MySQL test

.github/workflows/ci.yml

@@ -46,10 +46,37 @@ jobs:
             ${{ runner.os }}-
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
+
       - uses: julia-actions/julia-processcoverage@v1
       - uses: codecov/codecov-action@v1
         with:
           file: lcov.info
+  job1:
+    ## The type of runner that the job will run on,
+    ## here it runs on ubuntu latest
+    runs-on: ubuntu-latest
+    steps:
+      - name: step 1
+        ## Reference your environment variables
+        run: echo "The mysqlport is:${{secrets.MYSQL_PORT}}mysqluser:${{secrets.MYSQL_USER}}
+            mysqlhost:${{secrets.MYSQL_HOST}}
+            mysqlpassword:${{secrets.MYSQL_PASSWORD}}
+            postgresuser:${{secrets.POSTGRES_USER}}
+            postgreshost:${{secrets.POSTGRES_HOST}}
+            postgresport:${{secrets.POSTGRES_PORT}}
+            postgrespassword:${{secrets.POSTGRES_PASSWORD}}"
+  job2:
+    runs-on: ubuntu-latest
+    steps:
+      - name: step 1
+        ## Another way reference your environment variables
+        run: echo "The mysqlport is:${{secrets.MYSQL_PORT}}mysqluser:${{secrets.MYSQL_USER}}
+            mysqlhost:${{secrets.MYSQL_HOST}}
+            mysqlpassword:${{secrets.MYSQL_PASSWORD}}
+            postgresuser:${{secrets.POSTGRES_USER}}
+            postgreshost:${{secrets.POSTGRES_HOST}}
+            postgresport:${{secrets.POSTGRES_PORT}}
+            postgrespassword:${{secrets.POSTGRES_PASSWORD}}"
   docs:
     name: Documentation
     runs-on: ubuntu-latest
@@ -60,3 +87,4 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+

docs/make.jl

@@ -1,5 +1,23 @@
 using Documenter, Example
 
-makedocs(modules = [Example], sitename = "Example.jl")
+makedocs(;
+        modules = [DBConnector],
+        authors = "Jacob Zelko (aka TheCedarPrince) <[email protected]> and Fareeda",
+        repo =  "https://github.com/JuliaDatabases/DBConnector.jl",
+        sitename = "DBConnector.jl",
+        format = Documenter.HTML(;
+            prettyurls = get(ENV, "CI", "false") == "true",
+            canonical = "https://github.com/JuliaDatabases/DBConnector.jl"
+            edit_link = "dev",
+	footer = "Created by [Jacob Zelko](https://jacobzelko.com) & [Georgia Tech Research Institute](https://www.gtri.gatech.edu). [License](https://github.com/JuliaHealth/OMOPCDMCohortCreator.jl/blob/main/LICENSE)"
+    ),
+    pages = [
+        "Home" => "index.md",
+        "Functions" => "Functions.md"
+    ],
 
-deploydocs(repo = "github.com/quinnj/Example.jl.git", push_preview = true)
+)
+deploydocs(repo = "github.com/quinnj/Example.jl.git",
+             push_preview = true,
+
+    )

docs/src/Functions.md

@@ -0,0 +1,54 @@
+# Functions
+
+```@contents
+Pages = ["Functions.md"]
+```
+
+## _dbconnect()
+
+This Function is dedicated to expand the range of connection between The [OMOPCDMCohortCreator](https://github.com/JuliaHealth/OMOPCDMCohortCreator.jl) with databases.
+Databases exist are SQLite, MySQL, PostgreSQL.
+In the upcoming sections, we will learn about these tools.
+
+### SQLite
+
+Assuming your data exists on a SQLite database and you want to connect it to the OMOPCDMCohortCreator.
+
+calling the function
+
+``` _dbconnect(SQLite.Connection,"path/to/database.db") ```
+
+
+
+### MySQL
+
+Assuming your data exists on a MySQL database and you want to connect it to the OMOPCDMCohortCreator.
+
+Make sure that the server is running and using `MySQL.API`:
+
+```  systemctl status mysql ```
+
+calling the function
+
+``` _dbconnect(MySQL.Connection, "host_name", "username", "password"; db = "database_name" , port = port_num, unix_socket = "unix_socket_data_path" ) ```
+
+those parameters must exist:
+
+- host_name : if you are working on same machine server it will be "local host"
+
+- username
+- password
+
+Can be known by openning all the `.cnf` files until you find them. I wasn't lucky and opened around 5 till I found the right one. Don't give up!
+
+If unix_socket is not inserted, the default one is given 
+
+
+
+For any struggles MySQL related, [Read this](https://dev.mysql.com/doc/refman/8.0/en/starting-server.html)
+
+
+
+
+
+

docs/src/index.md

@@ -5,3 +5,6 @@ Example Julia package repo.
 ```@autodocs
 Modules = [Example]
 ```
+
+
+

src/jdbc.jl

@@ -8,23 +8,33 @@ function DBInterface.connect(::Type{JDBC.Connection}, args...; connection_string
     catch 
         println("JVM already initialized")
     end
-    JDBC.Connection(connection_string)
+    JDBC.DriverManager.getConnection(connection_string)
 end
 
 """
-Dispatch for LibPQ interface to DBInterface `prepare` function
-TODO: Not fully implemented yet
+Dispatch for JDBC interface to DBInterface `prepare` function
+BUG: Doesn't seem to work for all JDBC versions yet
 """
-# DBInterface.prepare(conn::JDBC.Connection, args...; kws...) =
-#     JDBC.prepareStatement(conn, args...; kws...)
+function DBInterface.prepare(conn::JDBC.JavaObject{Symbol("java.sql.Connection")}, args...; kws...)
+    stmt = JDBC.createStatement(conn)
+    result = executeQuery(stmt, args...)
+    return result
+end
+
+"""
+Workaround for JDBC interface to DBInterface's `execute` function
+"""
+function DBInterface.execute(conn::JDBC.JavaObject{Symbol("java.sql.ResultSet")}, args...; kws...)
+    JDBC.Source(conn)
+end
 
 """
-Workaround for LibPQ interface to DBInterface's `execute` function
+Workaround for JDBC interface to DBInterface's `execute` function
 """
-function DBInterface.execute(conn::Union{JDBC.Connection, JDBC.JPreparedStatement}, args...; kws...)
-    csr = JDBC.cursor(conn)
-    JDBC.execute!(csr, args..., kws...)
-    JDBC.Source(csr)
+function DBInterface.execute(conn::JDBC.JavaObject{Symbol("java.sql.Connection")}, args...; kws...)
+    stmt = JDBC.createStatement(conn)
+    result = executeQuery(stmt, args...)
+    JDBC.Source(result)
 end
 
 

src/mysql.jl

@@ -1,5 +1,10 @@
-function _dbconnect(conn_obj::Type{MySQL.Connection}, kwargs)
 
-    return DBInterface.connect(conn_obj; kwargs...)
+function _dbconnect(conn_obj::Type{MySQL.Connection}, host::String, user::String, password::String; db::String="", port::Integer=3306, unix_socket::Union{Nothing,String}=nothing, client_flag=API.CLIENT_MULTI_STATEMENTS, opts = Dict())
 
+    if unix_socket == nothing
+        unix_socket = API.MYSQL_DEFAULT_SOCKET
+    end
+
+    return DBInterface.connect(conn_obj,host, user, password, db=db, port=port, unix_socket=unix_socket, client_flag=client_flag, opts=opts )
 end
+

src/postgresql.jl

@@ -1,10 +1,12 @@
 """
 Dispatch for LibPQ interface to DBInterface `connect` function; not supported in LibPQ.jl package currently
+
 """
 DBInterface.connect(::Type{LibPQ.Connection}, args...; kws...) =
     LibPQ.Connection(args...; kws...)
 
-function _dbconnect(conn_obj::Type{LibPQ.Connection}; kwargs...)
+function _dbconnect(conn_obj::Type{LibPQ.Connection}, host::String, user::String, password::String; db::String="", port::Integer=3306, unix_socket::Union{Nothing,String}=nothing, client_flag=API.CLIENT_MULTI_STATEMENTS, opts = Dict())
+
     conn_string = ""
     for k in kwargs 
         conn_string = conn_string * "$(string(k.first))=$(k.second) "
@@ -16,6 +18,14 @@ function _dbconnect(conn_obj::Type{LibPQ.Connection}; kwargs...)
 
 end
 
+function _dbconnect(conn_obj::Type{LibPQ.Connection},  host::String, user::String, password::String; db::String="", port::Integer=3306, unix_socket::Union{Nothing,String}=nothing,  opts = Dict())
+    #conn = LibPQ.Connection("postgresql://postgres:postgres3@localhost:5432/mimic?user=postgres")
+
+    return DBInterface.connect(conn_obj, "postgresql://$user:$password@$host:$port/$db?user=$user")
+
+end
+
+
 """
 Workaround for LibPQ interface to DBInterface's `prepare` function; not supported in LibPQ.jl package currently
 """
@@ -27,5 +37,3 @@ Workaround for LibPQ interface to DBInterface's `execute` function; not supporte
 """
 DBInterface.execute(conn::Union{LibPQ.Connection, LibPQ.Statement}, args...; kws...) =
     LibPQ.execute(conn, args...; kws...)
-
-

src/sqlite.jl

@@ -1,5 +1,5 @@
-function _dbconnect(connector::Type{SQLite.DB}; file_path)
+function _dbconnect(connector::Type{SQLite.DB}, file_path::String)
 
-    return connector(file_path.second)
+    return connector(file_path)
 
 end

test/runtests.jl

@@ -1,4 +1,30 @@
-using Test, Example
+using Test
+using MySQL,SQLite, MySQL.API
 
-@test hello("Julia") == "Hello, Julia"
-@test domath(2.0) ≈ 7.0
+
+
+
+@testset "_dbconnect function for SQLite" begin
+
+    conn= _dbconnect(SQLite.DB, "DBConnector.jl/test/data/sqlite.db")
+    @test @isdefined conn
+
+end
+ """
+@testset "_dbconnect function for MySQL" begin
+
+    conn = _dbconnect(MySQL.Connection, ENV['mysqlhost'], ENV['mysqluser'], ENV['mysqlpassword'], db="MySQL", port= 3306)
+
+    @test typeof(conn) == MySQL.Connection
+    @test isopen(conn)
+    close(conn)
+
+end
+
+@testset "_dbconnect function for LibPQ" begin
+
+    conn= _dbconnect(LibPQ.Connection,  ENV['postgreshost'], ENV['postgresuser'], ENV['postgrespassword'], db = "mimic", port= 5432)
+    @test @isdefined conn
+
+end
+"""