Add feature upload-zenodo subcommand

README.md

@@ -51,7 +51,7 @@ This section describes some subcommands.
 
 ```bash
 $ yevis --help
-yevis 0.4.0
+yevis 0.5.8
 DDBJ(Bioinformatics and DDBJ Center)
 CLI tool that supports building a Yevis workflow registry with automated quality control
 
@@ -69,6 +69,7 @@ SUBCOMMANDS:
                      (`CI=true`))
     pull-request     Create a pull request based on the Yevis metadata files (after validation and testing)
     test             Test workflow based on the Yevis metadata files
+    upload-zenodo    Upload dataset to Zenodo
     validate         Validate schema and contents of the Yevis metadata file
 ```
 
@@ -78,7 +79,7 @@ Generate a workflow metadata file template from a primary workflow file URL.
 
 ```bash
 $ yevis make-template --help
-yevis-make-template 0.4.0
+yevis-make-template 0.5.8
 Generate a template file for the Yevis metadata file
 
 USAGE:
@@ -109,7 +110,7 @@ Validate schema and contents of the workflow metadata file.
 
 ```bash
 $ yevis validate --help
-yevis-validate 0.4.0
+yevis-validate 0.5.8
 Validate schema and contents of the Yevis metadata file
 
 USAGE:
@@ -159,7 +160,7 @@ Test workflow using [GA4GH WES](https://www.ga4gh.org/news/ga4gh-wes-api-enables
 
 ```bash
 $ yevis test --help
-yevis-test 0.4.0
+yevis-test 0.5.8
 Test workflow based on the Yevis metadata files
 
 USAGE:
@@ -232,7 +233,7 @@ Create a pull request after validation and testing.
 
 ```bash
 $ yevis pull-request --help
-yevis-pull-request 0.4.0
+yevis-pull-request 0.5.8
 Create a pull request based on the Yevis metadata files (after validation and testing)
 
 USAGE:
@@ -269,7 +270,7 @@ Upload files to Zenodo, generate TRS responses and deploy them on GitHub Pages.
 
 ```bash
 $ yevis publish --help
-yevis-publish 0.4.0
+yevis-publish 0.5.8
 Generate TRS responses and host them on GitHub Pages. (Basically used in the CI environment (`CI=true`))
 
 USAGE:
@@ -309,6 +310,40 @@ Note that the following four options:
 
 See the GitHub Actions section for more details.
 
+### upload-zenodo
+
+Upload files in the Yevis metadata to Zenodo and replace the metadata file with the Zenodo URL.
+
+```bash
+$ yevis upload-zenodo --help
+yevis-upload-zenodo 0.5.8
+Upload dataset to Zenodo
+
+USAGE:
+    yevis upload-zenodo [FLAGS] [OPTIONS] --repository <repository> [metadata-location]
+
+FLAGS:
+    -h, --help       Prints help information
+    -V, --version    Prints version information
+    -v, --verbose    Verbose mode
+
+OPTIONS:
+        --gh-token <github-token>                GitHub Personal Access Token
+    -o, --output <output>                        Path to the output file [default: yevis-metadata-uploaded.yml]
+    -r, --repository <repository>                GitHub repository that publishes TRS responses (format: <owner>/<repo>)
+        --zenodo-community <zenodo-community>    Community set in Zenodo deposition
+        --zenodo-host <zenodo-host>
+            Zenodo host. Uses zenodo.org by default and sandbox.zenodo.org for dev-mode
+
+        --zenodo-token <zenodo-token>
+            Zenodo Personal Access Token. You can generate it at
+            https://zenodo.org/account/settings/applications/tokens/new/
+
+ARGS:
+    <metadata-location>    Location of the Yevis metadata file (local file path or remote URL) [default: yevis-
+                           metadata.yml]
+```
+
 #### Generated TRS Responses
 
 Please note, as raised in the issue <https://github.com/ddbj/workflow-registry/issues/15> by @kinow, that the TRS responses generated by Yevis may not be fully compliant with the [TRS API](https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh/tool-registry-schemas/develop/openapi/openapi.yaml).
@@ -393,7 +428,7 @@ yevis 0.4.0
 
 ### Build binary
 
-Recommendation, build the binary using `musl``:
+Recommendation, build the binary using `musl`:
 
 ```bash
 $ docker run --rm -it -v $PWD:/home/rust/src ekidd/rust-musl-builder cargo build --release

src/args.rs

@@ -160,6 +160,47 @@ pub enum Args {
         #[structopt(short, long)]
         verbose: bool,
     },
+
+    #[structopt(setting(clap::AppSettings::ColoredHelp))]
+    /// Upload dataset to Zenodo.
+    UploadZenodo {
+        /// Location of the Yevis metadata file (local file path or remote URL).
+        #[structopt(default_value = "yevis-metadata.yml")]
+        metadata_location: String,
+
+        /// GitHub Personal Access Token.
+        #[structopt(long = "gh-token")]
+        github_token: Option<String>,
+
+        /// GitHub repository that publishes TRS responses (format: <owner>/<repo>).
+        #[structopt(short, long)]
+        repository: String,
+
+        /// Zenodo Personal Access Token. You can generate it at https://zenodo.org/account/settings/applications/tokens/new/.
+        #[structopt(long = "zenodo-token")]
+        zenodo_token: Option<String>,
+
+        /// Zenodo host. Uses zenodo.org by default and sandbox.zenodo.org for dev-mode.
+        #[structopt(long = "zenodo-host")]
+        zenodo_host: Option<String>,
+
+        /// Community set in Zenodo deposition.
+        #[structopt(long)]
+        zenodo_community: Option<String>,
+
+        /// Path to the output file.
+        #[structopt(
+            short,
+            long,
+            parse(from_os_str),
+            default_value = "yevis-metadata-uploaded.yml"
+        )]
+        output: PathBuf,
+
+        /// Verbose mode.
+        #[structopt(short, long)]
+        verbose: bool,
+    },
 }
 
 impl Args {
@@ -170,6 +211,7 @@ impl Args {
             Args::Test { verbose, .. } => *verbose,
             Args::PullRequest { verbose, .. } => *verbose,
             Args::Publish { verbose, .. } => *verbose,
+            Args::UploadZenodo { verbose, .. } => *verbose,
         }
     }
 
@@ -180,6 +222,7 @@ impl Args {
             Args::Test { github_token, .. } => github_token.clone(),
             Args::PullRequest { github_token, .. } => github_token.clone(),
             Args::Publish { github_token, .. } => github_token.clone(),
+            Args::UploadZenodo { github_token, .. } => github_token.clone(),
         }
     }
 }

src/main.rs

@@ -147,6 +147,29 @@ fn main() -> Result<()> {
 
             sub_cmd::publish(&meta_vec, &gh_token, &repository, with_test);
         }
+        args::Args::UploadZenodo {
+            metadata_location,
+            repository,
+            output,
+            zenodo_token,
+            zenodo_host,
+            zenodo_community,
+            ..
+        } => {
+            let meta_vec = sub_cmd::validate(vec![metadata_location], &gh_token);
+            let mut meta_loc = meta_vec
+                .into_iter()
+                .next()
+                .expect("Expected at least one metadata");
+            sub_cmd::upload_zenodo(
+                &mut meta_loc,
+                &output,
+                &zenodo_token,
+                &zenodo_host,
+                &zenodo_community,
+                &repository,
+            )?;
+        }
     };
     Ok(())
 }

src/sub_cmd.rs

@@ -4,6 +4,8 @@ pub mod pull_request;
 pub mod test;
 pub mod validate;
 
+use crate::zenodo;
+use anyhow::bail;
 use make_template::make_template as make_template_process;
 use publish::publish as publish_process;
 use pull_request::pull_request as pull_request_process;
@@ -147,3 +149,42 @@ pub fn publish(
         }
     };
 }
+
+pub fn upload_zenodo(
+    meta: &mut metadata::types::Metadata,
+    output: impl AsRef<Path>,
+    zenodo_token: &Option<impl AsRef<str>>,
+    zenodo_host: &Option<impl AsRef<str>>,
+    zenodo_community: &Option<impl AsRef<str>>,
+    repository: impl AsRef<str>,
+) -> Result<(), anyhow::Error> {
+    info!("{} upload-zenodo", "Running".green());
+    let token = match zenodo_token {
+        Some(zenodo_token) => zenodo_token.as_ref().to_string(),
+        None => match env::zenodo_token() {
+            Ok(token) => token,
+            Err(e) => {
+                bail!("{} to get Zenodo token with error: {}", "Failed".red(), e);
+            }
+        },
+    };
+    let host = match zenodo_host {
+        Some(zenodo_host) => zenodo_host.as_ref().to_string(),
+        None => env::zenodo_host(),
+    };
+    info!(
+        "Uploading wf_id: {}, version: {} to Zenodo",
+        meta.id, meta.version
+    );
+    zenodo::upload_zenodo(&host, &token, meta, repository, zenodo_community)?;
+    info!("Updating workflow metadata to Zenodo URL");
+    zenodo::update_metadata(&host, &token, meta)?;
+
+    info!("Writing uploaded metadata to {}", output.as_ref().display());
+    let file_ext = metadata::io::parse_file_ext(&output)?;
+    metadata::io::write_local(meta, &output, &file_ext)?;
+
+    info!("{} upload-zenodo", "Success".green());
+
+    Ok(())
+}

src/sub_cmd/validate.rs

@@ -44,36 +44,32 @@ pub fn validate_version(version: impl AsRef<str>) -> Result<()> {
 /// Change the license to `spdx_id`
 /// e.g., `apache-2.0` -> `Apache-2.0`
 fn validate_license(meta: &mut metadata::types::Metadata, gh_token: impl AsRef<str>) -> Result<()> {
-    let spdx_id: String = validate_with_github_license_api(gh_token, &meta.license)?;
-    validate_with_zenodo_license_api(&spdx_id)?;
+    let (key, spdx_id) = validate_with_github_license_api(gh_token, &meta.license)?;
+    validate_with_zenodo_license_api(&key)?;
     meta.license = spdx_id;
     Ok(())
 }
 
 #[derive(Debug, Deserialize)]
 struct LicenseResponse {
-    permissions: Vec<String>,
+    key: String,
     spdx_id: String,
 }
 
 /// https://docs.github.com/ja/rest/reference/licenses#get-a-license
-/// Ensure that `distribution` is included in `permissions` field.
+/// res: (key, spdx_id), e.g., ("mit", "MIT")
 fn validate_with_github_license_api(
     gh_token: impl AsRef<str>,
     license: impl AsRef<str>,
-) -> Result<String> {
+) -> Result<(String, String)> {
     let url = Url::parse(&format!(
         "https://api.github.com/licenses/{}",
         license.as_ref()
     ))?;
     let res = gh::get_request(gh_token, &url, &[])?;
     let res: LicenseResponse =
         serde_json::from_value(res).context("Failed to parse GitHub license API response")?;
-    ensure!(
-        res.permissions.contains(&String::from("distribution")),
-        "GitHub license API response does not contain `distribution` in `permissions` field"
-    );
-    Ok(res.spdx_id)
+    Ok((res.key, res.spdx_id))
 }
 
 /// https://developers.zenodo.org/?shell#retrieve41

src/zenodo.rs

@@ -52,7 +52,7 @@ pub fn upload_zenodo_and_commit_gh(
     Ok(())
 }
 
-fn upload_zenodo(
+pub fn upload_zenodo(
     host: impl AsRef<str>,
     token: impl AsRef<str>,
     meta: &mut metadata::types::Metadata,
@@ -222,7 +222,7 @@ fn update_deposition_files(
     Ok(())
 }
 
-fn update_metadata(
+pub fn update_metadata(
     host: impl AsRef<str>,
     token: impl AsRef<str>,
     meta: &mut metadata::types::Metadata,