docs: update init_mysql_db docstring, add detail to load medline example

.travis.yml

@@ -69,6 +69,6 @@ jobs:
       script:
         - git config --global user.name "semantic-release (via TravisCI)"
         - git config --global user.email "semantic-release@travis"
-        - semantic-release --post publish
+        - semantic-release publish
       after_script: skip
       after_success: skip

examples/literate_src/5_load_medline.jl

@@ -38,7 +38,8 @@ BioMedQuery.PubMed.create_tables!(conn);
 # ### Performing a Full Load
 # To run a full load, use the same code as above, but do not pass the test variable.
 # It is also possible to break up the load by passing which files to start and stop at -
-# simply pass `start_file=n and `end_file=p`.
+# simply pass `start_file=n and `end_file=p`. Currently the default end_file reflects the
+# last file of the 2019 baseline.
 #
 # After loading, it is recommended you add indexes to the tables, the `add_mysql_keys!`
 # function can be used to add a standard set of indexes.

src/DBUtils/mysql_db_utils.jl

@@ -4,7 +4,7 @@ using DataFrames
 
 """
     init_mysql_database(;host = "127.0.0.1", dbname="test",
-    username="root", pswd="", mysql_code=nothing, overwrite=false)
+    username="root", pswd="", mysql_code=nothing, overwrite=false, opts=Dict())
 
 Create a MySQL database using the code inside mysql_code
 
@@ -13,6 +13,7 @@ Create a MySQL database using the code inside mysql_code
 * `host`, `dbname`, `user`, `pswd`
 * `mysql_code::String`: String with MySQL code that crates all default tables
 * `overwrite::Bool` : Flag, if true and dbname exists, drops all database and re-creates it
+* `opts::Dict` : Dictionary containing MySQL connection options
 
 ### Output