From tomlin.9 at wright.edu Thu Jul 25 02:08:08 2013 From: tomlin.9 at wright.edu (Tomlin, Joshua James) Date: Thu, 25 Jul 2013 06:08:08 +0000 Subject: [BioSQL-l] BioSQL Help Message-ID: Hi, I'm on Mac os x 10.7.5 and am trying to setup biosql. I believe I have correctly installed MySQL, BioPython, and have the biosql-1.0.1 directory from the biosql wiki downloads page. I've tried following the instruction in the INSTALL text doc and all seemed to be going well untill I tried to load the schema to a database I created just to test. The issue I'm experiencing is when I run the "mysql -u root biosql < biosqldb-mysql.sql" command in Terminal I get an error that says "ERROR 1064 (42000) at line 49: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'TYPE=INNODB' at line 8" Any ideas? Thanks. From p.j.a.cock at googlemail.com Thu Jul 25 04:24:43 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 25 Jul 2013 09:24:43 +0100 Subject: [BioSQL-l] BioSQL Help In-Reply-To: References: Message-ID: On Thursday, July 25, 2013, Tomlin, Joshua James wrote: > Hi, I'm on Mac os x 10.7.5 and am trying to setup biosql. I believe I have > correctly installed MySQL, BioPython, and have the biosql-1.0.1 directory > from the biosql wiki downloads page. I've tried following the instruction > in the INSTALL text doc and all seemed to be going well untill I tried to > load the schema to a database I created just to test. > The issue I'm experiencing is when I run the "mysql -u root biosql < > biosqldb-mysql.sql" command in Terminal I get an error that says "ERROR > 1064 (42000) at line 49: You have an error in your SQL syntax; check the > manual that corresponds to your MySQL server version for the right syntax > to use near 'TYPE=INNODB' at line 8" > > Any ideas? > Thanks. > > Which version of MySQL do you have? Which version of the BioSQL schema do you have? The latest release or the latest from GitHub? My guess is you need this update, https://github.com/biosql/biosql/commit/f6697005c35976bb8744e9579390910f73e2945b Hilmar, can we do a release soon to ship this fix? Thanks, Peter From hlapp at drycafe.net Thu Jul 25 15:15:27 2013 From: hlapp at drycafe.net (Hilmar Lapp) Date: Thu, 25 Jul 2013 21:15:27 +0200 Subject: [BioSQL-l] BioSQL Help In-Reply-To: References: Message-ID: <36EE998A-6BFA-4AD8-9F1F-5195B6695802@drycafe.net> On Jul 25, 2013, at 10:24 AM, Peter Cock wrote: > On Thursday, July 25, 2013, Tomlin, Joshua James wrote: > >> Hi, I'm on Mac os x 10.7.5 and am trying to setup biosql. I believe I have >> correctly installed MySQL, BioPython, and have the biosql-1.0.1 directory >> from the biosql wiki downloads page. I've tried following the instruction >> in the INSTALL text doc and all seemed to be going well untill I tried to >> load the schema to a database I created just to test. >> The issue I'm experiencing is when I run the "mysql -u root biosql < >> biosqldb-mysql.sql" command in Terminal I get an error that says "ERROR >> 1064 (42000) at line 49: You have an error in your SQL syntax; check the >> manual that corresponds to your MySQL server version for the right syntax >> to use near 'TYPE=INNODB' at line 8" >> >> Any ideas? >> Thanks. >> >> > Which version of MySQL do you have? > > Which version of the BioSQL schema do you have? The latest release or the > latest from GitHub? > > My guess is you need this update, > https://github.com/biosql/biosql/commit/f6697005c35976bb8744e9579390910f73e2945b > > Hilmar, can we do a release soon to ship this fix? Yes, we should indeed absolutely do this. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From tomlin.9 at wright.edu Thu Jul 25 14:56:37 2013 From: tomlin.9 at wright.edu (Tomlin, Joshua James) Date: Thu, 25 Jul 2013 18:56:37 +0000 Subject: [BioSQL-l] FW: BioSQL Help In-Reply-To: References: , , Message-ID: ________________________________ From: Tomlin, Joshua James Sent: Thursday, July 25, 2013 12:11 PM To: Peter Cock Subject: RE: [BioSQL-l] BioSQL Help Hey Peter, thanks for the speedy reply! I actually played around with it a little more last night after I emailed the biosql mailing list and after some google searching and having a look at the biosqldb-mysql.sql file I actually fixed those TYPE to ENGINE lines and it seems to be functioning properly now..so you were right that was what was causing my error. So far it looks like I was able to create a new db and load the biosql schema now with that fix...although I'm new to mysql and am learning as I go so I'm not 100% certain its all functioning properly yet. BTW..These BioPython email lists have been a great resource to me so far, I appreciate it. Thanks again. ________________________________ From: Peter Cock [p.j.a.cock at googlemail.com] Sent: Thursday, July 25, 2013 4:24 AM To: Tomlin, Joshua James; BioSQL Subject: Re: [BioSQL-l] BioSQL Help On Thursday, July 25, 2013, Tomlin, Joshua James wrote: Hi, I'm on Mac os x 10.7.5 and am trying to setup biosql. I believe I have correctly installed MySQL, BioPython, and have the biosql-1.0.1 directory from the biosql wiki downloads page. I've tried following the instruction in the INSTALL text doc and all seemed to be going well untill I tried to load the schema to a database I created just to test. The issue I'm experiencing is when I run the "mysql -u root biosql < biosqldb-mysql.sql" command in Terminal I get an error that says "ERROR 1064 (42000) at line 49: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'TYPE=INNODB' at line 8" Any ideas? Thanks. Which version of MySQL do you have? Which version of the BioSQL schema do you have? The latest release or the latest from GitHub? My guess is you need this update, https://github.com/biosql/biosql/commit/f6697005c35976bb8744e9579390910f73e2945b Hilmar, can we do a release soon to ship this fix? Thanks, Peter From tomlin.9 at wright.edu Thu Jul 25 06:08:08 2013 From: tomlin.9 at wright.edu (Tomlin, Joshua James) Date: Thu, 25 Jul 2013 06:08:08 +0000 Subject: [BioSQL-l] BioSQL Help Message-ID: Hi, I'm on Mac os x 10.7.5 and am trying to setup biosql. I believe I have correctly installed MySQL, BioPython, and have the biosql-1.0.1 directory from the biosql wiki downloads page. I've tried following the instruction in the INSTALL text doc and all seemed to be going well untill I tried to load the schema to a database I created just to test. The issue I'm experiencing is when I run the "mysql -u root biosql < biosqldb-mysql.sql" command in Terminal I get an error that says "ERROR 1064 (42000) at line 49: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'TYPE=INNODB' at line 8" Any ideas? Thanks. From p.j.a.cock at googlemail.com Thu Jul 25 08:24:43 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 25 Jul 2013 09:24:43 +0100 Subject: [BioSQL-l] BioSQL Help In-Reply-To: References: Message-ID: On Thursday, July 25, 2013, Tomlin, Joshua James wrote: > Hi, I'm on Mac os x 10.7.5 and am trying to setup biosql. I believe I have > correctly installed MySQL, BioPython, and have the biosql-1.0.1 directory > from the biosql wiki downloads page. I've tried following the instruction > in the INSTALL text doc and all seemed to be going well untill I tried to > load the schema to a database I created just to test. > The issue I'm experiencing is when I run the "mysql -u root biosql < > biosqldb-mysql.sql" command in Terminal I get an error that says "ERROR > 1064 (42000) at line 49: You have an error in your SQL syntax; check the > manual that corresponds to your MySQL server version for the right syntax > to use near 'TYPE=INNODB' at line 8" > > Any ideas? > Thanks. > > Which version of MySQL do you have? Which version of the BioSQL schema do you have? The latest release or the latest from GitHub? My guess is you need this update, https://github.com/biosql/biosql/commit/f6697005c35976bb8744e9579390910f73e2945b Hilmar, can we do a release soon to ship this fix? Thanks, Peter From hlapp at drycafe.net Thu Jul 25 19:15:27 2013 From: hlapp at drycafe.net (Hilmar Lapp) Date: Thu, 25 Jul 2013 21:15:27 +0200 Subject: [BioSQL-l] BioSQL Help In-Reply-To: References: Message-ID: <36EE998A-6BFA-4AD8-9F1F-5195B6695802@drycafe.net> On Jul 25, 2013, at 10:24 AM, Peter Cock wrote: > On Thursday, July 25, 2013, Tomlin, Joshua James wrote: > >> Hi, I'm on Mac os x 10.7.5 and am trying to setup biosql. I believe I have >> correctly installed MySQL, BioPython, and have the biosql-1.0.1 directory >> from the biosql wiki downloads page. I've tried following the instruction >> in the INSTALL text doc and all seemed to be going well untill I tried to >> load the schema to a database I created just to test. >> The issue I'm experiencing is when I run the "mysql -u root biosql < >> biosqldb-mysql.sql" command in Terminal I get an error that says "ERROR >> 1064 (42000) at line 49: You have an error in your SQL syntax; check the >> manual that corresponds to your MySQL server version for the right syntax >> to use near 'TYPE=INNODB' at line 8" >> >> Any ideas? >> Thanks. >> >> > Which version of MySQL do you have? > > Which version of the BioSQL schema do you have? The latest release or the > latest from GitHub? > > My guess is you need this update, > https://github.com/biosql/biosql/commit/f6697005c35976bb8744e9579390910f73e2945b > > Hilmar, can we do a release soon to ship this fix? Yes, we should indeed absolutely do this. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From tomlin.9 at wright.edu Thu Jul 25 18:56:37 2013 From: tomlin.9 at wright.edu (Tomlin, Joshua James) Date: Thu, 25 Jul 2013 18:56:37 +0000 Subject: [BioSQL-l] FW: BioSQL Help In-Reply-To: References: , , Message-ID: ________________________________ From: Tomlin, Joshua James Sent: Thursday, July 25, 2013 12:11 PM To: Peter Cock Subject: RE: [BioSQL-l] BioSQL Help Hey Peter, thanks for the speedy reply! I actually played around with it a little more last night after I emailed the biosql mailing list and after some google searching and having a look at the biosqldb-mysql.sql file I actually fixed those TYPE to ENGINE lines and it seems to be functioning properly now..so you were right that was what was causing my error. So far it looks like I was able to create a new db and load the biosql schema now with that fix...although I'm new to mysql and am learning as I go so I'm not 100% certain its all functioning properly yet. BTW..These BioPython email lists have been a great resource to me so far, I appreciate it. Thanks again. ________________________________ From: Peter Cock [p.j.a.cock at googlemail.com] Sent: Thursday, July 25, 2013 4:24 AM To: Tomlin, Joshua James; BioSQL Subject: Re: [BioSQL-l] BioSQL Help On Thursday, July 25, 2013, Tomlin, Joshua James wrote: Hi, I'm on Mac os x 10.7.5 and am trying to setup biosql. I believe I have correctly installed MySQL, BioPython, and have the biosql-1.0.1 directory from the biosql wiki downloads page. I've tried following the instruction in the INSTALL text doc and all seemed to be going well untill I tried to load the schema to a database I created just to test. The issue I'm experiencing is when I run the "mysql -u root biosql < biosqldb-mysql.sql" command in Terminal I get an error that says "ERROR 1064 (42000) at line 49: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'TYPE=INNODB' at line 8" Any ideas? Thanks. Which version of MySQL do you have? Which version of the BioSQL schema do you have? The latest release or the latest from GitHub? My guess is you need this update, https://github.com/biosql/biosql/commit/f6697005c35976bb8744e9579390910f73e2945b Hilmar, can we do a release soon to ship this fix? Thanks, Peter