more external ident handling

4 files changed, 144 insertions, 10 deletions

diff --git a/rust/src/api_helpers.rs b/rust/src/api_helpers.rs
index f0f56a6b..ef07ee55 100644
--- a/rust/src/api_helpers.rs
+++ b/rust/src/api_helpers.rs
@@ -5,6 +5,8 @@ use diesel;
 use diesel::prelude::*;
 use errors::*;
 use uuid::Uuid;
+use regex::Regex;
+
 
 pub fn get_or_create_editgroup(editor_id: Uuid, conn: &PgConnection) -> Result<Uuid> {
     // check for current active
@@ -109,3 +111,85 @@ pub fn uuid2fcid(id: &Uuid) -> String {
     let raw = id.as_bytes();
     BASE32_NOPAD.encode(raw).to_lowercase()
 }
+
+pub fn check_pmcid(raw: &str) -> Result<()> {
+    lazy_static! {
+        static ref RE: Regex = Regex::new(r"^PMC\d+$").unwrap();
+    }
+    if RE.is_match(raw) {
+        Ok(())
+    } else {
+        Err(ErrorKind::MalformedExternalId(
+            format!("not a valid PubMed Central ID (PMCID): '{}' (expected, eg, 'PMC12345')", raw)
+        ).into())
+    }
+}
+
+pub fn check_pmid(raw: &str) -> Result<()> {
+    lazy_static! {
+        static ref RE: Regex  = Regex::new(r"^\d+$").unwrap();
+    }
+    if RE.is_match(raw) {
+        Ok(())
+    } else {
+        Err(ErrorKind::MalformedExternalId(
+            format!("not a valid PubMed ID (PMID): '{}' (expected, eg, '1234')", raw)
+        ).into())
+    }
+}
+
+pub fn check_wikidata_qid(raw: &str) -> Result<()> {
+    lazy_static! {
+        static ref RE: Regex  = Regex::new(r"^Q\d+$").unwrap();
+    }
+    if RE.is_match(raw) {
+        Ok(())
+    } else {
+        Err(ErrorKind::MalformedExternalId(
+            format!("not a valid Wikidata QID: '{}' (expected, eg, 'Q1234')", raw)
+        ).into())
+    }
+}
+
+pub fn check_doi(raw: &str) -> Result<()> {
+    lazy_static! {
+        static ref RE: Regex  = Regex::new(r"^10.\d{3,6}/.+$").unwrap();
+    }
+    if RE.is_match(raw) {
+        Ok(())
+    } else {
+        Err(ErrorKind::MalformedExternalId(
+            format!("not a valid DOI: '{}' (expected, eg, '10.1234/aksjdfh')", raw)
+        ).into())
+    }
+}
+
+pub fn check_issn(raw: &str) -> Result<()> {
+    lazy_static! {
+        static ref RE: Regex  = Regex::new(r"^\d{4}-\d{3}[0-9X]$").unwrap();
+    }
+    if RE.is_match(raw) {
+        Ok(())
+    } else {
+        Err(ErrorKind::MalformedExternalId(
+            format!("not a valid ISSN: '{}' (expected, eg, '1234-5678')", raw)
+        ).into())
+    }
+}
+
+pub fn check_orcid(raw: &str) -> Result<()> {
+    lazy_static! {
+        static ref RE: Regex  = Regex::new(r"^\d{4}-\d{4}-\d{4}-\d{4}$").unwrap();
+    }
+    if RE.is_match(raw) {
+        Ok(())
+    } else {
+        Err(ErrorKind::MalformedExternalId(
+            format!("not a valid ORCID: '{}' (expected, eg, '0123-4567-3456-6789')", raw)
+        ).into())
+    }
+}
+
+// TODO: make the above checks "more correct"
+// TODO: check ISBN-13
+// TODO: check hashes (SHA-1, etc)
diff --git a/rust/src/api_server.rs b/rust/src/api_server.rs
index 5aa075dd..64c028be 100644
--- a/rust/src/api_server.rs
+++ b/rust/src/api_server.rs
@@ -1,6 +1,6 @@
 //! API endpoint handlers
 
-use api_helpers::{accept_editgroup, fcid2uuid, get_or_create_editgroup, uuid2fcid};
+use api_helpers::*;
 use chrono;
 use database_models::*;
 use database_schema::{
@@ -95,6 +95,7 @@ fn container_row2entity(
     };
     Ok(ContainerEntity {
         issnl: rev.issnl,
+        wikidata_qid: rev.wikidata_qid,
         publisher: rev.publisher,
         name: rev.name,
         abbrev: rev.abbrev,
@@ -122,6 +123,7 @@ fn creator_row2entity(ident: Option<CreatorIdentRow>, rev: CreatorRevRow) -> Res
         given_name: rev.given_name,
         surname: rev.surname,
         orcid: rev.orcid,
+        wikidata_qid: rev.wikidata_qid,
         state: state,
         ident: ident_id,
         revision: Some(rev.id.to_string()),
@@ -249,6 +251,7 @@ fn release_row2entity(
         pmid: rev.pmid,
         pmcid: rev.pmcid,
         isbn13: rev.isbn13,
+        wikidata_qid: rev.wikidata_qid,
         volume: rev.volume,
         issue: rev.issue,
         pages: rev.pages,
@@ -304,6 +307,7 @@ impl Server {
     pub fn lookup_container_handler(&self, issnl: &str) -> Result<ContainerEntity> {
         let conn = self.db_pool.get().expect("db_pool error");
 
+        check_issn(issnl)?;
         let (ident, rev): (ContainerIdentRow, ContainerRevRow) = container_ident::table
             .inner_join(container_rev::table)
             .filter(container_rev::issnl.eq(issnl))
@@ -329,6 +333,7 @@ impl Server {
     pub fn lookup_creator_handler(&self, orcid: &str) -> Result<CreatorEntity> {
         let conn = self.db_pool.get().expect("db_pool error");
 
+        check_orcid(orcid)?;
         let (ident, rev): (CreatorIdentRow, CreatorRevRow) = creator_ident::table
             .inner_join(creator_rev::table)
             .filter(creator_rev::orcid.eq(orcid))
@@ -397,6 +402,7 @@ impl Server {
     pub fn lookup_release_handler(&self, doi: &str) -> Result<ReleaseEntity> {
         let conn = self.db_pool.get().expect("db_pool error");
 
+        check_doi(doi)?;
         let (ident, rev): (ReleaseIdentRow, ReleaseRevRow) = release_ident::table
             .inner_join(release_rev::table)
             .filter(release_rev::doi.eq(doi))
@@ -472,20 +478,27 @@ impl Server {
             None => get_or_create_editgroup(editor_id, &conn)?,
             Some(param) => fcid2uuid(&param)?,
         };
+        if let Some(ref extid) = entity.wikidata_qid {
+            check_wikidata_qid(extid)?;
+        }
+        if let Some(ref extid) = entity.issnl {
+            check_issn(extid)?;
+        }
 
         let edit: ContainerEditRow = diesel::sql_query(
-            "WITH rev AS ( INSERT INTO container_rev (name, publisher, issnl, abbrev, coden, extra_json)
-                        VALUES ($1, $2, $3, $4, $5, $6)
+            "WITH rev AS ( INSERT INTO container_rev (name, publisher, issnl, wikidata_qid, abbrev, coden, extra_json)
+                        VALUES ($1, $2, $3, $4, $5, $6, $7)
                         RETURNING id ),
                 ident AS ( INSERT INTO container_ident (rev_id)
                             VALUES ((SELECT rev.id FROM rev))
                             RETURNING id )
             INSERT INTO container_edit (editgroup_id, ident_id, rev_id) VALUES
-                ($7, (SELECT ident.id FROM ident), (SELECT rev.id FROM rev))
+                ($8, (SELECT ident.id FROM ident), (SELECT rev.id FROM rev))
             RETURNING *",
         ).bind::<diesel::sql_types::Text, _>(entity.name)
             .bind::<diesel::sql_types::Nullable<diesel::sql_types::Text>, _>(entity.publisher)
             .bind::<diesel::sql_types::Nullable<diesel::sql_types::Text>, _>(entity.issnl)
+            .bind::<diesel::sql_types::Nullable<diesel::sql_types::Text>, _>(entity.wikidata_qid)
             .bind::<diesel::sql_types::Nullable<diesel::sql_types::Text>, _>(entity.abbrev)
             .bind::<diesel::sql_types::Nullable<diesel::sql_types::Text>, _>(entity.coden)
             .bind::<diesel::sql_types::Nullable<diesel::sql_types::Json>, _>(entity.extra)
@@ -514,21 +527,28 @@ impl Server {
             None => get_or_create_editgroup(editor_id, &conn).expect("current editgroup"),
             Some(param) => fcid2uuid(&param)?,
         };
+        if let Some(ref extid) = entity.orcid {
+            check_orcid(extid)?;
+        }
+        if let Some(ref extid) = entity.wikidata_qid {
+            check_wikidata_qid(extid)?;
+        }
 
         let edit: CreatorEditRow = diesel::sql_query(
-            "WITH rev AS ( INSERT INTO creator_rev (display_name, given_name, surname, orcid, extra_json)
-                        VALUES ($1, $2, $3, $4, $5)
+            "WITH rev AS ( INSERT INTO creator_rev (display_name, given_name, surname, orcid, wikidata_qid, extra_json)
+                        VALUES ($1, $2, $3, $4, $5, $6)
                         RETURNING id ),
                 ident AS ( INSERT INTO creator_ident (rev_id)
                             VALUES ((SELECT rev.id FROM rev))
                             RETURNING id )
             INSERT INTO creator_edit (editgroup_id, ident_id, rev_id) VALUES
-                ($6, (SELECT ident.id FROM ident), (SELECT rev.id FROM rev))
+                ($7, (SELECT ident.id FROM ident), (SELECT rev.id FROM rev))
             RETURNING *",
         ).bind::<diesel::sql_types::Text, _>(entity.display_name)
             .bind::<diesel::sql_types::Nullable<diesel::sql_types::Text>, _>(entity.given_name)
             .bind::<diesel::sql_types::Nullable<diesel::sql_types::Text>, _>(entity.surname)
             .bind::<diesel::sql_types::Nullable<diesel::sql_types::Text>, _>(entity.orcid)
+            .bind::<diesel::sql_types::Nullable<diesel::sql_types::Text>, _>(entity.wikidata_qid)
             .bind::<diesel::sql_types::Nullable<diesel::sql_types::Json>, _>(entity.extra)
             .bind::<diesel::sql_types::Uuid, _>(editgroup_id)
             .get_result(conn)?;
@@ -644,6 +664,18 @@ impl Server {
             None => get_or_create_editgroup(editor_id, &conn).expect("current editgroup"),
             Some(param) => fcid2uuid(&param)?,
         };
+        if let Some(ref extid) = entity.doi {
+            check_doi(extid)?;
+        }
+        if let Some(ref extid) = entity.pmid {
+            check_pmid(extid)?;
+        }
+        if let Some(ref extid) = entity.pmcid {
+            check_pmcid(extid)?;
+        }
+        if let Some(ref extid) = entity.wikidata_qid {
+            check_wikidata_qid(extid)?;
+        }
 
         let work_id = match entity.work_id {
             Some(work_id) => fcid2uuid(&work_id)?,
@@ -668,14 +700,14 @@ impl Server {
         };
 
         let edit: ReleaseEditRow = diesel::sql_query(
-            "WITH rev AS ( INSERT INTO release_rev (title, release_type, release_status, release_date, doi, isbn13, volume, issue, pages, work_ident_id, container_ident_id, publisher, language, extra_json)
-                        VALUES ($1, $2, $3, $4, $5, $6, $7, $8, $9, $10, $11, $12, $13, $14)
+            "WITH rev AS ( INSERT INTO release_rev (title, release_type, release_status, release_date, doi, pmid, pmcid, wikidata_qid, isbn13, volume, issue, pages, work_ident_id, container_ident_id, publisher, language, extra_json)
+                        VALUES ($1, $2, $3, $4, $5, $6, $7, $8, $9, $10, $11, $12, $13, $14, $15, $16, $17)
                         RETURNING id ),
                 ident AS ( INSERT INTO release_ident (rev_id)
                             VALUES ((SELECT rev.id FROM rev))
                             RETURNING id )
             INSERT INTO release_edit (editgroup_id, ident_id, rev_id) VALUES
-                ($15, (SELECT ident.id FROM ident), (SELECT rev.id FROM rev))
+                ($18, (SELECT ident.id FROM ident), (SELECT rev.id FROM rev))
             RETURNING *",
         ).bind::<diesel::sql_types::Text, _>(entity.title)
             .bind::<diesel::sql_types::Nullable<diesel::sql_types::Text>, _>(entity.release_type)
@@ -683,6 +715,9 @@ impl Server {
             .bind::<diesel::sql_types::Nullable<diesel::sql_types::Date>, _>(
                 entity.release_date.map(|v| v.naive_utc().date()))
             .bind::<diesel::sql_types::Nullable<diesel::sql_types::Text>, _>(entity.doi)
+            .bind::<diesel::sql_types::Nullable<diesel::sql_types::Text>, _>(entity.pmid)
+            .bind::<diesel::sql_types::Nullable<diesel::sql_types::Text>, _>(entity.pmcid)
+            .bind::<diesel::sql_types::Nullable<diesel::sql_types::Text>, _>(entity.wikidata_qid)
             .bind::<diesel::sql_types::Nullable<diesel::sql_types::Text>, _>(entity.isbn13)
             .bind::<diesel::sql_types::Nullable<diesel::sql_types::Text>, _>(entity.volume)
             .bind::<diesel::sql_types::Nullable<diesel::sql_types::Text>, _>(entity.issue)
diff --git a/rust/src/api_wrappers.rs b/rust/src/api_wrappers.rs
index 8be661e1..e66f3ccd 100644
--- a/rust/src/api_wrappers.rs
+++ b/rust/src/api_wrappers.rs
@@ -35,6 +35,8 @@ macro_rules! wrap_entity_handlers {
                 Err(Error(ErrorKind::InvalidFatcatId(e), _)) =>
                     $get_resp::BadRequest(ErrorResponse {
                         message: ErrorKind::InvalidFatcatId(e).to_string() }),
+                Err(Error(ErrorKind::MalformedExternalId(e), _)) =>
+                    $get_resp::BadRequest(ErrorResponse { message: e.to_string() }),
                 Err(e) => {
                     error!("{}", e);
                     $get_resp::GenericError(ErrorResponse { message: e.to_string() })
@@ -58,6 +60,8 @@ macro_rules! wrap_entity_handlers {
                 Err(Error(ErrorKind::InvalidFatcatId(e), _)) =>
                     $post_resp::BadRequest(ErrorResponse {
                         message: ErrorKind::InvalidFatcatId(e).to_string() }),
+                Err(Error(ErrorKind::MalformedExternalId(e), _)) =>
+                    $post_resp::BadRequest(ErrorResponse { message: e.to_string() }),
                 Err(e) => {
                     error!("{}", e);
                     $post_resp::GenericError(ErrorResponse { message: e.to_string() })
@@ -81,6 +85,8 @@ macro_rules! wrap_entity_handlers {
                 Err(Error(ErrorKind::InvalidFatcatId(e), _)) =>
                     $post_batch_resp::BadRequest(ErrorResponse {
                         message: ErrorKind::InvalidFatcatId(e).to_string() }),
+                Err(Error(ErrorKind::MalformedExternalId(e), _)) =>
+                    $post_batch_resp::BadRequest(ErrorResponse { message: e.to_string() }),
                 Err(e) => {
                     error!("{}", e);
                     $post_batch_resp::GenericError(ErrorResponse { message: e.to_string() })
@@ -127,6 +133,8 @@ macro_rules! wrap_lookup_handler {
                     $get_resp::FoundEntity(entity),
                 Err(Error(ErrorKind::Diesel(::diesel::result::Error::NotFound), _)) =>
                     $get_resp::NotFound(ErrorResponse { message: format!("Not found: {}", $idname) }),
+                Err(Error(ErrorKind::MalformedExternalId(e), _)) =>
+                    $get_resp::BadRequest(ErrorResponse { message: e.to_string() }),
                 Err(e) => {
                     error!("{}", e);
                     $get_resp::BadRequest(ErrorResponse { message: e.to_string() })
diff --git a/rust/src/lib.rs b/rust/src/lib.rs
index fd871f55..eff487b3 100644
--- a/rust/src/lib.rs
+++ b/rust/src/lib.rs
@@ -17,6 +17,9 @@ extern crate serde_json;
 #[macro_use]
 extern crate log;
 extern crate data_encoding;
+extern crate regex;
+#[macro_use]
+extern crate lazy_static;
 
 pub mod api_helpers;
 pub mod api_server;
@@ -39,6 +42,10 @@ mod errors {
                 description("invalid fatcat identifier syntax")
                 display("invalid fatcat identifier (expect 26-char base32 encoded): {}", id)
             }
+            MalformedExternalId(id: String) {
+                description("external identifier doesn't match required pattern")
+                display("external identifier doesn't match required pattern")
+            }
         }
     }
 }