I have set up SIDB, and am able to upload and store images now, but when using the upload interface, the drop down menu next to the template selection drop down doesnt display any choices. As such, I'm not able to choose 3-D as an option so cannot input the required information that this option allows. Beyond this, everything seems to be working well.
Any help will be greatly appreciated!
Darren E. Brust
Kent State University
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My first guess is that the table 'filetypes' is not present in the postgres database, or that it contains no data. To check this, you will have to connect to the postgres database server directly. To do so, type (assuming you are running a UNIX box):
psql -U postgres sidb
(where postgres is your database user and sidb the name of your database. You entered these data when you installed sidb, otherwise check in the file sidb/includes/config_inc.php)
Once connected type:
\d filetypes
If the table is not listed enter the following:
CREATE TABLE "filetypes" (
"name" character varying,
"extensions" character varying,
"sortid" int2
);
This should create the table
To check for the table contents, type:
SELECT * FROM filetypes;
If there is nothing there, type (or better, copy):
COPY "filetypes" FROM stdin;
2-D tiff;tif;jpg;jpeg;png;gif;psd 1
multipage \N 10
3-D TIF;tif;pic;PIC 20
ICS ICS;IDS;ics;ids 21
other \N 30
\.
And to finish it off:
CREATE UNIQUE INDEX "filetypes_name_key" on "filetypes" using btree ( "name" "varchar_ops" );
If this table (with content) was there to begin with,let me know and I'll look into it more.
Best regards,
Nico
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Thanks for the help! I found that the table did in fact exist, but, it was empty. So, I tried numerous ways to enter the data that you gave, but I keep getting the same result:
ERROR: copy: line 1, Missing data for column "extensions"
lost synchronization with server, resetting connection
I'm really not sure what I'm doing wrong. I've highlighted directly out of the email and typed it manually and got the same results. Any ideas?
Thanks!
Darren
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I am sure you are not doing anything wrong (if anyone is, it is me). Your observation also explains why the data were not inserted in the first place. For now try (in psql):
INSERT INTO filetypes VALUES ('2-D','tiff;tif;jpg;jpeg;png;gif;psd',1);
INSERT INTO filetypes VALUES ('multiplage',NULL,10);
INSERT INTO filetypes VALUES ('3-D','TIF;tif;PIC',20);
INSERT INTO filetypes VALUES ('ICS','ICS;IDS;ICS;ids',21);
INSERT INTO filetype VALUES ('other',NULL,30);
And if this fails I made some typos..
Just outoff curiosity, did you do a fresh install of 0.31, or did you upgrade (if so, from wchih version?). Also, which postgres version are you using?
Best, Nico
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I am using a fresh install of 0.31, and using postgress version 7.3.5.
With your help, I was able to make the drop down menu's work, so now I can choose 2-D and 3-D images. I did, however, have to tell it that I had huygens installed in order to get the 3-D working. I cant seem to locate huygens2t on their website unfortunatly, only a regular version with a licsense attatched. If you have a copy of 2t sitting around, or know how to get it, I'd be gratefull.
I have run into another image, however. When editing php.ini, I set the two variables, post_max and upload_max to 2048M. When I do this, it will not let me log in to the system. Actually, anything larget than 2000M and I cant log in to the system. It simply keeps re-displaying the login screen like I didnt type anything at all.
And, for the last problem, when I choose 3-D, I get the following error for the microscope fields, right above the yellow and purple boxes for optical parameters and refractive indexes. A /d microscopes reveals that the table does exist, and it does in fact have information in it, there just seems to be some trouble with "sortkey."
Illegal operation performed!
Reported error:
Could not execute query SELECT microscopeid,microscope FROM microscopes ORDER BY sortkey;!
Errormessage reported from database:
ERROR: Attribute "sortkey" not found
I really appreciate the help, and hope that I am not being to much of a bother. This database is proving to be extrememly usefull and is becoming an important tool in our research. We're finally bridging the "building gaps" between the cs and biology departments!
Thanks again,
Darren
Kent State University
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
To make matters more complicated, huygens2t has been renamed into huscript. Simply download the huygens package from the www.svi.nl website, ignore all the license stuff, locate huscript (on linux probably in /usr/local/svi/bin/huscript) and substitute huygens2t in sidb for huscript. When there is no license key available, huscript (and huygens itself for that matter) will operate in 'freeware'mode. Sidb only uses functions available in freeware mode.
I am not sure why you want to set POST_MAX and UPLOAD_MAX higher than 2GB. You might not even have that amount of RAM in your machine (otherwise, you have a real nice beast there). I would suspect that php uses ints to store those variables, and those might max out around 2GB (not sure, never run into that problem yet). If you really want to put such large files into SIDB, it will be better to save the files in your home directory on the server and work out the settings needed to let SIDB move those files into the database system (but I am working on problems with files larger than 2GB even with that solution).
Sorry about all that database trouble, I'll do a fresh install myself and see if I can fix these bugs. For now type the following in psql:
ALTER TABLE microscopes ADD COLUMN sortkey int;
Great that SIDB is helpful!
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
We definatly have enough RAM on the machine. We are working with parallel and and distributed rendering of large data sets, and 1GB was to small right off the bat, so the next logical size to limit to was 2GB. What is funny is that it was working for a time, until I made some updgrades to packages etc when trying to fix some other problems.
The ALTER TABLE fixed the problems, we're golden now. I have downloaded the huygens stuff, so now I'll get that working, no problem. Thanks for all your help, its been much appreciated!
Darren E. Brust
Kent State University
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hello!
I have set up SIDB, and am able to upload and store images now, but when using the upload interface, the drop down menu next to the template selection drop down doesnt display any choices. As such, I'm not able to choose 3-D as an option so cannot input the required information that this option allows. Beyond this, everything seems to be working well.
Any help will be greatly appreciated!
Darren E. Brust
Kent State University
Hi Darren
Thanks for trying out SIDB!
My first guess is that the table 'filetypes' is not present in the postgres database, or that it contains no data. To check this, you will have to connect to the postgres database server directly. To do so, type (assuming you are running a UNIX box):
psql -U postgres sidb
(where postgres is your database user and sidb the name of your database. You entered these data when you installed sidb, otherwise check in the file sidb/includes/config_inc.php)
Once connected type:
\d filetypes
If the table is not listed enter the following:
CREATE TABLE "filetypes" (
"name" character varying,
"extensions" character varying,
"sortid" int2
);
This should create the table
To check for the table contents, type:
SELECT * FROM filetypes;
If there is nothing there, type (or better, copy):
COPY "filetypes" FROM stdin;
2-D tiff;tif;jpg;jpeg;png;gif;psd 1
multipage \N 10
3-D TIF;tif;pic;PIC 20
ICS ICS;IDS;ics;ids 21
other \N 30
\.
And to finish it off:
CREATE UNIQUE INDEX "filetypes_name_key" on "filetypes" using btree ( "name" "varchar_ops" );
If this table (with content) was there to begin with,let me know and I'll look into it more.
Best regards,
Nico
Nico,
Thanks for the help! I found that the table did in fact exist, but, it was empty. So, I tried numerous ways to enter the data that you gave, but I keep getting the same result:
ERROR: copy: line 1, Missing data for column "extensions"
lost synchronization with server, resetting connection
I'm really not sure what I'm doing wrong. I've highlighted directly out of the email and typed it manually and got the same results. Any ideas?
Thanks!
Darren
I am sure you are not doing anything wrong (if anyone is, it is me). Your observation also explains why the data were not inserted in the first place. For now try (in psql):
INSERT INTO filetypes VALUES ('2-D','tiff;tif;jpg;jpeg;png;gif;psd',1);
INSERT INTO filetypes VALUES ('multiplage',NULL,10);
INSERT INTO filetypes VALUES ('3-D','TIF;tif;PIC',20);
INSERT INTO filetypes VALUES ('ICS','ICS;IDS;ICS;ids',21);
INSERT INTO filetype VALUES ('other',NULL,30);
And if this fails I made some typos..
Just outoff curiosity, did you do a fresh install of 0.31, or did you upgrade (if so, from wchih version?). Also, which postgres version are you using?
Best, Nico
Nico,
I am using a fresh install of 0.31, and using postgress version 7.3.5.
With your help, I was able to make the drop down menu's work, so now I can choose 2-D and 3-D images. I did, however, have to tell it that I had huygens installed in order to get the 3-D working. I cant seem to locate huygens2t on their website unfortunatly, only a regular version with a licsense attatched. If you have a copy of 2t sitting around, or know how to get it, I'd be gratefull.
I have run into another image, however. When editing php.ini, I set the two variables, post_max and upload_max to 2048M. When I do this, it will not let me log in to the system. Actually, anything larget than 2000M and I cant log in to the system. It simply keeps re-displaying the login screen like I didnt type anything at all.
And, for the last problem, when I choose 3-D, I get the following error for the microscope fields, right above the yellow and purple boxes for optical parameters and refractive indexes. A /d microscopes reveals that the table does exist, and it does in fact have information in it, there just seems to be some trouble with "sortkey."
Illegal operation performed!
Reported error:
Could not execute query SELECT microscopeid,microscope FROM microscopes ORDER BY sortkey;!
Errormessage reported from database:
ERROR: Attribute "sortkey" not found
I really appreciate the help, and hope that I am not being to much of a bother. This database is proving to be extrememly usefull and is becoming an important tool in our research. We're finally bridging the "building gaps" between the cs and biology departments!
Thanks again,
Darren
Kent State University
To make matters more complicated, huygens2t has been renamed into huscript. Simply download the huygens package from the www.svi.nl website, ignore all the license stuff, locate huscript (on linux probably in /usr/local/svi/bin/huscript) and substitute huygens2t in sidb for huscript. When there is no license key available, huscript (and huygens itself for that matter) will operate in 'freeware'mode. Sidb only uses functions available in freeware mode.
I am not sure why you want to set POST_MAX and UPLOAD_MAX higher than 2GB. You might not even have that amount of RAM in your machine (otherwise, you have a real nice beast there). I would suspect that php uses ints to store those variables, and those might max out around 2GB (not sure, never run into that problem yet). If you really want to put such large files into SIDB, it will be better to save the files in your home directory on the server and work out the settings needed to let SIDB move those files into the database system (but I am working on problems with files larger than 2GB even with that solution).
Sorry about all that database trouble, I'll do a fresh install myself and see if I can fix these bugs. For now type the following in psql:
ALTER TABLE microscopes ADD COLUMN sortkey int;
Great that SIDB is helpful!
We definatly have enough RAM on the machine. We are working with parallel and and distributed rendering of large data sets, and 1GB was to small right off the bat, so the next logical size to limit to was 2GB. What is funny is that it was working for a time, until I made some updgrades to packages etc when trying to fix some other problems.
The ALTER TABLE fixed the problems, we're golden now. I have downloaded the huygens stuff, so now I'll get that working, no problem. Thanks for all your help, its been much appreciated!
Darren E. Brust
Kent State University