Fix #27 #35 #39 #40

[bartcharbon]

#40 Downloading very big datasets (> 60.000 rows) results in timeout bug
Timeout is now configurable (in seconds) with the -t parameter

#39 MappedBy downloads as entity instead of attribute bug
Fixed

#35 Download with metadata should be the default enhancement
-m option is replaced with -d (data only).

#27 I have to enter required admin password even if I want to download public data.
Fixed: password is now only required if an account is specified, account is no longer a required option

[marikaris]

I tried this(to test #27):
-f test1.xlsx -i -u https://molgenis01.gcc.rug.nl/ demo_borrel -o -d

I receive a lot of error messages, but it downloads (with metadata though...):

downloading from: https://molgenis01.gcc.rug.nl//api/v2/sys_Language
Oct 12, 2017 8:30:26 AM org.molgenis.downloader.client.MolgenisRestApiClient streamEntityData
SEVERE: null
org.json.JSONException: JSONObject["meta"] not found.
	at org.json.JSONObject.get(JSONObject.java:471)
	at org.json.JSONObject.getJSONObject(JSONObject.java:636)
	at org.molgenis.downloader.client.MolgenisRestApiClient.streamEntityData(MolgenisRestApiClient.java:140)
	at org.molgenis.downloader.api.MolgenisClient.streamEntityData(MolgenisClient.java:19)
	at org.molgenis.downloader.client.MolgenisRestApiClient.streamMetadata(MolgenisRestApiClient.java:181)
	at org.molgenis.downloader.emx.EMXClient.downloadEMX(EMXClient.java:49)
	at org.molgenis.downloader.Downloader.run(Downloader.java:141)
	at org.molgenis.downloader.Downloader.main(Downloader.java:53)

downloading from: https://molgenis01.gcc.rug.nl//api/v2/sys_md_Tag
Oct 12, 2017 8:30:26 AM org.molgenis.downloader.client.MolgenisRestApiClient streamEntityData
SEVERE: null
org.json.JSONException: JSONObject["meta"] not found.
	at org.json.JSONObject.get(JSONObject.java:471)
	at org.json.JSONObject.getJSONObject(JSONObject.java:636)
	at org.molgenis.downloader.client.MolgenisRestApiClient.streamEntityData(MolgenisRestApiClient.java:140)
	at org.molgenis.downloader.api.MolgenisClient.streamEntityData(MolgenisClient.java:19)
	at org.molgenis.downloader.client.MolgenisRestApiClient.streamMetadata(MolgenisRestApiClient.java:182)
	at org.molgenis.downloader.emx.EMXClient.downloadEMX(EMXClient.java:49)
	at org.molgenis.downloader.Downloader.run(Downloader.java:141)
	at org.molgenis.downloader.Downloader.main(Downloader.java:53)

downloading from: https://molgenis01.gcc.rug.nl//api/v2/sys_md_Package
downloading from: https://molgenis01.gcc.rug.nl//api/v2/sys_md_Attribute
downloading from: https://molgenis01.gcc.rug.nl/api/v2/sys_md_Attribute?start=100
downloading from: https://molgenis01.gcc.rug.nl//api/v2/sys_md_EntityType
downloading from: https://molgenis01.gcc.rug.nl//api/v2/demo_borrel?num=1
downloading from: https://molgenis01.gcc.rug.nl//api/v2/demo_borrel

And this (to test #35):
-f test.xlsx -i -u https://molgenis01.gcc.rug.nl/ demo_borrel -o
Error, but file downloads with metadata:

SEVERE: null
org.json.JSONException: JSONObject["meta"] not found.
	at org.json.JSONObject.get(JSONObject.java:471)
	at org.json.JSONObject.getJSONObject(JSONObject.java:636)
	at org.molgenis.downloader.client.MolgenisRestApiClient.streamEntityData(MolgenisRestApiClient.java:140)
	at org.molgenis.downloader.api.MolgenisClient.streamEntityData(MolgenisClient.java:19)
	at org.molgenis.downloader.client.MolgenisRestApiClient.streamMetadata(MolgenisRestApiClient.java:181)
	at org.molgenis.downloader.emx.EMXClient.downloadEMX(EMXClient.java:49)
	at org.molgenis.downloader.Downloader.run(Downloader.java:141)
	at org.molgenis.downloader.Downloader.main(Downloader.java:53)