Fix JSON tag casing, error handling, and documentation inconsistencies from PR #73 review

config/config.go

@@ -23,7 +23,8 @@ func (in *Param) IsFile() bool {
 }
 
 func (in *Param) IsDir() bool {
-	return strings.ToLower(in.Type) == "path"
+	t := strings.ToLower(in.Type)
+	return t == "path" || t == "dir"
 }
 
 func TrimPrefix(s string) string {
@@ -38,5 +39,6 @@ func (in *ParamRequest) IsFile() bool {
 }
 
 func (in *ParamRequest) IsDir() bool {
-	return strings.ToLower(in.Type) == "path"
+	t := strings.ToLower(in.Type)
+	return t == "path" || t == "dir"
 }

docs/docs/config.md

@@ -1,8 +1,8 @@
 ---
-title: Paramaters
+title: Parameters
 ---
 
-## Paramaters Variables
+## Parameters Variables
 
 Playbooks can be parameterized. They are defined in the `params` section of the playbook YAML file.
 

docs/docs/inputs/index.md

@@ -23,7 +23,7 @@ The `table` loader is a good starting point because it demonstrates the typical
 params:
   gafFile:
     type: File
-    value: ../../source/go/goa_human.gaf.gz
+    default: ../../source/go/goa_human.gaf.gz
 
 inputs:
   gafLoad:

docs/docs/schema.md

@@ -87,7 +87,7 @@ Loads data from a SQLite database.
 
 ### `transpose`
 Loads a TSV and transposes it (making rows from columns).
-- `input`: Path to the file.
+- `path`: Path to the file.
 - `rowSkip`: Rows to skip.
 - `sep`: Separator.
 - `useDB`: Use a temporary disk database for large transpositions.

extractors/sqldump_step.go

@@ -15,7 +15,7 @@
 )
 
 type SQLDumpStep struct {
-	Path   string   `json:"Path" jsonschema_description:"Path to the SQL dump file"`
+	Path   string   `json:"path" jsonschema_description:"Path to the SQL dump file"`
 	Tables []string `json:"tables" jsonschema_description:"Array of transforms for the different tables in the SQL dump"`
 }
 
@@ -59,7 +59,7 @@
 	go func() {
 		defer fhd.Close()
 		defer close(out)
 		tableColumns := map[string][]string{}
 		data, _ := io.ReadAll(hd)
 		parser := sqlparser.Parser{}
 		tokens := parser.NewStringTokenizer(string(data))

extractors/tabular_load.go

@@ -16,7 +16,7 @@ import (
 )
 
 type TableLoadStep struct {
-	Path         string   `json:"Path" jsonschema_description:"TSV to be transformed"`
+	Path         string   `json:"path" jsonschema_description:"TSV to be transformed"`
 	RowSkip      int      `json:"rowSkip" jsonschema_description:"Number of header rows to skip"`
 	Columns      []string `json:"columns" jsonschema_description:"Manually set names of columns"`
 	ExtraColumns string   `json:"extraColumns" jsonschema_description:"Columns beyond originally declared columns will be placed in this array"`

extractors/transpose_load.go

@@ -271,7 +271,7 @@ func transposeInDB(workdir string, c csvReader, out chan map[string]any) error {
 }
 
 func transposeInTable(workdir string, fieldSize int, c csvReader, out chan map[string]any) error {
-
+	defer close(out)
 	table, err := os.Create(filepath.Join(workdir, "transpose"))
 	if err != nil {
 		return err
@@ -316,12 +316,14 @@ func transposeInTable(workdir string, fieldSize int, c csvReader, out chan map[s
 	columns := []string{}
 	for row := int64(0); row < rowCount; row++ {
 		buf := make([]byte, fieldSize)
-		_, err := table.ReadAt(buf, row*stepSize)
-		tmp := bytes.Split(buf, []byte{0})
-		if err == nil {
-			columns = append(columns, string(tmp[0]))
-		} else {
+		n, err := table.ReadAt(buf, row*stepSize)
+		if err != nil && err != io.EOF {
 			logger.Error("Column error", "message", err)
+			continue
+		}
+		if n > 0 {
+			tmp := bytes.Split(buf[:n], []byte{0})
+			columns = append(columns, string(tmp[0]))
 		}
 	}
 
@@ -341,7 +343,6 @@ func transposeInTable(workdir string, fieldSize int, c csvReader, out chan map[s
 		out <- record
 	}
 	table.Close()
-	close(out)
 	os.RemoveAll(workdir)
 	return nil
 }

go.sum

@@ -22,8 +22,6 @@ github.com/beorn7/perks v1.0.1 h1:VlbKKnNfV8bJzeqoa4cOKqO6bYr3WgKZxO8Z16+hsOM=
 github.com/beorn7/perks v1.0.1/go.mod h1:G2ZrVWU2WbWT9wwq4/hrbKbnv/1ERSJQ0ibhJ6rlkpw=
 github.com/bitly/go-simplejson v0.5.0 h1:6IH+V8/tVMab511d5bn4M7EwGXZf9Hj6i2xSwkNEM+Y=
 github.com/bitly/go-simplejson v0.5.0/go.mod h1:cXHtHw4XUPsvGaxgjIAn8PhEWG9NfngEKAMDJEczWVA=
-github.com/bmeg/flame v0.0.0-20231228021014-450efb0021a6 h1:7cacs+zs6d9oP0ylXMrmb6PlH8773WEnj/yohQRZkiA=
-github.com/bmeg/flame v0.0.0-20231228021014-450efb0021a6/go.mod h1:XA9wVP0ORyATjjwdbwkjq/yaimsnreixGUR62sGMWsY=
 github.com/bmeg/flame v0.0.0-20250730184845-2dc57651053c h1:ktjBmJUTaHjRoabJio6+P/GPGNjm640gQi3OfcSlnBI=
 github.com/bmeg/flame v0.0.0-20250730184845-2dc57651053c/go.mod h1:telO7T1SSr9Ejv9nm//xcSMCQWynGFll08bnGMwBO/o=
 github.com/bmeg/golib v0.0.0-20200725232156-e799a31439fc h1:/0v/ZcXYjGs44InmjECrls31onIbVKVu1Q/E2cmnCEU=

test/command_line_test.go

@@ -60,15 +60,15 @@ func TestCommandLines(t *testing.T) {
 	// read in conf, ie config.yaml in this case
 	for _, c := range conf {
 		cmd := exec.Command("../sifter", "run", c.Playbook)
-		fmt.Printf("Running: %s\n", c.Playbook)
+		t.Logf("Running: %s\n", c.Playbook)
 		err = cmd.Run()
 		if err != nil {
 			t.Errorf("Failed running %s: %s", c.Playbook, err)
 		} else {
 			for i, chk := range c.Outputs {
 				// iterate through expected output paths
 				path := filepath.Join(filepath.Dir(c.Playbook), chk)
-				fmt.Printf("Checking %s \n", path)
+				t.Logf("Checking %s \n", path)
 				if stat, err := os.Stat(path); err == nil {
 					if stat.Size() > 0 {
 						file, err := os.Open(path)

test/resources/transpose_test.tsv

@@ -0,0 +1,4 @@
+gene	sample1	sample2	sample3
+EGFR	5.2	3.1	7.4
+KRAS	2.5	1.8	3.2
+TP53	6.1	4.5	5.8