Refactor of AlgebraicRelations

.buildkite/build_docs.sh

@@ -0,0 +1,17 @@
+#!/bin/bash
+
+
+pwd; hostname; date
+
+if [ $# -ne 1 ]; then
+    echo "Usage: $0 VERSION"
+    echo "Example: $0 1.10.0"
+    exit 1
+fi
+
+VERSION=$1
+
+module load julia/$VERSION
+
+echo "Building documentation..."
+julia --project=docs -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.status(); Pkg.instantiate(); include("docs/make.jl")'

.buildkite/jobscript.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+pwd; hostname; date
+
+module load julia
+
+echo "Running Tests..."
+julia --project -e 'using Pkg; Pkg.status(); Pkg.test()'
+
+echo "Building Documentation..."
+julia --project=docs -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.status(); Pkg.instantiate(); include("docs/make.jl")'

.buildkite/pipeline.yml

@@ -0,0 +1,7 @@
+steps:
+
+  - label: ":arrow_down: Load AlgebraicJulia pipeline"
+    command: |
+      curl -s https://raw.githubusercontent.com/AlgebraicJulia/.github/main/buildkite/pipeline.yml | buildkite-agent pipeline upload
+
+  - wait

.buildkite/run_tests.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+pwd; hostname; date
+
+if [ $# -ne 1 ]; then
+    echo "Usage: $0 VERSION"
+    echo "Example: $0 1.10.0"
+    exit 1
+fi
+
+VERSION=$1
+
+module load julia/$VERSION
+
+echo "Running tests..."
+julia --project -e "using Pkg; Pkg.status(); Pkg.test()"

Project.toml

@@ -4,22 +4,34 @@ authors = ["bosonbaas <[email protected]>"]
 version = "0.3.1"
 
 [deps]
-AlgebraicPetri = "4f99eebe-17bf-4e98-b6a1-2c4f205a959b"
-AutoHashEquals = "15f4f7f2-30c1-5605-9d31-71845cf9641f"
 Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+FunSQL = "cf6cc811-59f4-4a10-b258-a8547a8f6407"
+JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 LibPQ = "194296ae-ab2e-5f79-8cd4-7183a0a5a0d1"
+Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
+SQLite = "0aa819cd-b072-5ff4-a722-6bc24af294d9"
+Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
+
+[weakdeps]
+DuckDB = "d2f5444f-75bc-4fdf-ac35-56f514c445e1"
+LibPQ = "2196b101-3ac0-4e12-b5a8-532424305d17"
+MySQL = "39abe10b-433b-5dbd-92d4-e302a9df00cd"
+
+[extensions]
+DuckDBAlgRelExt = "DuckDB"
+LibPQAlgRelExt = "LibPQ"
+MySQLACSetsExt = "MySQL"
+SQLiteAlgRelExt = "SQLite"
 
 [compat]
-AlgebraicPetri = "0.6, 0.7"
-AutoHashEquals = "0.2.0, 1, 2"
-Catlab = "0.14"
+Catlab = "0.16"
 DataFrames = "1.0"
-LibPQ = "1.4.0"
-julia = "1.0"
+Reexport = "1.2.2"
+SQLite = "1.6.1"
+julia = "1.6"
 
 [extras]
-SQLite = "0aa819cd-b072-5ff4-a722-6bc24af294d9"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]

ext/DuckDBAlgRelExt.jl

@@ -0,0 +1,35 @@
+module SQLiteInterop
+  using AlgebraicRelations.Schemas
+  using Catlab.CategoricalAlgebra
+  using Tables
+  using ...SQLite
+
+  function AlgebraicRelations.SQLSchema(db::SQLite.DB)
+    sch = SQLSchema()
+    tables = [t.name for t in SQLite.tables(db)]
+    tab_ind = add_parts!(sch, :Table, length(tables), tname=tables)
+    tab2ind = Dict([tables[t] => t for t in tab_ind])
+
+    col2ind = Dict{String, Dict{String, Int64}}()
+    for t in tables
+      col2ind[t] = Dict{String, Int64}()
+      cols = SQLite.columns(db, t)
+      for c in 1:length(cols.cid)
+        type = cols.type[c]
+        if cols.pk[c] == 1
+          type *= " PRIMARY KEY"
+        end
+        c_ind = add_part!(sch, :Column, table=tab2ind[t], cname=cols.name[c], type=type)
+        col2ind[t][cols.name[c]] = c_ind
+      end
+    end
+    for t in tables
+      res = DBInterface.execute(db, "PRAGMA foreign_key_list($t);")
+      for r in res
+        add_part!(sch, :FK, from = col2ind[t][r.from],
+                            to = col2ind[r.table][r.to])
+      end
+    end
+    sch
+  end
+end

ext/LibPQAlgRelExt.jl

@@ -0,0 +1,35 @@
+module SQLiteInterop
+  using AlgebraicRelations.Schemas
+  using Catlab.CategoricalAlgebra
+  using Tables
+  using ...SQLite
+
+  function AlgebraicRelations.SQLSchema(db::SQLite.DB)
+    sch = SQLSchema()
+    tables = [t.name for t in SQLite.tables(db)]
+    tab_ind = add_parts!(sch, :Table, length(tables), tname=tables)
+    tab2ind = Dict([tables[t] => t for t in tab_ind])
+
+    col2ind = Dict{String, Dict{String, Int64}}()
+    for t in tables
+      col2ind[t] = Dict{String, Int64}()
+      cols = SQLite.columns(db, t)
+      for c in 1:length(cols.cid)
+        type = cols.type[c]
+        if cols.pk[c] == 1
+          type *= " PRIMARY KEY"
+        end
+        c_ind = add_part!(sch, :Column, table=tab2ind[t], cname=cols.name[c], type=type)
+        col2ind[t][cols.name[c]] = c_ind
+      end
+    end
+    for t in tables
+      res = DBInterface.execute(db, "PRAGMA foreign_key_list($t);")
+      for r in res
+        add_part!(sch, :FK, from = col2ind[t][r.from],
+                            to = col2ind[r.table][r.to])
+      end
+    end
+    sch
+  end
+end

ext/MySQLAlgRelExt.jl

@@ -0,0 +1,35 @@
+module SQLiteInterop
+  using AlgebraicRelations.Schemas
+  using Catlab.CategoricalAlgebra
+  using Tables
+  using ...SQLite
+
+  function AlgebraicRelations.SQLSchema(db::SQLite.DB)
+    sch = SQLSchema()
+    tables = [t.name for t in SQLite.tables(db)]
+    tab_ind = add_parts!(sch, :Table, length(tables), tname=tables)
+    tab2ind = Dict([tables[t] => t for t in tab_ind])
+
+    col2ind = Dict{String, Dict{String, Int64}}()
+    for t in tables
+      col2ind[t] = Dict{String, Int64}()
+      cols = SQLite.columns(db, t)
+      for c in 1:length(cols.cid)
+        type = cols.type[c]
+        if cols.pk[c] == 1
+          type *= " PRIMARY KEY"
+        end
+        c_ind = add_part!(sch, :Column, table=tab2ind[t], cname=cols.name[c], type=type)
+        col2ind[t][cols.name[c]] = c_ind
+      end
+    end
+    for t in tables
+      res = DBInterface.execute(db, "PRAGMA foreign_key_list($t);")
+      for r in res
+        add_part!(sch, :FK, from = col2ind[t][r.from],
+                            to = col2ind[r.table][r.to])
+      end
+    end
+    sch
+  end
+end

ext/SQLiteAlgRelExt.jl

@@ -0,0 +1,36 @@
+module SQLiteAlgRelExt
+
+using AlgebraicRelations
+using Catlab.CategoricalAlgebra
+using Tables
+using SQLite
+
+function AlgebraicRelations.SQLSchema(db::SQLite.DB)
+  sch = SQLSchema()
+  tables = [t.name for t in SQLite.tables(db)]
+  tab_ind = add_parts!(sch, :Table, length(tables), tname=tables)
+  tab2ind = Dict([tables[t] => t for t in tab_ind])
+
+  col2ind = Dict{String, Dict{String, Int64}}()
+  for t in tables
+    col2ind[t] = Dict{String, Int64}()
+    cols = SQLite.columns(db, t)
+    for c in 1:length(cols.cid)
+      type = cols.type[c]
+      if cols.pk[c] == 1
+        type *= " PRIMARY KEY"
+      end
+      c_ind = add_part!(sch, :Column, table=tab2ind[t], cname=cols.name[c], type=type)
+      col2ind[t][cols.name[c]] = c_ind
+    end
+  end
+  for t in tables
+    res = DBInterface.execute(db, "PRAGMA foreign_key_list($t);")
+    for r in res
+      add_part!(sch, :FK, from = col2ind[t][r.from],
+                          to = col2ind[r.table][r.to])
+    end
+  end
+  sch
+end
+end

src/AlgebraicRelations.jl

@@ -1,6 +1,11 @@
 module AlgebraicRelations
-  include("DB.jl")
-  include("Queries.jl")
-  include("Interface.jl")
-  include("Presentations.jl")
+
+using Reexport
+
+include("Schemas.jl")
+include("Queries.jl")
+
+@reexport using .Schemas
+@reexport using .Queries
+
 end