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-rw-r--r--rust/src/api_helpers.rs84
-rw-r--r--rust/src/api_server.rs55
-rw-r--r--rust/src/api_wrappers.rs8
-rw-r--r--rust/src/lib.rs7
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")
+ }
}
}
}
generated by cgit v1.2.3 (git 2.39.1) at 2024-11-11 19:39:01 +0000