ENH Add load_sample_from_yaml function

To load a single sample from an YAML file

NGLess/BuiltinModules/Samples.hs

@@ -1,13 +1,19 @@
+{-# LANGUAGE CPP #-}
 {- Copyright 2022 NGLess Authors
  - License: MIT
  -}
 
 module BuiltinModules.Samples
     ( loadModule
+#ifdef IS_BUILDING_TEST
+    , executeLoadSample
+    , executeLoadSampleList
+#endif
     ) where
 
 import qualified Data.ByteString as B
 import qualified Data.Text as T
+import           Data.List (find)
 import           Data.Default (def)
 import qualified Data.Aeson as Aeson
 import qualified Data.Aeson.Types as Aeson
@@ -104,23 +110,46 @@ executeLoadSampleList (NGOString fname) _ = do
         Left err -> throwSystemError ("Could not sample information file "++ (T.unpack fname) ++ ". Error was `" ++ show err ++ "`")
 executeLoadSampleList arg _ = throwShouldNotOccur ("load_sample_list called with argument: " ++ show arg)
 
-
-load_sample_list_Function = Function
-    { funcName = FuncName "load_sample_list"
-    , funcArgType = Just NGLString
-    , funcArgChecks = []
-    , funcRetType = NGList NGLReadSet
-    , funcKwArgs = []
-    , funcAllowsAutoComprehension = True
-    , funcChecks = [FunctionCheckMinNGLessVersion (1,5)
-                   ,FunctionCheckReturnAssigned]
-    }
+executeLoadSample :: NGLessObject -> KwArgsValues -> NGLessIO NGLessObject
+executeLoadSample fname kwargs = do
+    sample <- lookupStringOrScriptError "load_sample_from_yaml arguments" "sample" kwargs
+    samples <- executeLoadSampleList fname []
+    case samples of
+        NGOList l -> case find (\(NGOReadSet n _) -> n == sample) l of
+            Just s -> return s
+            _ -> throwDataError ("load_sample_from_yaml: sample " ++ show sample ++ " not found in file " ++ show fname)
+        _ -> throwShouldNotOccur "load_sample_from_yaml: sample list is not a list"
+
+
+yamlFunctions =
+    [ Function
+        { funcName = FuncName "load_sample_list"
+        , funcArgType = Just NGLString
+        , funcArgChecks = []
+        , funcRetType = NGList NGLReadSet
+        , funcKwArgs = [ArgInformation "sample" True (NGList NGLString) []]
+        , funcAllowsAutoComprehension = True
+        , funcChecks = [FunctionCheckMinNGLessVersion (1,5)
+                       ,FunctionCheckReturnAssigned]
+        }
+    , Function
+        { funcName = FuncName "load_sample_from_yaml"
+        , funcArgType = Just NGLString
+        , funcArgChecks = []
+        , funcRetType = NGList NGLReadSet
+        , funcKwArgs = []
+        , funcAllowsAutoComprehension = True
+        , funcChecks = [FunctionCheckMinNGLessVersion (1,5)
+                       ,FunctionCheckReturnAssigned]
+        }
+    ]
 
 loadModule :: T.Text -> NGLessIO Module
 loadModule _ = return def
     { modInfo = ModInfo "builtin.samples" "1.5"
-    , modFunctions = [load_sample_list_Function]
+    , modFunctions = yamlFunctions
     , runFunction = \case
                         "load_sample_list" -> executeLoadSampleList
+                        "load_sample_from_yaml" -> executeLoadSample
                         _ -> error "NOT POSSIBLE"
     }

Tests-Src/Tests.hs

@@ -49,6 +49,7 @@ import Tests.Language (tgroup_Language)
 import Tests.LoadFQDirectory (tgroup_LoadFQDirectory)
 import Tests.NGLessAPI (tgroup_NGLessAPI)
 import Tests.Parse (tgroup_Parse)
+import Tests.Samples (tgroup_Samples)
 import Tests.Select (tgroup_Select)
 import Tests.Types (tgroup_Types)
 import Tests.Validation (tgroup_Validation)
@@ -63,6 +64,7 @@ test_Types      = [tgroup_Types]
 test_NGLessAPI  = [tgroup_NGLessAPI]
 test_Vector     = [tgroup_Vector]
 test_IntGroups  = [tgroup_IntGroups]
+test_Samples    = [tgroup_Samples]
 test_Select     = [tgroup_Select]
 test_Language   = [tgroup_Language]
 test_LoadFqDir  = [tgroup_LoadFQDirectory]

Tests-Src/Tests/FastQ.hs

@@ -21,7 +21,7 @@ import qualified Data.Conduit.List as CL
 
 import Interpretation.FastQ
 import Interpretation.Substrim
-import Tests.Utils
+import Tests.Utils (asTempFile)
 import Data.FastQ
 import Utils.Here
 import Utils.Conduit

Tests-Src/Tests/Samples.hs

@@ -0,0 +1,49 @@
+{-# LANGUAGE TemplateHaskell, QuasiQuotes #-}
+
+{- Copyright 2022 NGLess Authors
+ - License: MIT
+ -}
+module Tests.Samples
+    ( tgroup_Samples
+    ) where
+
+import Test.Tasty.TH
+import Test.Tasty.HUnit
+import qualified Data.ByteString as B
+import qualified Data.Text as T
+import           Control.Monad.IO.Class (liftIO)
+
+import BuiltinModules.Samples
+import Language
+import Utils.Here
+import Tests.Utils (asTempFile, testNGLessIO)
+
+simpleYaml :: B.ByteString
+simpleYaml = [here|
+samples:
+  sample1:
+    - paired:
+        - sample/sample1a.1.fq.gz
+        - sample/sample1a.2.fq.gz
+  sample2:
+    - paired:
+        - sample/sample2a.1.fq.gz
+        - sample/sample2a.2.fq.gz
+|]
+
+tgroup_Samples = $(testGroupGenerator)
+
+getSampleName (NGOReadSet name _) = name
+
+case_load_samples :: Assertion
+case_load_samples = testNGLessIO $ do
+    simpleYamlF <- asTempFile simpleYaml "yaml"
+    NGOList samples <- executeLoadSampleList (NGOString $ T.pack simpleYamlF) []
+    liftIO $ length samples @?= 2
+    liftIO $ (getSampleName $ head samples) @?= "sample1"
+    liftIO $ (getSampleName $ last samples) @?= "sample2"
+    NGOReadSet n _ <- executeLoadSample (NGOString $ T.pack simpleYamlF) [("sample", NGOString "sample1")]
+    liftIO $ n @?= "sample1"
+
+
+

docs/sources/yaml-list.md

@@ -53,3 +53,14 @@ It can also be used with the [parallel module](stdlib.html) module's `run_for_al
         if len(read) < 45:
             discard
     ...
+
+## Loading a single sample from an YAML file
+
+The function `load_sample_from_yaml` (which takes a YAML file and a mandatory
+`sample` argument) will return a single sample (identified by the `sample`
+argument).
+
+    ngless "1.5"
+    input = load_sample_from_yaml('list.yaml', sample='sample-id')
+    ...
+