diff options
Diffstat (limited to 'rust/src/database_entity_crud.rs')
| -rw-r--r-- | rust/src/database_entity_crud.rs | 626 |
1 files changed, 618 insertions, 8 deletions
diff --git a/rust/src/database_entity_crud.rs b/rust/src/database_entity_crud.rs index e97e134b..b8ff195a 100644 --- a/rust/src/database_entity_crud.rs +++ b/rust/src/database_entity_crud.rs @@ -1,11 +1,13 @@ +use sha1::Sha1; +use chrono; use diesel::prelude::*; use diesel::{self, insert_into}; use database_schema::*; use database_models::*; use errors::*; use fatcat_api::models::*; -use api_helpers::{FatCatId, DbConn}; +use api_helpers::*; use uuid::Uuid; use std::marker::Sized; use std::str::FromStr; @@ -55,7 +57,7 @@ pub trait EntityCrud where Self: Sized { fn db_get_history(conn: &DbConn, ident: FatCatId, limit: Option<i64>) -> Result<Vec<EntityHistoryEntry>>; // Entity-specific Methods - fn from_row(conn: &DbConn, rev_row: Self::RevRow, ident_row: Option<Self::IdentRow>) -> Result<Self>; + fn db_from_row(conn: &DbConn, rev_row: Self::RevRow, ident_row: Option<Self::IdentRow>) -> Result<Self>; fn db_insert_rev(&self, conn: &DbConn) -> Result<Uuid>; fn db_insert_revs(conn: &DbConn, models: &[&Self]) -> Result<Vec<Uuid>>; } @@ -80,7 +82,7 @@ macro_rules! generic_db_get { .inner_join($rev_table::table) .first(conn)?; - Self::from_row(conn, rev, Some(ident)) + Self::db_from_row(conn, rev, Some(ident)) } } } @@ -92,12 +94,13 @@ macro_rules! generic_db_get_rev { .find(rev_id) .first(conn)?; - Self::from_row(conn, rev, None) + Self::db_from_row(conn, rev, None) } } } macro_rules! generic_db_create { + // TODO: this path should call generic_db_create_batch ($ident_table: ident, $edit_table: ident) => { fn db_create(&self, conn: &DbConn, edit_context: &EditContext) -> Result<Self::EditRow> { let rev_id = self.db_insert_rev(conn)?; @@ -128,7 +131,7 @@ macro_rules! generic_db_create_batch { is_live: edit_context.autoapprove, redirect_id: None, }) - .collect::<Vec<WorkIdentNewRow>>()) + .collect::<Vec<Self::IdentNewRow>>()) .returning($ident_table::id) .get_results(conn)?; let edits: Vec<Self::EditRow> = insert_into($edit_table::table) @@ -141,7 +144,7 @@ macro_rules! generic_db_create_batch { prev_rev: None, extra_json: edit_context.extra_json.clone(), }) - .collect::<Vec<WorkEditNewRow>>()) + .collect::<Vec<Self::EditNewRow>>()) .get_results(conn)?; Ok(edits) } @@ -209,7 +212,7 @@ macro_rules! generic_db_delete { macro_rules! generic_db_get_history { ($edit_table:ident) => { fn db_get_history(conn: &DbConn, ident: FatCatId, limit: Option<i64>) -> Result<Vec<EntityHistoryEntry>> { - let limit = limit.unwrap_or(50); // XXX: make a static + let limit = limit.unwrap_or(50); // TODO: make a static let rows: Vec<(EditgroupRow, ChangelogRow, Self::EditRow)> = editgroup::table .inner_join(changelog::table) @@ -239,6 +242,613 @@ macro_rules! generic_db_insert_rev { } } +impl EntityCrud for ContainerEntity { + type EditRow = ContainerEditRow; + type EditNewRow = ContainerEditNewRow; + type IdentRow = ContainerIdentRow; + type IdentNewRow = ContainerIdentNewRow; + type RevRow = ContainerRevRow; + + generic_parse_editgroup_id!(); + generic_db_get!(container_ident, container_rev); + generic_db_get_rev!(container_rev); + generic_db_create!(container_ident, container_edit); + generic_db_create_batch!(container_ident, container_edit); + generic_db_update!(container_ident, container_edit); + generic_db_delete!(container_ident, container_edit); + generic_db_get_history!(container_edit); + generic_db_insert_rev!(); + + fn db_from_row(_conn: &DbConn, rev_row: Self::RevRow, ident_row: Option<Self::IdentRow>) -> Result<Self> { + + let (state, ident_id, redirect_id) = match ident_row { + Some(i) => ( + Some(i.state().unwrap().shortname()), + Some(FatCatId::from_uuid(&i.id).to_string()), + i.redirect_id.map(|u| FatCatId::from_uuid(&u).to_string()), + ), + None => (None, None, None), + }; + + Ok(ContainerEntity { + issnl: rev_row.issnl, + wikidata_qid: rev_row.wikidata_qid, + publisher: rev_row.publisher, + name: rev_row.name, + abbrev: rev_row.abbrev, + coden: rev_row.coden, + state: state, + ident: ident_id, + revision: Some(rev_row.id.to_string()), + redirect: redirect_id, + extra: rev_row.extra_json, + editgroup_id: None, + }) + } + + fn db_insert_revs(conn: &DbConn, models: &[&Self]) -> Result<Vec<Uuid>> { + + // first verify external identifier syntax + for entity in models { + if let Some(ref extid) = entity.wikidata_qid { + check_wikidata_qid(extid)?; + } + if let Some(ref extid) = entity.issnl { + check_issn(extid)?; + } + } + + let rev_ids: Vec<Uuid> = insert_into(container_rev::table) + .values(models.iter() + .map(|model| ContainerRevNewRow { + name: model.name.clone(), + publisher: model.publisher.clone(), + issnl: model.issnl.clone(), + wikidata_qid: model.wikidata_qid.clone(), + abbrev: model.abbrev.clone(), + coden: model.coden.clone(), + extra_json: model.extra.clone() + }) + .collect::<Vec<ContainerRevNewRow>>()) + .returning(container_rev::id) + .get_results(conn)?; + Ok(rev_ids) + } +} + +impl EntityCrud for CreatorEntity { + type EditRow = CreatorEditRow; + type EditNewRow = CreatorEditNewRow; + type IdentRow = CreatorIdentRow; + type IdentNewRow = CreatorIdentNewRow; + type RevRow = CreatorRevRow; + + generic_parse_editgroup_id!(); + generic_db_get!(creator_ident, creator_rev); + generic_db_get_rev!(creator_rev); + generic_db_create!(creator_ident, creator_edit); + generic_db_create_batch!(creator_ident, creator_edit); + generic_db_update!(creator_ident, creator_edit); + generic_db_delete!(creator_ident, creator_edit); + generic_db_get_history!(creator_edit); + generic_db_insert_rev!(); + + fn db_from_row(_conn: &DbConn, rev_row: Self::RevRow, ident_row: Option<Self::IdentRow>) -> Result<Self> { + let (state, ident_id, redirect_id) = match ident_row { + Some(i) => ( + Some(i.state().unwrap().shortname()), + Some(FatCatId::from_uuid(&i.id).to_string()), + i.redirect_id.map(|u| FatCatId::from_uuid(&u).to_string()), + ), + None => (None, None, None), + }; + Ok(CreatorEntity { + display_name: rev_row.display_name, + given_name: rev_row.given_name, + surname: rev_row.surname, + orcid: rev_row.orcid, + wikidata_qid: rev_row.wikidata_qid, + state: state, + ident: ident_id, + revision: Some(rev_row.id.to_string()), + redirect: redirect_id, + editgroup_id: None, + extra: rev_row.extra_json, + }) + } + + fn db_insert_revs(conn: &DbConn, models: &[&Self]) -> Result<Vec<Uuid>> { + + // first verify external identifier syntax + for entity in models { + if let Some(ref extid) = entity.orcid { + check_orcid(extid)?; + } + if let Some(ref extid) = entity.wikidata_qid { + check_wikidata_qid(extid)?; + } + } + + let rev_ids: Vec<Uuid> = insert_into(creator_rev::table) + .values(models.iter() + .map(|model| CreatorRevNewRow { + display_name: model.display_name.clone(), + given_name: model.given_name.clone(), + surname: model.surname.clone(), + orcid: model.orcid.clone(), + wikidata_qid: model.wikidata_qid.clone(), + extra_json: model.extra.clone() + }) + .collect::<Vec<CreatorRevNewRow>>()) + .returning(creator_rev::id) + .get_results(conn)?; + Ok(rev_ids) + } +} + +impl EntityCrud for FileEntity { + type EditRow = FileEditRow; + type EditNewRow = FileEditNewRow; + type IdentRow = FileIdentRow; + type IdentNewRow = FileIdentNewRow; + type RevRow = FileRevRow; + + generic_parse_editgroup_id!(); + generic_db_get!(file_ident, file_rev); + generic_db_get_rev!(file_rev); + generic_db_create!(file_ident, file_edit); + generic_db_create_batch!(file_ident, file_edit); + generic_db_update!(file_ident, file_edit); + generic_db_delete!(file_ident, file_edit); + generic_db_get_history!(file_edit); + generic_db_insert_rev!(); + + fn db_from_row(conn: &DbConn, rev_row: Self::RevRow, ident_row: Option<Self::IdentRow>) -> Result<Self> { + let (state, ident_id, redirect_id) = match ident_row { + Some(i) => ( + Some(i.state().unwrap().shortname()), + Some(FatCatId::from_uuid(&i.id).to_string()), + i.redirect_id.map(|u| FatCatId::from_uuid(&u).to_string()), + ), + None => (None, None, None), + }; + + let releases: Vec<FatCatId> = file_release::table + .filter(file_release::file_rev.eq(rev_row.id)) + .get_results(conn)? + .into_iter() + .map(|r: FileReleaseRow| FatCatId::from_uuid(&r.target_release_ident_id)) + .collect(); + + let urls: Vec<FileEntityUrls> = file_rev_url::table + .filter(file_rev_url::file_rev.eq(rev_row.id)) + .get_results(conn)? + .into_iter() + .map(|r: FileRevUrlRow| FileEntityUrls { + rel: r.rel, + url: r.url, + }) + .collect(); + + Ok(FileEntity { + sha1: rev_row.sha1, + sha256: rev_row.sha256, + md5: rev_row.md5, + size: rev_row.size.map(|v| v as i64), + urls: Some(urls), + mimetype: rev_row.mimetype, + releases: Some(releases.iter().map(|fcid| fcid.to_string()).collect()), + state: state, + ident: ident_id, + revision: Some(rev_row.id.to_string()), + redirect: redirect_id, + editgroup_id: None, + extra: rev_row.extra_json, + }) + } + + fn db_insert_revs(conn: &DbConn, models: &[&Self]) -> Result<Vec<Uuid>> { + + let rev_ids: Vec<Uuid> = insert_into(file_rev::table) + .values(models.iter() + .map(|model| FileRevNewRow { + size: model.size, + sha1: model.sha1.clone(), + sha256: model.sha256.clone(), + md5: model.md5.clone(), + mimetype: model.mimetype.clone(), + extra_json: model.extra.clone() + }) + .collect::<Vec<FileRevNewRow>>()) + .returning(file_rev::id) + .get_results(conn)?; + + let mut file_release_rows: Vec<FileReleaseRow> = vec![]; + let mut file_url_rows: Vec<FileRevUrlNewRow> = vec![]; + + for (model, rev_id) in models.iter().zip(rev_ids.iter()) { + match &model.releases { + None => (), + Some(release_list) => { + let these_release_rows: Vec<FileReleaseRow> = release_list + .iter() + .map(|r| FileReleaseRow { + file_rev: rev_id.clone(), + target_release_ident_id: fcid2uuid(r) + // XXX: shouldn't expect + .expect("invalid fatcat identifier"), + }) + .collect(); + file_release_rows.extend(these_release_rows); + } + }; + + match &model.urls { + None => (), + Some(url_list) => { + let these_url_rows: Vec<FileRevUrlNewRow> = url_list + .into_iter() + .map(|u| FileRevUrlNewRow { + file_rev: rev_id.clone(), + rel: u.rel.clone(), + url: u.url.clone(), + }) + .collect(); + file_url_rows.extend(these_url_rows); + } + }; + } + + if !file_release_rows.is_empty() { + // TODO: shouldn't it be "file_rev_release"? + insert_into(file_release::table) + .values(file_release_rows) + .execute(conn)?; + } + + if !file_url_rows.is_empty() { + insert_into(file_rev_url::table) + .values(file_url_rows) + .execute(conn)?; + } + + Ok(rev_ids) + } +} + +impl EntityCrud for ReleaseEntity { + type EditRow = ReleaseEditRow; + type EditNewRow = ReleaseEditNewRow; + type IdentRow = ReleaseIdentRow; + type IdentNewRow = ReleaseIdentNewRow; + type RevRow = ReleaseRevRow; + + generic_parse_editgroup_id!(); + generic_db_get!(release_ident, release_rev); + generic_db_get_rev!(release_rev); + //generic_db_create!(release_ident, release_edit); + //generic_db_create_batch!(release_ident, release_edit); + generic_db_update!(release_ident, release_edit); + generic_db_delete!(release_ident, release_edit); + generic_db_get_history!(release_edit); + generic_db_insert_rev!(); + + fn db_create(&self, conn: &DbConn, edit_context: &EditContext) -> Result<Self::EditRow> { + let mut edits = Self::db_create_batch(conn, edit_context, &vec![self])?; + // probably a more elegant way to destroy the vec and take first element + Ok(edits.pop().unwrap()) + } + + fn db_create_batch(conn: &DbConn, edit_context: &EditContext, models: &[&Self]) -> Result<Vec<Self::EditRow>> { + // This isn't the generic implementation because we need to create Work entities for each + // of the release entities passed (at least in the common case) + + // Generate the set of new work entities to insert (usually one for each release, but some + // releases might be pointed to a work already) + let mut new_work_models: Vec<&WorkEntity> = vec![]; + for entity in models { + if entity.work_id.is_none() { + new_work_models.push(&WorkEntity { + ident: None, + revision: None, + redirect: None, + state: None, + editgroup_id: None, + extra: None, + }); + }; + } + + // create the works, then pluck the list of idents from the result + let new_work_edits = WorkEntity::db_create_batch(conn, edit_context, new_work_models.as_slice())?; + let mut new_work_ids: Vec<Uuid> = new_work_edits.iter().map(|edit| edit.ident_id).collect(); + + // Copy all the release models, and ensure that each has work_id set, using the new work + // idents. There should be one new work ident for each release missing one. + let models_with_work_ids: Vec<Self> = models.iter().map(|model| { + let mut model = (*model).clone(); + if model.work_id.is_none() { + model.work_id = Some(FatCatId::from_uuid(&new_work_ids.pop().unwrap()).to_string()) + } + model + }).collect(); + let model_refs: Vec<&Self> = models_with_work_ids.iter().map(|s| s).collect(); + let models = model_refs.as_slice(); + + // The rest here is copy/pasta from the generic (how to avoid copypasta?) + let rev_ids: Vec<Uuid> = Self::db_insert_revs(conn, models)?; + let ident_ids: Vec<Uuid> = insert_into(release_ident::table) + .values(rev_ids.iter() + .map(|rev_id| Self::IdentNewRow { + rev_id: Some(rev_id.clone()), + is_live: edit_context.autoapprove, + redirect_id: None, + }) + .collect::<Vec<Self::IdentNewRow>>()) + .returning(release_ident::id) + .get_results(conn)?; + let edits: Vec<Self::EditRow> = insert_into(release_edit::table) + .values(rev_ids.into_iter().zip(ident_ids.into_iter()) + .map(|(rev_id, ident_id)| Self::EditNewRow { + editgroup_id: edit_context.editgroup_id.to_uuid(), + rev_id: Some(rev_id), + ident_id: ident_id, + redirect_id: None, + prev_rev: None, + extra_json: edit_context.extra_json.clone(), + }) + .collect::<Vec<Self::EditNewRow>>()) + .get_results(conn)?; + Ok(edits) + } + + fn db_from_row(conn: &DbConn, rev_row: Self::RevRow, ident_row: Option<Self::IdentRow>) -> Result<Self> { + let (state, ident_id, redirect_id) = match ident_row { + Some(i) => ( + Some(i.state().unwrap().shortname()), + Some(FatCatId::from_uuid(&i.id).to_string()), + i.redirect_id.map(|u| FatCatId::from_uuid(&u).to_string()), + ), + None => (None, None, None), + }; + + let refs: Vec<ReleaseRef> = release_ref::table + .filter(release_ref::release_rev.eq(rev_row.id)) + .order(release_ref::index_val.asc()) + .get_results(conn) + .expect("fetch release refs") + .into_iter() + .map(|r: ReleaseRefRow| ReleaseRef { + index: r.index_val, + key: r.key, + extra: r.extra_json, + container_title: r.container_title, + year: r.year, + title: r.title, + locator: r.locator, + target_release_id: r.target_release_ident_id.map(|v| FatCatId::from_uuid(&v).to_string()), + }) + .collect(); + + let contribs: Vec<ReleaseContrib> = release_contrib::table + .filter(release_contrib::release_rev.eq(rev_row.id)) + .order(( + release_contrib::role.asc(), + release_contrib::index_val.asc(), + )) + .get_results(conn) + .expect("fetch release refs") + .into_iter() + .map(|c: ReleaseContribRow| ReleaseContrib { + index: c.index_val, + raw_name: c.raw_name, + role: c.role, + extra: c.extra_json, + creator_id: c.creator_ident_id.map(|v| FatCatId::from_uuid(&v).to_string()), + creator: None, + }) + .collect(); + + let abstracts: Vec<ReleaseEntityAbstracts> = release_rev_abstract::table + .inner_join(abstracts::table) + .filter(release_rev_abstract::release_rev.eq(rev_row.id)) + .get_results(conn)? + .into_iter() + .map( + |r: (ReleaseRevAbstractRow, AbstractsRow)| ReleaseEntityAbstracts { + sha1: Some(r.0.abstract_sha1), + mimetype: r.0.mimetype, + lang: r.0.lang, + content: Some(r.1.content), + }, + ) + .collect(); + + Ok(ReleaseEntity { + title: rev_row.title, + release_type: rev_row.release_type, + release_status: rev_row.release_status, + release_date: rev_row.release_date + .map(|v| chrono::DateTime::from_utc(v.and_hms(0, 0, 0), chrono::Utc)), + doi: rev_row.doi, + pmid: rev_row.pmid, + pmcid: rev_row.pmcid, + isbn13: rev_row.isbn13, + core_id: rev_row.core_id, + wikidata_qid: rev_row.wikidata_qid, + volume: rev_row.volume, + issue: rev_row.issue, + pages: rev_row.pages, + files: None, + container: None, + container_id: rev_row.container_ident_id.map(|u| FatCatId::from_uuid(&u).to_string()), + publisher: rev_row.publisher, + language: rev_row.language, + work_id: Some(FatCatId::from_uuid(&rev_row.work_ident_id).to_string()), + refs: Some(refs), + contribs: Some(contribs), + abstracts: Some(abstracts), + state: state, + ident: ident_id, + revision: Some(rev_row.id.to_string()), + redirect: redirect_id, + editgroup_id: None, + extra: rev_row.extra_json, + }) + } + + fn db_insert_revs(conn: &DbConn, models: &[&Self]) -> Result<Vec<Uuid>> { + + // first verify external identifier syntax + for entity in models { + 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 rev_ids: Vec<Uuid> = insert_into(release_rev::table) + .values(models.iter() + .map(|model| ReleaseRevNewRow { + title: model.title.clone(), + release_type: model.release_type.clone(), + release_status: model.release_status.clone(), + release_date: model.release_date.map(|v| v.naive_utc().date()), + doi: model.doi.clone(), + pmid: model.pmid.clone(), + pmcid: model.pmcid.clone(), + wikidata_qid: model.wikidata_qid.clone(), + isbn13: model.isbn13.clone(), + core_id: model.core_id.clone(), + volume: model.volume.clone(), + issue: model.issue.clone(), + pages: model.pages.clone(), + work_ident_id: model.work_id + .clone() + .map(|s| FatCatId::from_str(&s).expect("invalid fatcat identifier").to_uuid()) + .expect("release_revs must have a work_id by the time they are inserted; this is an internal soundness error"), + container_ident_id: model.container_id + .clone() + .map(|s| FatCatId::from_str(&s).expect("invalid fatcat identifier").to_uuid()), + publisher: model.publisher.clone(), + language: model.language.clone(), + extra_json: model.extra.clone() + }) + .collect::<Vec<ReleaseRevNewRow>>()) + .returning(release_rev::id) + .get_results(conn)?; + + let mut release_ref_rows: Vec<ReleaseRefNewRow> = vec![]; + let mut release_contrib_rows: Vec<ReleaseContribNewRow> = vec![]; + + for (model, rev_id) in models.iter().zip(rev_ids.iter()) { + match &model.refs { + None => (), + Some(ref_list) => { + let these_ref_rows: Vec<ReleaseRefNewRow> = ref_list + .iter() + .map(|r| ReleaseRefNewRow { + release_rev: rev_id.clone(), + target_release_ident_id: r.target_release_id + .clone() + .map(|v| fcid2uuid(&v).expect("valid fatcat identifier")), + index_val: r.index, + key: r.key.clone(), + container_title: r.container_title.clone(), + year: r.year, + title: r.title.clone(), + locator: r.locator.clone(), + extra_json: r.extra.clone(), + }) + .collect(); + release_ref_rows.extend(these_ref_rows); + } + }; + + match &model.contribs { + None => (), + Some(contrib_list) => { + let these_contrib_rows: Vec<ReleaseContribNewRow> = contrib_list + .iter() + .map(|c| ReleaseContribNewRow { + release_rev: rev_id.clone(), + creator_ident_id: c.creator_id + .clone() + // XXX: shouldn't have these expects + .map(|v| fcid2uuid(&v).expect("valid fatcat identifier")), + raw_name: c.raw_name.clone(), + index_val: c.index, + role: c.role.clone(), + extra_json: c.extra.clone(), + }) + .collect(); + release_contrib_rows.extend(these_contrib_rows); + } + }; + + // TODO: this part still isn't parallelized + if let Some(abstract_list) = &model.abstracts { + // For rows that specify content, we need to insert the abstract if it doesn't exist + // already + let new_abstracts: Vec<AbstractsRow> = abstract_list + .iter() + .filter(|ea| ea.content.is_some()) + .map(|c| AbstractsRow { + sha1: Sha1::from(c.content.clone().unwrap()).hexdigest(), + content: c.content.clone().unwrap(), + }) + .collect(); + if !new_abstracts.is_empty() { + // Sort of an "upsert"; only inserts new abstract rows if they don't already exist + insert_into(abstracts::table) + .values(&new_abstracts) + .on_conflict(abstracts::sha1) + .do_nothing() + .execute(conn)?; + } + let release_abstract_rows: Vec<ReleaseRevAbstractNewRow> = abstract_list + .into_iter() + .map(|c| ReleaseRevAbstractNewRow { + release_rev: rev_id.clone(), + abstract_sha1: match c.content { + Some(ref content) => Sha1::from(content).hexdigest(), + // XXX: shouldn't have these expects + None => c.sha1.clone().expect("either abstract_sha1 or content is required"), + }, + lang: c.lang.clone(), + mimetype: c.mimetype.clone(), + }) + .collect(); + insert_into(release_rev_abstract::table) + .values(release_abstract_rows) + .execute(conn)?; + } + } + + if !release_ref_rows.is_empty() { + insert_into(release_ref::table) + .values(release_ref_rows) + .execute(conn)?; + } + + if !release_contrib_rows.is_empty() { + insert_into(release_contrib::table) + .values(release_contrib_rows) + .execute(conn)?; + } + + Ok(rev_ids) + } +} + impl EntityCrud for WorkEntity { type EditRow = WorkEditRow; type EditNewRow = WorkEditNewRow; @@ -256,7 +866,7 @@ impl EntityCrud for WorkEntity { generic_db_get_history!(work_edit); generic_db_insert_rev!(); - fn from_row(conn: &DbConn, rev_row: Self::RevRow, ident_row: Option<Self::IdentRow>) -> Result<Self> { + fn db_from_row(_conn: &DbConn, rev_row: Self::RevRow, ident_row: Option<Self::IdentRow>) -> Result<Self> { let (state, ident_id, redirect_id) = match ident_row { Some(i) => ( |