fix: MySQL tests now work on MacOS

Homebrew-configured versions of MySQL:

1. Only create a user with the same name as the current user (no root)
2. Don't allow that user to login using 127.0.0.1 (but works with "localhost")

The tests have been modified to take this into consideration

src/DBUtils/mysql_db_utils.jl

@@ -21,11 +21,11 @@ Create a MySQL database using the code inside mysql_code
 
 """
 function init_mysql_database(host="127.0.0.1",
-    user="root", pwd="", dbname="test"; overwrite=false, opts = Dict())
+    user="root", pswd="", dbname="test"; overwrite=false, opts = Dict())
 
     opts[MySQL.API.MYSQL_SET_CHARSET_NAME] = "utf8mb4"
 
-    con = MySQL.connect(host, user, pwd, opts=opts)
+    con = MySQL.connect(host, user, pswd, opts=opts)
 
     init_mysql_database(con, dbname, overwrite)
 end

test/dbutils_mysql.jl

@@ -5,7 +5,7 @@ using MySQL
 
     dbname="pubmed_test"
 
-    conn = DBUtils.init_mysql_database("127.0.0.1", "root", "", dbname)
+    conn = DBUtils.init_mysql_database(MYSQL_HOST, MYSQL_USER, MYSQL_PASSWORD, dbname)
     PubMed.create_tables!(conn)
 
     println(conn)

test/processes_mysql.jl

@@ -13,9 +13,9 @@ const verbose = false
 
 
 #************************ MYSQL **********************************************
-const host="127.0.0.1" #If want to hide - use enviroment variables instead
-const mysql_usr="root"
-const mysql_pswd=""
+const host=MYSQL_HOST #If want to hide - use enviroment variables instead
+const mysql_usr=MYSQL_USER
+const mysql_pswd=MYSQL_PASSWORD
 const dbname="pubmed_processes_test"
 const dbname_pmid ="pmid_processes_test"
 const medline_file = 1

test/pubmed.jl

@@ -56,11 +56,11 @@ import Base.parse
             println("-----------------------------------------")
             println("       Test Save PMID MySQL     ")
             dbname = "entrez_test"
-            host = "127.0.0.1";
-            user = "root"
-            pwd = ""
+            host = MYSQL_HOST
+            user = MYSQL_USER
+            pswd = MYSQL_PASSWORD
 
-            conn = DBUtils.init_mysql_database(host, user, pwd, dbname)
+            conn = DBUtils.init_mysql_database(host, user, pswd, dbname)
             PubMed.create_pmid_table!(conn)
             PubMed.save_pmids!(conn, ids)
 
@@ -78,11 +78,11 @@ import Base.parse
         println("       Testing MySQL Saving")
 
         dbname = "efetch_test"
-        host = "127.0.0.1";
-        user = "root"
-        pwd = ""
+        host = MYSQL_HOST
+        user = MYSQL_USER
+        pswd = MYSQL_PASSWORD
 
-        conn = DBUtils.init_mysql_database(host, user, pwd, dbname)
+        conn = DBUtils.init_mysql_database(host, user, pswd, dbname)
         PubMed.create_tables!(conn)
         @time PubMed.save_efetch!(conn, efetch_doc, false, true)
 

test/runtests.jl

@@ -17,7 +17,6 @@ using MySQL
 using SQLite
 using DataStreams
 
-
 #For now this corresponds to JULIACIBot... since we aren't testing anywhere else
 global CI = get(ENV, "CI", "false")=="true"
 global TRAVIS = get(ENV, "TRAVIS", "false")=="true"
@@ -39,6 +38,21 @@ all_tests = [
             ("processes_df.jl",     "       Testing: Processes DataFrame")
             ]
 if !CI_SKIP_MYSQL
+    # on MacOS host name must be localhost
+    if Sys.isapple()
+        global const MYSQL_HOST = "localhost"
+    else
+        global const MYSQL_HOST = "127.0.0.1"
+    end
+
+    if Sys.isapple()
+        global const MYSQL_USER = get(ENV, "MYSQL_USER", get(ENV, "LOGNAME", "root"))
+    else
+        global const MYSQL_USER = get(ENV, "MYSQL_USER", "root")
+    end
+
+    global const MYSQL_PASSWORD = get(ENV, "MYSQL_PASSWORD", "")
+
     push!(all_tests, ("dbutils_mysql.jl",    "       Testing: DBUtils MySQL"))
     push!(all_tests, ("processes_mysql.jl",  "       Testing: Processes MySQL"))
 end