Fix tests

examples/literate_src/1_pubmed_search_and_save.jl

@@ -79,7 +79,7 @@ all_pmids(conn_sqlite)
 tables = ["author_ref", "mesh_desc", "mesh_qual", "mesh_heading"]
 for t in tables
     query_str = "SELECT * FROM $t LIMIT 5;"
-    q = SQLite.query(conn_sqlite, query_str)
+    q = SQLite.Query(conn_sqlite, query_str)
     println(q)
 end
 

examples/runexamples.jl

@@ -1,6 +1,7 @@
 all_examples = [
     ("literate_src/1_pubmed_search_and_save.jl",    " Running Example: Search and Save"),
-    ("literate_src/2_umls_map_and_filter.jl",       " Running Example: MeSH/UMLS Map and Filter"),
+    # TODO how can we run UMLS examples?
+    # ("literate_src/2_umls_map_and_filter.jl",       " Running Example: MeSH/UMLS Map and Filter"),
     ("literate_src/4_pubmed_export_citations.jl",   " Running Example: Export Citations"),
     ("literate_src/5_load_medline.jl", " Running Example: Load MEDLINE")
     ]

src/PubMed/pubmed_sql_utils.jl

@@ -511,8 +511,7 @@ function db_insert!(db::MySQL.Connection, csv_path::String = pwd(), csv_prefix::
             path = joinpath(csv_path, "$(csv_prefix)$(table).csv")
             drop_csv && push!(paths,path)
 
-            headers = CSV.read(path, DataFrame, rows = 1)
-            # return headers
+            headers = CSV.read(path, limit=1)
 
             cols = String.(getfield(headers, :colindex).names)
             if !col_match(db, table, cols)

test/ct.jl

@@ -11,12 +11,16 @@ using ZipFile
 
     #test all files are .xml
     not_xml = false
-    r = ZipFile.Reader(fout);
-    for f in r.files
-        if !occursin(r"^.*\.xml.*$", f.name)
-          not_xml = true
-          break
+    r = ZipFile.Reader(fout)
+    try
+        for f in r.files
+            if !occursin(r"^.*\.xml.*$", f.name)
+              not_xml = true
+              break
+            end
         end
+    finally
+        close(r)
     end
 
     @test not_xml == false

test/dbutils_sqlite.jl

@@ -2,8 +2,7 @@ using SQLite
 
 @testset "SQLite DBUtils" begin
 
-    db_path = "test_db.sqlite"
-    conn = SQLite.DB(db_path)
+    conn = SQLite.DB()
     PubMed.create_tables!(conn)
 
     #check collection of tables
@@ -19,8 +18,4 @@ using SQLite
 
     @test length(sel[1]) == 1
     @test sel[1][1] == 1234
-
-    if isfile(db_path)
-        rm(db_path)
-    end
 end

test/processes_sqlite.jl

@@ -9,14 +9,8 @@ const verbose = false
 const umls_user = get(ENV, "UMLS_USER", "")
 const umls_pswd = get(ENV, "UMLS_PSSWD", "")
 #************************ SQLite **************************
-const db_path="./test_processes.sqlite"
-#***************************************************************************
 
-if isfile(db_path)
-    rm(db_path)
-end
-
-const conn_sql = SQLite.DB(db_path)
+const conn_sql = SQLite.DB()
 PubMed.create_tables!(conn_sql)
 
 @testset "Save and Search" begin
@@ -63,9 +57,5 @@ global credentials_set = get(ENV, "TRAVIS_SECURE_ENV_VARS", "true")=="true" && u
 
 end
 
-# remove temp files
-if isfile(db_path)
-    rm(db_path)
-end
 println("------------End Test Processes SQLite-----------")
 println("------------------------------------------------")

test/pubmed.jl

@@ -154,9 +154,7 @@ import Base.parse
         println("-----------------------------------------")
         println("       Testing SQLite Saving")
 
-        db_path = "./test_db.db"
-
-        conn = SQLite.DB(db_path)
+        conn = SQLite.DB()
         PubMed.create_tables!(conn)
         PubMed.save_efetch!(conn, efetch_doc,false, true)
 
@@ -187,11 +185,6 @@ import Base.parse
             count = q[1][1]
             @test count > 0
         end
-
-        # remove temp files
-        if isfile(db_path)
-            rm(db_path)
-        end
     end
 
 

test/runtests.jl

@@ -3,6 +3,11 @@
 #
 using Test
 
+# Hack: force the loading of MbedTLS as otherwise it conflicts with the version in LibCURL
+# Entropy() was chosen as a fairly quick exported function
+using MbedTLS
+MbedTLS.Entropy()
+
 using XMLDict
 using BioMedQuery.Processes
 using BioMedQuery.PubMed