feat: add module for objects common between clts and wfs

onnovalkering · Mar 19, 2020 · ea31209 · ea31209
1 parent e9e5095
commit ea31209
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Showing 4 changed files with 198 additions and 159 deletions.
diff --git a/src/lib.rs b/src/lib.rs
@@ -2,5 +2,6 @@
 extern crate failure;
 
 pub mod v11_clt;
+pub mod v11_cm;
 pub mod v11_wf;
 pub mod v11;
diff --git a/src/v11_clt.rs b/src/v11_clt.rs
@@ -1,3 +1,4 @@
+use crate::v11_cm::{Any, CwlType, Documentation, Format, SecondaryFiles};
 use serde::{Deserialize, Serialize};
 use serde_with::skip_serializing_none;
 use serde_yaml::Value as YValue;
@@ -16,9 +17,9 @@ pub struct CommandLineTool {
 
     pub cwl_version: String,
 
-    pub doc: Option<CommandLineToolDoc>,
+    pub doc: Option<Documentation>,
 
-    pub hints: Option<YValue>,
+    pub hints: Option<YValue>, // TODO
 
     pub id: Option<String>,
 
@@ -30,13 +31,13 @@ pub struct CommandLineTool {
 
     pub permanent_fail_codes: Option<Vec<u32>>,
 
-    pub requirements: Option<YValue>,
+    pub requirements: Option<YValue>, // TODO
 
-    pub stderr: Option<CommandLineToolStderr>,
+    pub stderr: Option<String>,
 
-    pub stdin: Option<CommandLineToolStdin>,
+    pub stdin: Option<String>,
 
-    pub stdout: Option<CommandLineToolStdout>,
+    pub stdout: Option<String>,
 
     pub success_codes: Option<Vec<u32>>,
 
@@ -47,8 +48,7 @@ pub struct CommandLineTool {
 #[derive(Clone, Debug, Deserialize, Serialize)]
 pub enum CommandLineToolArgument {
     Argument(String),
-    Expression(YValue),
-    CommandLineBinding(CommandLineBinding),
+    Binding(CommandLineBinding),
 }
 
 #[skip_serializing_none]
@@ -67,54 +67,40 @@ pub struct CommandLineBinding {
 
     pub shell_quote: Option<bool>,
 
-    pub value_from: Option<CommandLineBindingValueFrom>,
+    pub value_from: Option<String>,
 }
 
 #[serde(untagged, rename_all = "camelCase")]
 #[derive(Clone, Debug, Deserialize, Serialize)]
 pub enum CommandLineBindingPosition {
     Position(u32),
-    Expression(YValue)
-}
-
-#[serde(untagged, rename_all = "camelCase")]
-#[derive(Clone, Debug, Deserialize, Serialize)]
-pub enum CommandLineBindingValueFrom {
-    ValueFrom(String),
-    Expression(YValue)
+    Expression(String)
 }
 
 #[serde(untagged, rename_all = "camelCase")]
 #[derive(Clone, Debug, Deserialize, Serialize)]
 pub enum CommandLineToolBaseCommand {
-    BaseCommand(String),
-    Array(Vec<String>)
-}
-
-#[serde(untagged, rename_all = "camelCase")]
-#[derive(Clone, Debug, Deserialize, Serialize)]
-pub enum CommandLineToolDoc {
-    Doc(String),
-    Array(Vec<String>)
+    Command(String),
+    CommandWithArguments(Vec<String>)
 }
 
 #[serde(untagged, rename_all = "camelCase")]
 #[derive(Clone, Debug, Deserialize, Serialize)]
 pub enum CommandLineToolInput {
-    Array(Vec<CommandInputParameter>),
-    Map(Map<CommandInputParameter>),
-    Types(Map<YValue>)
+    ParameterArray(Vec<CommandInputParameter>),
+    ParameterMap(Map<CommandInputParameter>),
+    TypeMap(Map<CommandLineToolInputType>)
 }
 
 #[skip_serializing_none]
 #[serde(rename_all = "camelCase")]
 #[derive(Clone, Debug, Deserialize, Serialize)]
 pub struct CommandInputParameter {
-    pub default: Option<YValue>,
+    pub default: Option<Any>,
 
-    pub doc: Option<CommandLineToolDoc>,
+    pub doc: Option<Documentation>,
 
-    pub format: Option<CommandLineParameterFormat>,
+    pub format: Option<Format>,
 
     pub id: Option<String>,
 
@@ -126,58 +112,42 @@ pub struct CommandInputParameter {
 
     pub load_listing: Option<String>,
 
-    #[serde(rename = "type")]
-    pub param_type: YValue,
+    pub r#type: CommandInputParameterType,
 
-    pub secondary_files: Option<CommandLineSecondaryFiles>,
+    pub secondary_files: Option<SecondaryFiles>,
 
     pub streamable: Option<bool>,
 }
 
 #[serde(untagged, rename_all = "camelCase")]
 #[derive(Clone, Debug, Deserialize, Serialize)]
-pub enum CommandLineSecondaryFiles {
-    SecondaryFile(SecondaryFileSchema),
-    Array(Vec<SecondaryFileSchema>),
-}
-
-#[skip_serializing_none]
-#[serde(rename_all = "camelCase")]
-#[derive(Clone, Debug, Deserialize, Serialize)]
-pub struct SecondaryFileSchema {
-    pub pattern: SecondaryFileSchemaPattern,
-    pub required: Option<SecondaryFileSchemaRequired>
+pub enum CommandInputParameterType {
+    Type(CommandLineToolInputType),
+    TypeArray(Vec<CommandLineToolInputType>)
 }
 
 #[serde(untagged, rename_all = "camelCase")]
 #[derive(Clone, Debug, Deserialize, Serialize)]
-pub enum SecondaryFileSchemaPattern {
-    Pattern(String),
-    Expression(YValue)
-}
-
-#[serde(untagged, rename_all = "camelCase")]
-#[derive(Clone, Debug, Deserialize, Serialize)]
-pub enum SecondaryFileSchemaRequired {
-    Required(bool),
-    Expression(YValue)
+pub enum CommandLineToolInputType {
+    CwlType(CwlType),
+    Schema(YValue), // TODO
 }
 
 #[serde(untagged, rename_all = "camelCase")]
 #[derive(Clone, Debug, Deserialize, Serialize)]
 pub enum CommandLineToolOutput {
-    Array(Vec<CommandOutputParameter>),
-    Map(Map<CommandOutputParameter>),
-    Types(Map<YValue>)
+    ParameterArray(Vec<CommandOutputParameter>),
+    ParameterMap(Map<CommandOutputParameter>),
+    TypeMap(Map<CommandLineToolOutputType>)
 }
 
 #[skip_serializing_none]
 #[serde(rename_all = "camelCase")]
 #[derive(Clone, Debug, Deserialize, Serialize)]
 pub struct CommandOutputParameter {
-    pub doc: Option<CommandLineToolDoc>,
+    pub doc: Option<Documentation>,
 
-    pub format: Option<CommandLineParameterFormat>,
+    pub format: Option<Format>,
 
     pub id: Option<String>,
 
@@ -189,39 +159,23 @@ pub struct CommandOutputParameter {
 
     pub load_listing: Option<String>,
 
-    #[serde(rename = "type")]
-    pub param_type: YValue,
+    pub r#type: CommandOutputParameterType,
 
-    pub secondary_files: Option<CommandLineSecondaryFiles>,
+    pub secondary_files: Option<SecondaryFiles>,
 
     pub streamable: Option<bool>,
 }
 
 #[serde(untagged, rename_all = "camelCase")]
 #[derive(Clone, Debug, Deserialize, Serialize)]
-pub enum CommandLineParameterFormat {
-    Format(String),
-    Array(Vec<String>),
-    Expression(YValue),
+pub enum CommandOutputParameterType {
+    Type(CommandLineToolOutputType),
+    TypeArray(Vec<CommandLineToolOutputType>)
 }
 
 #[serde(untagged, rename_all = "camelCase")]
 #[derive(Clone, Debug, Deserialize, Serialize)]
-pub enum CommandLineToolStderr {
-    Stderr(String),
-    Expression(YValue)
-}
-
-#[serde(rename_all = "camelCase")]
-#[derive(Clone, Debug, Deserialize, Serialize)]
-pub enum CommandLineToolStdin {
-    Stdin(String),
-    Expression(YValue)
-}
-
-#[serde(rename_all = "camelCase")]
-#[derive(Clone, Debug, Deserialize, Serialize)]
-pub enum CommandLineToolStdout {
-    Stdout(String),
-    Expression(YValue)
+pub enum CommandLineToolOutputType {
+    CwlType(CwlType),
+    Schema(YValue), // TODO
 }
diff --git a/src/v11_cm.rs b/src/v11_cm.rs
@@ -0,0 +1,110 @@
+use serde::{Deserialize, Serialize};
+use serde_with::skip_serializing_none;
+use serde_yaml::Value as YValue;
+
+#[serde(untagged, rename_all = "camelCase")]
+#[derive(Clone, Debug, Deserialize, Serialize)]
+pub enum SecondaryFiles {
+    Schema(SecondaryFileSchema),
+    Schemas(Vec<SecondaryFileSchema>),
+}
+
+#[skip_serializing_none]
+#[serde(rename_all = "camelCase")]
+#[derive(Clone, Debug, Deserialize, Serialize)]
+pub struct SecondaryFileSchema {
+    pattern: String,
+    required: SecondaryFileSchemaRequired,
+}
+
+#[serde(untagged, rename_all = "camelCase")]
+#[derive(Clone, Debug, Deserialize, Serialize)]
+pub enum SecondaryFileSchemaRequired {
+    Boolean(bool),
+    Expression(String),
+}
+
+#[serde(untagged, rename_all = "camelCase")]
+#[derive(Clone, Debug, Deserialize, Serialize)]
+pub enum Any {
+    Any(YValue)
+}
+
+#[serde(untagged, rename_all = "camelCase")]
+#[derive(Clone, Debug, Deserialize, Serialize)]
+pub enum CwlType {
+    Null,
+    Boolean(bool),
+    Int(i32),
+    Long(i64),
+    Float(f32),
+    Double(f64),
+    Str(String),
+    File(File),
+    Directory(Directory),
+}
+
+#[skip_serializing_none]
+#[serde(rename_all = "camelCase")]
+#[derive(Clone, Debug, Deserialize, Serialize)]
+pub struct File {
+    pub class: String,
+
+    pub location: Option<String>,
+
+    pub path: Option<String>,
+
+    pub basename: Option<String>,
+
+    pub dirname: Option<String>,
+
+    pub nameroot: Option<String>,
+
+    pub nameext: Option<String>,
+
+    pub checksum: Option<String>,
+
+    pub size: Option<i64>,
+
+    pub secondary_files: Option<Vec<FileOrDirectory>>,
+
+    pub format: Option<String>,
+
+    pub contents: Option<String>,
+}
+
+#[skip_serializing_none]
+#[serde(rename_all = "camelCase")]
+#[derive(Clone, Debug, Deserialize, Serialize)]
+pub struct Directory {
+    pub class: String,
+
+    pub location: Option<String>,
+
+    pub path: Option<String>,
+
+    pub basename: Option<String>,
+
+    pub listing: Option<Vec<FileOrDirectory>>,
+}
+
+#[serde(untagged, rename_all = "camelCase")]
+#[derive(Clone, Debug, Deserialize, Serialize)]
+pub enum FileOrDirectory {
+    File(File),
+    Directory(Directory),
+}
+
+#[serde(untagged, rename_all = "camelCase")]
+#[derive(Clone, Debug, Deserialize, Serialize)]
+pub enum Documentation {
+    SingleLine(String),
+    MultiLine(Vec<String>)
+}
+
+#[serde(untagged, rename_all = "camelCase")]
+#[derive(Clone, Debug, Deserialize, Serialize)]
+pub enum Format {
+    Format(String),
+    Formats(Vec<String>),
+}