I installed ggsd on our linux box, but when I try to create user or any other option from the left menu I get this error msg.
The database is created and we are using MySql. I can see that the installation created the user root and this is the one I am using to enter the site. I see the screen I am getting for create users is different from the one in the doc. Any hint?
Error #5: 2010-05-10 09:56:18
Error in call to authenticate from create_user.php
I'm sorry you've had issues using GGSD. I'm currently away from the office at a conference, so a more detailed explanation and solution might take a few days.
But one thing I see is that there is a bug in the fact that err_msg is suppose to be a variable that contains the real error message, but is actually a bare word. I'll change the code in cvs and put a new release up.
I've gone into the code and this error is being generated by the sub-routine authenticateRoot from the sql_lib.inc library. If you could please open sql_lib.inc in a text editor and change line 434 from return err_msg; to return $err_msg; and then save the change. Then redo your above action and send the real error message that will help me alot solve the issue.
But there appears to be a problem querying the database.
Thanks for your help.
Lead GGSD developer
Thank you Aaron. Yes, we saw that the process of the msg error seem to have a problem. We passed the login stage, but not I am getting the message that I am not authorized to enter individuas. genes, etc. (You are not an authorized user of this website!!) . And I am the root and was able to create database and users. I also found a alter table query refering to a wrong field name. I can fix that, but I am wondering how many errors I will find down the road. Do you have users really using this tool? Did they fix the bugs on their own?
Error #16: 2010-05-11 09:55:15
Error in call to updateRecord from alter_user_priveleges.php
Error in call to updateRecord
Unable to execute sql query: UPDATE user_database_link_table SET user_privileges = 'administrative', last_updated = '2010-05-11 09:55:15' WHERE user_database_link_id = '2'
MDB2 Error: no such field
I'm so sorry this installation has been buggy!! Yes, I developed this in collaboration with a group in my old department, and am further developing it for my new group. But have made some alterations since putting up on sourceforge that are different than what the old group are running, and I have obviosly missed some dependencies in the code. So either people have fixed the bugs themselves, or given up because you are the first person to ask for help. Thanks so much for your patience, I'm truely sorry about the problems. I really do want to help you manage your data.
I have found the problem of the above error message. I updated the schema and changed the field user_privileges to database_privileges, and missed this use of the old field name in the alter user function.
So let me understand the issues you are having:
1) You've run the setup script and everything appears to have worked.
2) You can log into the system using user name 'root' and create users and a database
3) When you then try and actually load data into the created database you get the "you are not an authorized user" error message.
If you select one of the "Search" tools, are you allowed to log in? My guess is that the issues are stemming from the missed change in db field name.
Are you/your group able/willing to wait a week for me to get back to work where I'll go through my testing routine for the system and do an installation from scratch to identify bugs that I might of created on the last update??
Yes, we can wait.
Right now, I can logon using the root user I created during installation and I can create and delete tables and users.
When I click on insert individuals or any of the other functions I get either not authorized user or I am asked to enter username/password and database, but then I get the not authorized msg again. this is also true for the search/download tools.
It would be great if we can use this tool. We will need to write several queries for the users of our research group, so, we might be able to collaborate somehow.
Please keep me posted. When you are done, I can download it again.
Great, thanks for your patience. With this information in hand I know where to look.
Feedback and collaboration could be very helpful. If you want you can email me at firstname.lastname@example.org so we can take this offline.
I'll keep you posted about the new release. Thanks for helping this project.
I haven't forgotten anything. Had a lot of emails/work to catch up on after my trip, as well as recovering from jet lag. Will have a new version for you early next week.
I haven't yet completed the complete retesting of the new package. I need to submit two papers before Friday. Once those are submitted I'll do a top-to-bottom stress test of the system.
FYI, the first insertions of the first marker/genotype data can take a while. For example, if you have Illumina 550K genotypes for > 1000 individuals it might take a couple of days. I know this is horrible performance, but it is a limitation of MySQL's indexing, key generation and my own non-optimized sql statements. I've been working hard on this, and it is the next major upgrade for version 3.0.
Let me know how things go, and if you still run into troubles I'll get you a fix a lot faster this time.
I've just discovered a minor logic flow problem.
After you perform any administrative opertations as root, LOG OUT before clicking on any of the other non-administrative links. The session variable of which database being worked on is not set in the administrative section, so when you click on any of the other links the insertions/searches are not set up properly. Logging out of the administrative section corrects this.
I'm fixing now and will upload a new release today.
Just to explain further to post #9. This is why you get the not authorized user message when you click on any of the non-administrative links after logging into the administrative section.
Thank you for working on this. On Tuesday, I will install the most updated build and test it out. Looking forward to it.
I wanted to check in to see if I fixed your problem, or if you encountered another issues.
I did not have time to re-install it, but it is in my plans to do it by next Tuesday. I will get in touch with you as soon as I test it.
Thank you so much,