequenceSegments())
     {
-      return false;
+      filenames.setTagValue(Filenames::Tag::OUTPUT_SEQUENCE_SEGMENT_NAME, sequence_segment.getSequenceSegmentName());
+      process(sequence_segment, application_handler->sequenceHandler_, {}, filenames);
     }
-    sequence_segment_observable_ = &application_handler->sequenceHandler_;
-    process(application_handler->sequenceHandler_.getSequenceSegments()[0], SequenceHandler(), {}, filenames);
     return true;
   }
 
diff --git a/src/smartpeak/source/core/SequenceSegmentProcessors/StoreQuantitationMethods.cpp b/src/smartpeak/source/core/SequenceSegmentProcessors/StoreQuantitationMethods.cpp
@@ -71,17 +71,12 @@ namespace SmartPeak
 
   bool StoreQuantitationMethods::onFilePicked(const std::filesystem::path& directory, ApplicationHandler* application_handler)
   {
-    if (application_handler->sequenceHandler_.getSequenceSegments().size() == 0)
-    {
-      LOGE << "File cannot be written without first loading the sequence.";
-      return false;
-    }
+    Filenames filenames;
+    filenames.setTagValue(Filenames::Tag::FEATURES_OUTPUT_PATH, directory.generic_string());
+    static_filenames_ = false;
     for (auto& sequence_segment : application_handler->sequenceHandler_.getSequenceSegments())
     {
-      Filenames filenames;
-      filenames.setTagValue(Filenames::Tag::FEATURES_OUTPUT_PATH, directory.generic_string());
       filenames.setTagValue(Filenames::Tag::OUTPUT_SEQUENCE_SEGMENT_NAME, sequence_segment.getSequenceSegmentName());
-      static_filenames_ = false;
       process(sequence_segment, application_handler->sequenceHandler_, {}, filenames);
     }
     return true;
diff --git a/src/smartpeak/source/core/SequenceSegmentProcessors/StoreStandardsConcentrations.cpp b/src/smartpeak/source/core/SequenceSegmentProcessors/StoreStandardsConcentrations.cpp
@@ -56,17 +56,16 @@ namespace SmartPeak
     return ParameterSet();
   }
 
-  bool StoreStandardsConcentrations::onFilePicked(const std::filesystem::path& filename, ApplicationHandler* application_handler)
+  bool StoreStandardsConcentrations::onFilePicked(const std::filesystem::path& directory, ApplicationHandler* application_handler)
   {
-    if (application_handler->sequenceHandler_.getSequence().size() == 0)
+    Filenames filenames;
+    filenames.setTagValue(Filenames::Tag::FEATURES_OUTPUT_PATH, directory.generic_string());
+    static_filenames_ = false;
+    for (auto& sequence_segment : application_handler->sequenceHandler_.getSequenceSegments())
     {
-      LOGE << "File cannot be loaded without first loading the sequence.";
-      return false;
+      filenames.setTagValue(Filenames::Tag::OUTPUT_SEQUENCE_SEGMENT_NAME, sequence_segment.getSequenceSegmentName());
+      process(sequence_segment, application_handler->sequenceHandler_, {}, filenames);
     }
-    Filenames filenames;
-    filenames.setFullPath("standardsConcentrations", filename);
-    sequence_segment_observable_ = &application_handler->sequenceHandler_;
-    process(application_handler->sequenceHandler_.getSequenceSegments()[0], SequenceHandler(), {}, filenames);
     return true;
   }
 
diff --git a/src/widgets/source/ui/FilePicker.cpp b/src/widgets/source/ui/FilePicker.cpp
@@ -349,7 +349,7 @@ namespace SmartPeak
       {
         auto dir = pfd::select_folder(
           title,
-          default_file_name
+          ""
         ).result();
         LOGD << "Selected dir: " << dir;
         picked_pathname_ = dir;

Original file line number	Diff line number	Diff line change
`@@ -47,21 +47,16 @@ namespace SmartPeak`
`47`	`47`	`return { };`
`48`	`48`	`}`
`49`	`49`
`50`		`- bool StoreFeatureBackgroundEstimations::onFilePicked(const std::filesystem::path& filename, ApplicationHandler* application_handler)`
	`50`	`+ bool StoreFeatureBackgroundEstimations::onFilePicked(const std::filesystem::path& directory, ApplicationHandler* application_handler)`
`51`	`51`	`{`
`52`	`52`	`Filenames filenames;`
`53`		`- if (!FeatureFiltersUtils::onFilePicked(`
`54`		`- filename,`
`55`		`- application_handler,`
`56`		`- filenames,`
`57`		`- "featureBackgroundEstimationComponents",`
`58`		`- "featureBackgroundEstimationComponentGroups",`
`59`		`- feature_filter_mode_))`
	`53`	`+ filenames.setTagValue(Filenames::Tag::FEATURES_OUTPUT_PATH, directory.generic_string());`
	`54`	`+ static_filenames_ = false;`
	`55`	`+ for (auto& sequence_segment : application_handler->sequenceHandler_.getSequenceSegments())`
`60`	`56`	`{`
`61`		`- return false;`
	`57`	`+ filenames.setTagValue(Filenames::Tag::OUTPUT_SEQUENCE_SEGMENT_NAME, sequence_segment.getSequenceSegmentName());`
	`58`	`+ process(sequence_segment, application_handler->sequenceHandler_, {}, filenames);`
`62`	`59`	`}`
`63`		`- sequence_segment_observable_ = &application_handler->sequenceHandler_;`
`64`		`- process(application_handler->sequenceHandler_.getSequenceSegments()[0], SequenceHandler(), {}, filenames);`
`65`	`60`	`return true;`
`66`	`61`	`}`
`67`	`62`
Original file line number	Diff line number	Diff line change
`@@ -71,6 +71,7 @@ namespace SmartPeak`
`71`	`71`	`return false;`
`72`	`72`	`}`
`73`	`73`	`sequence_segment_observable_ = &application_handler->sequenceHandler_;`
	`74`	`+ // have only one copy per sequence, so just take the 1st one`
`74`	`75`	`process(application_handler->sequenceHandler_.getSequenceSegments()[0], SequenceHandler(), {}, filenames);`
`75`	`76`	`return true;`
`76`	`77`	`}`
Original file line number	Diff line number	Diff line change
`@@ -56,17 +56,16 @@ namespace SmartPeak`
`56`	`56`	`return ParameterSet();`
`57`	`57`	`}`
`58`	`58`
`59`		`- bool StoreStandardsConcentrations::onFilePicked(const std::filesystem::path& filename, ApplicationHandler* application_handler)`
	`59`	`+ bool StoreStandardsConcentrations::onFilePicked(const std::filesystem::path& directory, ApplicationHandler* application_handler)`
`60`	`60`	`{`
`61`		`- if (application_handler->sequenceHandler_.getSequence().size() == 0)`
	`61`	`+ Filenames filenames;`
	`62`	`+ filenames.setTagValue(Filenames::Tag::FEATURES_OUTPUT_PATH, directory.generic_string());`
	`63`	`+ static_filenames_ = false;`
	`64`	`+ for (auto& sequence_segment : application_handler->sequenceHandler_.getSequenceSegments())`
`62`	`65`	`{`
`63`		`- LOGE << "File cannot be loaded without first loading the sequence.";`
`64`		`- return false;`
	`66`	`+ filenames.setTagValue(Filenames::Tag::OUTPUT_SEQUENCE_SEGMENT_NAME, sequence_segment.getSequenceSegmentName());`
	`67`	`+ process(sequence_segment, application_handler->sequenceHandler_, {}, filenames);`
`65`	`68`	`}`
`66`		`- Filenames filenames;`
`67`		`- filenames.setFullPath("standardsConcentrations", filename);`
`68`		`- sequence_segment_observable_ = &application_handler->sequenceHandler_;`
`69`		`- process(application_handler->sequenceHandler_.getSequenceSegments()[0], SequenceHandler(), {}, filenames);`
`70`	`69`	`return true;`
`71`	`70`	`}`
`72`	`71`
Original file line number	Diff line number	Diff line change
`@@ -349,7 +349,7 @@ namespace SmartPeak`
`349`	`349`	`{`
`350`	`350`	`auto dir = pfd::select_folder(`
`351`	`351`	`title,`
`352`		`- default_file_name`
	`352`	`+ ""`
`353`	`353`	`).result();`
`354`	`354`	`LOGD << "Selected dir: " << dir;`
`355`	`355`	`picked_pathname_ = dir;`