Merge #67

67: Restore additional tests r=ibacher a=ibacher



Co-authored-by: Ian <ian_bacher@brown.edu>

.travis.yml

@@ -22,35 +22,42 @@ notifications:
 sudo: false
 
 addons:
-  mariadb: '10.4'
+  # mariadb: '10.0'
+  homebrew:
+    packages:
+    - mariadb
+    update: true
 
-script:
+services:
+  - mysql
+
+before_script:
   - if [ "$TRAVIS_OS_NAME" == "osx" ]; then . ./ci/travis/before_install-osx.sh; fi
-  - export OLD_PATH=$LD_LIBRARY_PATH
-  - export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:`mariadb_config --libs | cut -d ' ' -f1 | sed 's/-L//'`
-after_script:
-  - export LD_LIBRARY_PATH=$OLD_PATH
-  - unset OLD_PATH
+  - export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:`mysql_config --libs | cut -d ' ' -f1 | sed 's/-L//'`
+
 after_success:
   - julia -e 'import Pkg; Pkg.instantiate(); Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder())'
 
+matrix:
+  allow_failures:
+  - julia: 1.2
+
 jobs:
-    - stage: tests
+  include:
+    - stage: test
       os: osx
       julia: 1.1
-      env: GROUP=Test
       script:
         - julia -e 'import Pkg; Pkg.build(); Pkg.test(coverage=false);'
       after_success: skip
-    - stage: examples
+    - stage: example
       os: linux
       julia: 1.1
-      env: GROUP=Examples
       script:
         - julia -e 'import Pkg; Pkg.instantiate(); include(joinpath(@__DIR__, "examples", "runexamples.jl"))'
     - stage: deploy documentation
       julia: 1.1
       os: linux
       script:
-        - julia -e 'import Pkg; Pkg.instantiate(); Pkg.add("Documenter"); include(joinpath("docs", "make.jl"))'
+        - julia -e 'import Pkg; Pkg.instantiate(); Pkg.add("Documenter"); Pkg.add("Literate"); include(joinpath("docs", "make.jl"))'
       after_success: skip

Project.toml

@@ -1,7 +1,7 @@
 name = "BioMedQuery"
 uuid = "e96904bf-1073-5077-9b57-b0ce0ff5555a"
 author = ["Brown Center for Biomedical Informatics"]
-version = '0.6.4'
+version = "0.6.5"
 
 [deps]
 BioServices = "a0d4ced5-b29c-5395-b614-ca030a679c4b"
@@ -19,11 +19,12 @@ SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 XMLDict = "228000da-037f-5747-90a9-8195ccbf91a5"
 
 [compat]
-julia = ">=0.7"
+julia = ">=1.0"
 
 [extras]
+MbedTLS = "739be429-bea8-5141-9913-cc70e7f3736d"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 ZipFile = "a5390f91-8eb1-5f08-bee0-b1d1ffed6cea"
 
 [targets]
-test = ["Test", "ZipFile"]
+test = ["MbedTLS", "Test", "ZipFile"]

ci/travis/before_install-osx.sh

@@ -5,8 +5,12 @@ echo Running before_install-osx.sh...
 echo "------------------------------------------"
 
 # Install and start MySQL on OSX
-echo ">>> brew install mariadb"
-brew update
-brew install mariadb
+echo ">>> configure mariadb"
+mkdir -p /usr/local/etc/my.cnf.d
+echo "[mysqld]" > $HOME/.my.cnf
+echo "secure_file_priv = \"\" ">> $HOME/.my.cnf
+echo "default_authentication_plugin = mysql_native_password" >> $HOME/.my.cnf
+echo "local_infile = 1" >> $HOME/.my.cnf
+
 echo ">>> mysql.server start"
 mysql.server start

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