Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Better type resolution #46

Merged
merged 15 commits into from
Feb 15, 2024
Merged

Better type resolution #46

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
15 commits
Select commit Hold shift + click to select a range
50b7d81
Generic implementation of rebase()
xitology Jan 10, 2024
ff5c249
Generic implementation of label()
xitology Jan 10, 2024
64eab4f
Refactoring rendering pipeline to improve type resolution
xitology Feb 2, 2024
9903b2d
Fix missing columns in recursive subquery
xitology Feb 6, 2024
f911244
MS Windows does not like aux.jl
xitology Feb 6, 2024
2ba7e52
Join: bias resolution towards the right branch
xitology Feb 6, 2024
bad05c1
Allow IntAutoDefine to be generated by resolve()
xitology Feb 7, 2024
32c8495
Remove references to REFERENCE_ERROR_TYPE.AMBIGUOUS_NAME
xitology Feb 7, 2024
a07a665
make resolve() idempotent
xitology Feb 7, 2024
e3cee4a
Fix CTE shadowing
xitology Feb 12, 2024
2509106
Fix linking isolated subqueries within iterate()
xitology Feb 13, 2024
a43e24d
Bound() -> Nested(), etc
xitology Feb 13, 2024
a27cd78
Add BoundVariableNode
xitology Feb 14, 2024
c83dd99
IntAutoDefineNode -> PaddingNode
xitology Feb 14, 2024
19212e0
Rename FromKnot -> FromIterate, IntJoin -> RoutedJoin
xitology Feb 15, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
66 changes: 33 additions & 33 deletions docs/src/examples/index.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -655,45 +655,45 @@ query.
("concept_1"."vocabulary_id" = 'SNOMED') AND
("concept_1"."concept_code" = '22298006')
UNION ALL
SELECT "concept_3"."concept_id"
FROM "base_1" AS "concept_2"
SELECT "concept_2"."concept_id"
FROM "base_1" AS "base_2"
JOIN (
SELECT
"concept_relationship_1"."concept_id_1",
"concept_relationship_1"."concept_id_2"
FROM "concept_relationship" AS "concept_relationship_1"
WHERE ("concept_relationship_1"."relationship_id" = 'Is a')
) AS "concept_relationship_2" ON ("concept_2"."concept_id" = "concept_relationship_2"."concept_id_2")
JOIN "concept" AS "concept_3" ON ("concept_relationship_2"."concept_id_1" = "concept_3"."concept_id")
) AS "concept_relationship_2" ON ("base_2"."concept_id" = "concept_relationship_2"."concept_id_2")
JOIN "concept" AS "concept_2" ON ("concept_relationship_2"."concept_id_1" = "concept_2"."concept_id")
),
"base_3" ("concept_id") AS (
SELECT "concept_4"."concept_id"
FROM "concept" AS "concept_4"
"base_4" ("concept_id") AS (
SELECT "concept_3"."concept_id"
FROM "concept" AS "concept_3"
WHERE
("concept_4"."vocabulary_id" = 'SNOMED') AND
("concept_4"."concept_code" = '70422006')
("concept_3"."vocabulary_id" = 'SNOMED') AND
("concept_3"."concept_code" = '70422006')
UNION ALL
SELECT "concept_6"."concept_id"
FROM "base_3" AS "concept_5"
SELECT "concept_4"."concept_id"
FROM "base_4" AS "base_5"
JOIN (
SELECT
"concept_relationship_3"."concept_id_1",
"concept_relationship_3"."concept_id_2"
FROM "concept_relationship" AS "concept_relationship_3"
WHERE ("concept_relationship_3"."relationship_id" = 'Is a')
) AS "concept_relationship_4" ON ("concept_5"."concept_id" = "concept_relationship_4"."concept_id_2")
JOIN "concept" AS "concept_6" ON ("concept_relationship_4"."concept_id_1" = "concept_6"."concept_id")
) AS "concept_relationship_4" ON ("base_5"."concept_id" = "concept_relationship_4"."concept_id_2")
JOIN "concept" AS "concept_4" ON ("concept_relationship_4"."concept_id_1" = "concept_4"."concept_id")
)
SELECT
"condition_occurrence_1"."person_id",
"condition_occurrence_1"."condition_start_date"
FROM "condition_occurrence" AS "condition_occurrence_1"
JOIN (
SELECT "base_2"."concept_id"
FROM "base_1" AS "base_2"
LEFT JOIN "base_3" AS "base_4" ON ("base_2"."concept_id" = "base_4"."concept_id")
WHERE ("base_4"."concept_id" IS NULL)
) AS "concept_7" ON ("condition_occurrence_1"."condition_concept_id" = "concept_7"."concept_id")
SELECT "base_3"."concept_id"
FROM "base_1" AS "base_3"
LEFT JOIN "base_4" AS "base_6" ON ("base_3"."concept_id" = "base_6"."concept_id")
WHERE ("base_6"."concept_id" IS NULL)
) AS "base_7" ON ("condition_occurrence_1"."condition_concept_id" = "base_7"."concept_id")
ORDER BY "condition_occurrence_1"."condition_occurrence_id"
=#

Expand Down Expand Up @@ -920,34 +920,34 @@ Now we have all the components to construct the final query:
("concept_1"."vocabulary_id" = 'SNOMED') AND
("concept_1"."concept_code" = '22298006')
UNION ALL
SELECT "concept_3"."concept_id"
FROM "base_1" AS "concept_2"
SELECT "concept_2"."concept_id"
FROM "base_1" AS "base_2"
JOIN (
SELECT
"concept_relationship_1"."concept_id_1",
"concept_relationship_1"."concept_id_2"
FROM "concept_relationship" AS "concept_relationship_1"
WHERE ("concept_relationship_1"."relationship_id" = 'Is a')
) AS "concept_relationship_2" ON ("concept_2"."concept_id" = "concept_relationship_2"."concept_id_2")
JOIN "concept" AS "concept_3" ON ("concept_relationship_2"."concept_id_1" = "concept_3"."concept_id")
) AS "concept_relationship_2" ON ("base_2"."concept_id" = "concept_relationship_2"."concept_id_2")
JOIN "concept" AS "concept_2" ON ("concept_relationship_2"."concept_id_1" = "concept_2"."concept_id")
),
"base_3" ("concept_id") AS (
SELECT "concept_4"."concept_id"
FROM "concept" AS "concept_4"
"base_4" ("concept_id") AS (
SELECT "concept_3"."concept_id"
FROM "concept" AS "concept_3"
WHERE
("concept_4"."vocabulary_id" = 'Visit') AND
("concept_4"."concept_code" = 'IP')
("concept_3"."vocabulary_id" = 'Visit') AND
("concept_3"."concept_code" = 'IP')
UNION ALL
SELECT "concept_6"."concept_id"
FROM "base_3" AS "concept_5"
SELECT "concept_4"."concept_id"
FROM "base_4" AS "base_5"
JOIN (
SELECT
"concept_relationship_3"."concept_id_1",
"concept_relationship_3"."concept_id_2"
FROM "concept_relationship" AS "concept_relationship_3"
WHERE ("concept_relationship_3"."relationship_id" = 'Is a')
) AS "concept_relationship_4" ON ("concept_5"."concept_id" = "concept_relationship_4"."concept_id_2")
JOIN "concept" AS "concept_6" ON ("concept_relationship_4"."concept_id_1" = "concept_6"."concept_id")
) AS "concept_relationship_4" ON ("base_5"."concept_id" = "concept_relationship_4"."concept_id_2")
JOIN "concept" AS "concept_4" ON ("concept_relationship_4"."concept_id_1" = "concept_4"."concept_id")
)
SELECT
"condition_occurrence_3"."person_id",
Expand All @@ -962,13 +962,13 @@ Now we have all the components to construct the final query:
"condition_occurrence_1"."person_id",
"condition_occurrence_1"."condition_start_date"
FROM "condition_occurrence" AS "condition_occurrence_1"
JOIN "base_1" AS "base_2" ON ("condition_occurrence_1"."condition_concept_id" = "base_2"."concept_id")
JOIN "base_1" AS "base_3" ON ("condition_occurrence_1"."condition_concept_id" = "base_3"."concept_id")
ORDER BY "condition_occurrence_1"."condition_occurrence_id"
) AS "condition_occurrence_2"
WHERE (EXISTS (
SELECT NULL AS "_"
FROM "visit_occurrence" AS "visit_occurrence_1"
JOIN "base_3" AS "base_4" ON ("visit_occurrence_1"."visit_concept_id" = "base_4"."concept_id")
JOIN "base_4" AS "base_6" ON ("visit_occurrence_1"."visit_concept_id" = "base_6"."concept_id")
WHERE
("visit_occurrence_1"."person_id" = "condition_occurrence_2"."person_id") AND
("condition_occurrence_2"."condition_start_date" BETWEEN "visit_occurrence_1"."visit_start_date" AND "visit_occurrence_1"."visit_end_date")
Expand Down
60 changes: 36 additions & 24 deletions docs/src/guide/index.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1283,13 +1283,13 @@ immediate subtypes as the function:

DBInterface.execute(conn, q) |> DataFrame
#=>
2×7 DataFrame
2×10 DataFrame
Row │ concept_id concept_name domain_id vocabulary_id conc ⋯
│ Int64 String String String Stri ⋯
─────┼──────────────────────────────────────────────────────────────────────────
1 │ 4329847 Myocardial infarction Condition SNOMED Clin ⋯
2 │ 312327 Acute myocardial infarction Condition SNOMED Clin
3 columns omitted
6 columns omitted
=#

But how can we fetch not just immediate, but all of the subtypes of a concept?
Expand Down Expand Up @@ -1317,50 +1317,62 @@ This is exactly the action of the [`Iterate`](@ref) node.

render(conn, q) |> print
#=>
WITH RECURSIVE "concept_2" ("concept_id", "concept_name", "domain_id", "vocabulary_id", "concept_class_id", "standard_concept", "concept_code") AS (
WITH RECURSIVE "__1" ("concept_id", "concept_name", "domain_id", "vocabulary_id", "concept_class_id", "standard_concept", "concept_code", "valid_start_date", "valid_end_date", "invalid_reason") AS (
SELECT
"concept_1"."concept_id",
"concept_1"."concept_name",
"concept_1"."domain_id",
"concept_1"."vocabulary_id",
"concept_1"."concept_class_id",
"concept_1"."standard_concept",
"concept_1"."concept_code"
"concept_1"."concept_code",
"concept_1"."valid_start_date",
"concept_1"."valid_end_date",
"concept_1"."invalid_reason"
FROM "concept" AS "concept_1"
WHERE ("concept_1"."concept_name" = 'Myocardial infarction')
UNION ALL
SELECT
"concept_3"."concept_id",
"concept_3"."concept_name",
"concept_3"."domain_id",
"concept_3"."vocabulary_id",
"concept_3"."concept_class_id",
"concept_3"."standard_concept",
"concept_3"."concept_code"
FROM "concept" AS "concept_3"
"concept_2"."concept_id",
"concept_2"."concept_name",
"concept_2"."domain_id",
"concept_2"."vocabulary_id",
"concept_2"."concept_class_id",
"concept_2"."standard_concept",
"concept_2"."concept_code",
"concept_relationship_2"."valid_start_date",
"concept_relationship_2"."valid_end_date",
"concept_relationship_2"."invalid_reason"
FROM "concept" AS "concept_2"
JOIN (
SELECT
"concept_relationship_1"."valid_start_date",
"concept_relationship_1"."valid_end_date",
"concept_relationship_1"."invalid_reason",
"concept_relationship_1"."concept_id_2",
"concept_relationship_1"."concept_id_1"
FROM "concept_relationship" AS "concept_relationship_1"
WHERE ("concept_relationship_1"."relationship_id" = 'Is a')
) AS "concept_relationship_2" ON ("concept_3"."concept_id" = "concept_relationship_2"."concept_id_1")
JOIN "concept_2" AS "concept_4" ON ("concept_relationship_2"."concept_id_2" = "concept_4"."concept_id")
) AS "concept_relationship_2" ON ("concept_2"."concept_id" = "concept_relationship_2"."concept_id_1")
JOIN "__1" AS "__2" ON ("concept_relationship_2"."concept_id_2" = "__2"."concept_id")
)
SELECT
"concept_5"."concept_id",
"concept_5"."concept_name",
"concept_5"."domain_id",
"concept_5"."vocabulary_id",
"concept_5"."concept_class_id",
"concept_5"."standard_concept",
"concept_5"."concept_code"
FROM "concept_2" AS "concept_5"
"concept_3"."concept_id",
"concept_3"."concept_name",
"concept_3"."domain_id",
"concept_3"."vocabulary_id",
"concept_3"."concept_class_id",
"concept_3"."standard_concept",
"concept_3"."concept_code",
"concept_3"."valid_start_date",
"concept_3"."valid_end_date",
"concept_3"."invalid_reason"
FROM "__1" AS "concept_3"
=#

DBInterface.execute(conn, q) |> DataFrame
#=>
6×7 DataFrame
6×10 DataFrame
Row │ concept_id concept_name domain_id vocabulary_id ⋯
│ Int64 String String String ⋯
─────┼──────────────────────────────────────────────────────────────────────────
Expand All @@ -1370,6 +1382,6 @@ This is exactly the action of the [`Iterate`](@ref) node.
4 │ 438170 Acute myocardial infarction of i… Condition SNOMED
5 │ 438438 Acute myocardial infarction of a… Condition SNOMED ⋯
6 │ 444406 Acute subendocardial infarction Condition SNOMED
3 columns omitted
6 columns omitted
=#

Loading
Loading