helenadeus / s3db Goto Github PK

* What is the URL of your deployment?
<http://biodata.mdanderson.org/s3db/>

* What steps will reproduce the problem?
1. Get rule id for 'Researcher' 'has' 'initials'.

[NOTE] Replace KEYNAME with actual key value
$ curl "http://biodata.mdanderson.org/s3db/S3QL.php?
key=KEYNAME&query=<S3QL><from>rules</from><where><project_id>80192</project_id>
</where></S3QL>" | tidy -q -i

If we skim the results (about 65-70% of way down), the associated rule id is 
3705.
This step is purely informational to show how I came up with the rule id used 
in the
next step.

2. Get statements related to R3705:

$ curl "http://biodata.mdanderson.org/s3db/S3QL.php?
key=KEYNAME&query=<S3QL><from>statements</from><where><project_id>80192</proje
ct_id><rule_id>3705</rule_id></where></S3QL>"

* What is the expected output? What do you see instead?

Here's what I get back. All headers and no data.

<TABLE><TR><TD>statement_id</TD><TD>value</TD><TD>notes</TD><TD>file_name</
TD><TD>file_size</TD><TD>rule_id</TD><TD>resource_id</TD><TD>project_id</TD><T
D>created_on</TD><TD>created_by</TD><TD>subject</TD><TD>verb</TD><TD>object<
/TD><TD>description</TD><TD>instance_id</TD><TD>item_id</TD><TD>permission_leve
l</TD><TD>assigned_permission</TD><TD>effective_permission</TD><TD>uid</TD><TD
>uri</TD></TR></TABLE>

I expected to get back results that match the following:

$ curl "http://biodata.mdanderson.org/s3db/S3QL.php?
key=KEYNAME&query=<S3QL><from>statements</from><where><rule_id>3705</rule_id><
/where></S3QL>" | tidy -q -i

* What version of the product are you using? On what operating system?
S3DB 3.5.2 (as of 2009/03/10 when issue reported)
Redhat 5.2

* Please provide any additional information below.

This is the same HTTP GET query that had been working for over a month. So what 
changed 
since 2009/03/04?

http://biodata.mdanderson.org/s3db/S3QL.php?query=<S3QL><key>YourKey</key><updat
e>group</update><where><group_id>5435</group_id><name>Test+Group+100</name></whe
re></S3QL>&format=xml


What is the URL of your deployment?
http://biodata.mdanderson.org/s3db/

What steps will reproduce the problem?
1. Create a group called "Test Group"
2. Use the above link with proper key (and the group_id) to try to modify
the name of the group
3. You got a normal return message with no error. But the actual group name
become 'null'

What is the expected output? What do you see instead?


What version of the product are you using? On what operating system?


Please provide any additional information below.

WAMP has removed PECL package from its latest versions - PECL is necessary to 
intall S3DB

If you are a windows user and use WAMP to deploy s3db, please install a WAMP 
version that has been deployed WITH PECL (any version released between 
11/21/2007 and 07/11/2009). The list of all WAMP version can be found in 
sourceforge: http://sourceforge.net/projects/wampserver/files/)

What steps will reproduce the problem?
1. login use my account swu3, which has the admin privilege
2. java_service_account was created by swu3
3. permission levels was set correctly on the bioinfo project

What is the expected output? What do you see instead?

swu3 account should have admin privilege. But instead, it lost the admin
privilege and can not manage user and can not see all the projects that
previous can see
java_service_account lost the permission to create item 

This is urgent!!!

What is the URL of your deployment?
http://aleph.inesc-id.pt/s3db/main.php
What steps will reproduce the problem?
1.do a s3ql api query with a login_id with more then 30 chars
2.
3.

What is the expected output? What do you see instead?
Expected:no error in the database

I see: ERROR:  value too long for type character varying(30)
STATEMENT:  insert into s3db_access_log (login_timestamp, session_id,
login_id, ip) values(now(),
'key:wVMY3o2Aai5BOvN','http:google:[email protected]','143.210.172.221')


What version of the product are you using? On what operating system?
3.5.9, linux

Please provide any additional information below.
i changed the column login_id to varchar(255);
before it was a varchar(30) column.

What is the URL of your deployment?
http://ibl.mdanderson.org/TCGA/
What steps will reproduce the problem?
1.Try to select the value from a query
2.http://ibl.mdanderson.org/TCGA/S3QL.php?query=<S3QL><key>yTLV4SFcUtLGBKF</key>
<select>value</select><from>statements</from><where><rule_id>68</rule_id></where
></S3QL>
3.The result is empty

What is the expected output? What do you see instead?
I expect to receive  anumber that I know that exists. It shows an empty
result, as if value was empty (but it isn't).

What version of the product are you using? On what operating system?


Please provide any additional information below.

What steps will reproduce the problem?
- The SPARQL tab interface does not retrieve collections on IE

What is the expected output? What do you see instead?
- Once a project is selected in the SPARQL tab, collections from that project 
should be displayed

Please use labels and text to provide additional information.
- Mozilla firefox and google chrome browser have been tested and are working

What is the URL of your deployment?
http://aleph.inesc-id.pt/s3db/

What steps will reproduce the problem?
1.login with user name + password to retrieve a key 
2. use that key in subsequent s3ql queries
3.some query return the expect result and others return
error, code:1, message:invalid key...

What is the expected output? What do you see instead?
3.some query return the expect result and others return
error, code:1, message:invalid key...

in the postgres log we can see:
STATEMENT:  insert into s3db_deployment (deployment_id, url, publickey,
checked_on, checked_valid) values ('', '', '', now(), '')
ERROR:  invalid input syntax for type timestamp: ""

What version of the product are you using? On what operating system?
S3DB-3.5.7; D1313779; linux; apache; postgres 8.3.3

Please provide any additional information below.

because s3db is deployed in different databases, it should use an
intermediary logic layer so when you are inserting  
database values the intermediary layers would convert that datatype
from php to the right representation of that datatype for each
database.
cleary the check_valid field is of type timestamp and does not accept
'' (string) values on postgres 8.3.3. . Maybe in the other databases
it is accept.
the logic layer is usually called ORM when the logic code is on object
programming and does this conversion automatically. 
It's a suggestion.

What is the URL of your deployment?
localhost

What steps will reproduce the problem?
1.update rule query
2.bad documentation
3.

What is the expected output? What do you see instead?
error_code  message
0   rule updated


What version of the product are you using? On what operating system?
3.5.9
windows xp 32bit


Please provide any additional information below.
Documentation says:
Update  Where (Required)    Where (Optional)
rule    rule_id     subject, verb, object, notes, validation

but the query:
<S3QL><update>rule</update><where><rule_id>137</rule_id><notes>test</notes>
</where></S3QL>
doesn't work

It requires subject_id, verb_id, object_id as well to work:
<S3QL><update>rule</update><where><rule_id>137</rule_id><notes>test</notes>
<subject_id>76</subject_id><validation></validation><verb_id>80</verb_id><o
bject_id>134</object_id></where></S3QL>

What is the URL of your deployment?

What steps will reproduce the problem?
1.
2.
3.

What is the expected output? What do you see instead?


What version of the product are you using? On what operating system?


Please provide any additional information below.

What is the URL of your deployment?
http://mdadqss3db05/s3db/S3QL.php?query=<S3QL><key>kEolQJJlOaMSmCm</key><select>
item_id</select><from>items</from><where><project_id>3780</project_id></where></
S3QL>

What steps will reproduce the problem?
1. The item_id back empty.
2. The same url when used in other projects to return the item_id way.
3.

What is the expected output? What do you see instead?

The expected result is all item_id of the project. He did not return me
anything.

What version of the product are you using? On what operating system?


Please provide any additional information below.

What is the URL of your deployment?

What steps will reproduce the problem?
1.<S3QL><select>*</select><from>users</from><where><project_id>[project_id]
</project_id></where></S3QL>
2.<S3QL><select>*</select><from>users</from><where><project_id>[project_id]
</project_id><user_id>[a user_id not listed in the answer to 
1)]</user_id></where></S3QL> 

What is the expected output? 

empty reply

What do you see instead?

info on [a user_id not listed in the answer to 1)]

What is the URL of your deployment?
any url would present this problem

What steps will reproduce the problem?
1.Different computers doing the same KIND of query at the same time
OR
2.One user doing the same query at the same time using different browsers
(firefox and safari, as exemple)
MAYBE
3.Querying THE SAME PROJECT at the same time

What is the expected output? What do you see instead?
I know that one of my queries should always return an array with size 3. If
I do something like I described above, I notice that I receive answares
with one or 2 arrays sometimes.

What version of the product are you using? On what operating system?


Please provide any additional information below.
My concern is, this query I know that has size 3. How about the others,
that have variable size?

What is the URL of your deployment?
http://ibl.mdanderson.org
What steps will reproduce the problem?
1.Try to access a txt file and store its content in a variable (using
javascript)
2.http://ibl.mdanderson.org/TCGA/download.php?statement_id=217&download=no&key=y
TLV4SFcUtLGBKF
3.

What is the expected output? What do you see instead?
I need to convert the text files in text when I call jasonpp
format=json&callback=call, so I can store the text values in a json object,
but that doesn't happen.

What version of the product are you using? On what operating system?
I am using javascript

Please provide any additional information below.

What is the URL of your deployment?
http://dqsbcb01.mdanderson.edu/s3db

What steps will reproduce the problem?
1. Insert a statement with the '&madash' character, you can copy this from
any web page such as 
http://www.chron.com/disp/story.mpl/ap/top/all/6618447.html

WASHINGTON — Law enforcement agents raided residences in New York City
before dawn Monday as part of a terrorism investigation.

2. I have already input one of this in the database. The problem is when we
want to query this statement

3. Try this query:
http://dqsbcb01.mdanderson.edu/s3db/S3QL.php?query=<S3QL><key>yourkey</key><sele
ct>*</select><from>statements</from><where><project_id>16762</project_id><subjec
t>Project</subject></where></S3QL>&format=xml


What is the expected output? What do you see instead?
It suppose to return an XML doucument. 
Instead we got an error message:

XML Parsing Error: undefined entity
Location:
http://dqsbcb01.mdanderson.edu/s3db/S3QL.php?query=%3CS3QL%3E%3Ckey%3Eyourkey%3C
/key%3E%3Cselect%3E*%3C/select%3E%3Cfrom%3Estatements%3C/from%3E%3Cwhere%3E%3Cpr
oject_id%3E16762%3C/project_id%3E%3Csubject%3EProject%3C/subject%3E%3C/where%3E%
3C/S3QL%3E&format=xml
Line Number 2078, Column 16:    <value>GENEVA &Atilde;&cent;&Acirc;�&Acirc;�
The World Climate Conference has approved the creation of a new climate
forecasting system to help countries adapt to climate change and enable
them to better prepare for natural disasters, officials said Friday.</value>
----------------------^


What version of the product are you using? On what operating system?
S3DB   3.5.7
    D1378171

Please provide any additional information below.

Look like it does not handle the html or xml entities. Any &4221; kind of
characters will cause this problem

Some versions of WAMP are not very happy with s3db's URI redirection. If
you are getting an "Internal Server Error" message when you setup S3DB,
simply move the file called .htaccess into the folder /uri

What is the URL of your deployment?

http://www.isbiotechnology.com

What steps will reproduce the problem?
1. I open the pahe http://localhost/s3db
2. I fill the form in basic mode and create the database
3. The procedure fails

What is the expected output? What do you see instead?

It is espected the database creation and the final configuration page 
instead the browser give the follow message: HTTP 500 internal error.

What version of the product are you using? On what operating system?

I am using the version 3.5 on a windows 7 with a wamp server. I have 
downloaded the full application s3db + wamp

Please provide any additional information below.

What is the URL of your deployment?
https://biodata.mdanderson.org/s3db

What steps will reproduce the problem?
1.
https://biodata.mdanderson.org/s3db/S3QL.php?query=<S3QL><key>yourkey</key><upda
te>statement</update><where><statement_id>8391</statement_id><value>To+see+if+th
e+owner+can+edit+this+project+with%27s+apostrophe</value></where></S3QL>&format=
xml
here %27 is the encoded value for apostrophe(')

What is the expected output? What do you see instead?
Update failed, error code 2

What is the URL of your deployment?

What steps will reproduce the problem?
Specifying the fields to return instead of using "*".

wget -q -O -
'http://vor.mdanderson.edu:8088/s3db/S3QL.php?key=...&query=<S3QL><select>item_i
d,value</select><from>statements</from><where><rule_id>18305</rule_id><value>238
04</value><project_id>11344</project_id></where></S3QL>&format=xml'

What is the expected output? What do you see instead?

Get nothing.  Expect to see fields.



What version of the product are you using? On what operating system?


Please provide any additional information below.

What is the URL of your deployment?
https://biodata.mdanderson.org/s3db

What steps will reproduce the problem?
Using the API to:
1. Create an item, in the "notes" field, have some single quotes in it.
When you create the item, single quotes are work fine
2. The use the API to update this "notes" field. If the content of this
"notes" field contain single quote ('), you can not update it.
Example, in this command:
https://biodata.mdanderson.org/s3db/S3QL.php?query=<S3QL><key>yourkey</key><upda
te>item</update><where><item_id>6968</item_id><notes>Shaolong%27s+Test+on+April+
3+fgdfgdf</notes></where></S3QL>&format=xml

Here %27 is the encoded format of the single quote(')



What is the expected output? What do you see instead?
Expected to update. 
Instead, it get nothing back. No error message at all.

What is the URL of your deployment?
http://s3db.github.com/

What steps will reproduce the problem?
1. download s3db
2. try to install it
3. try to setup the database

What is the expected output? What do you see instead?
Expected is that something happens when you click the Create Table button in 
the screenshot. Instead, nothing happens when you do this. The page is stuck. 
Refreshing the page produces an error since until now no admin user has been 
created.

What version of the product are you using? On what operating system?
3.5.14 with windows 7

Please provide any additional information below.

What is the URL of your deployment?

What steps will reproduce the problem?
1.http://aleph.inesc-id.pt/s3db/S3QL.php?
key=Po2x9Uq6MR5SBiz&format=json&query=%3CS3QL%3E%3Cselect%3E*%3C/select%3E%
3Cfrom%3Estatements%3C/from%3E%3Cwhere%3E%3Csubject_id%3E26514%3C/subject_i
d%3E%3C/where%3E%3C/S3QL%3E&jsonp=
2.
3.

What is the expected output? What do you see instead?
expected statements from subject_id 26514 and I'm getting the 
entire database statements

the documentation says
select
statement_id, item_id, rule_id, value, file_name, file_size, subject, 
subject_id, verb, verb_id, object, object_id,
notes (deprecated), resource_id (deprecated), instance_id (deprecated),  
project_id (deprecated) 
from
statements

but putting a parameter in subject_id does not work

What version of the product are you using? On what operating system?
S3DB   3.5.9 D1313779,linux

Please provide any additional information below.

http://biodata.mdanderson.org/s3db/S3QL.php?query=<S3QL><key>vW4Q7hoCQMCMcTD</ke
y><insert>user</insert><where><login>rockey</login><email>rockeywu%40yahoo.com</
email><username>Rockey+Wu</username><address>5215+Cheena+Drive</address><city>Ho
uston</city><country>USA</country><postal_code>77096</postal_code></where></S3QL
>&format=xml


What is the URL of your deployment?
http://biodata.mdanderson.org/s3db

What steps will reproduce the problem?
1. Create user using the API, specify username, address, city, country,
state, zip code

What is the expected output? What do you see instead?
user successfully created, but the username is not the one we input (the
real name), instead, it take the login value. Other information (address,
city, state, country, zip code) does not saved.

This is same when you try to update these values

What is the URL of your deployment?
Not relevant

What steps will reproduce the problem?
1. Go to "Documentation" at http://s3db.org


What is the expected output? What do you see instead?

Expect: clear statement of documented version
See: Nothing about version

What version of the product are you using? On what operating system?


Please provide any additional information below.

What is the URL of your deployment?

http://biodata.mdanderson.org/

What steps will reproduce the problem?
1. Run attached Python script which attempts to insert statements both
with and without 'project_id" as criteria.

What is the expected output? What do you see instead?

One should always get a response from a query, either as
a success, or as an error. Instead, nothing is returned.

If this is considered an error, maybe something like:
    errcode, 'criteria invalid in this context', field
      where:
        errcode = S3DB error code
        field      = name of criteria that caused problem [in this example, project_id]

What version of the product are you using? On what operating system?

S3DB 3.5.2 (D1356676)
RHEL 5.2

Also occurs for:

S3DB 3.5.7 (D1378171)
RHEL 5.3

Please provide any additional information below.

Problem described above verified for inserting statements and instances. Other
types of inserts not tried.

What is the URL of your deployment?
http://s3db.virtual.vps-host.net/s3db/

What steps will reproduce the problem?
1.add remote rule
2.
3.

What is the expected output? What do you see instead?
Expected to create a new rule, but it doesn't.

What version of the product are you using? On what operating system?
Internet Explorer and Firefox on Vista.

Please provide any additional information below.

What is the URL of your deployment?

http://dqsbcb01.mdanderson.edu/s3db

What steps will reproduce the problem?
1. Start terminal process and resize to width of screen.
$ ssh dqsbcb01
$ cd /usr/local/apache2/logs
$ tail -F error_log
2. Login to S3DB via web browser.
3. View terminal again after login.

What is the expected output? What do you see instead?

Nothing.

[<timestamp>] [error] [ip addr] File does not exist: 
/usr/local/apache2/htdocs/s3db/'.S3DB_URI_BASE.', referer: 
http://dqsbcb01.mdanderson.edu/s3db/home.php

What version of the product are you using? On what operating system?

S3DB 3.5.7 (D1378171)
RHEL 5.3

Please provide any additional information below.

This is happening for multiple PHP scripts, not just the one referenced above.
Other known ones include: 'admin/edituser.php', 'access_keys.php',
'frames/HeaderFrame.php'. Currently have insufficient access using MDACC
account on this system to see what other PHP scripts might be affected.

What is the URL of your deployment?
biohypo.org

What steps will reproduce the problem?
1.delete collection and all dependencies, on a collection with 4000 items
each item 9 statements 
2.try to create the same collection with the same rules
3.some rules cannot be created

What is the expected output? What do you see instead?
that the deleted rules inside the deleted collection could 
be created again.
What we saw was: some of the rules where not deleted in the database.
because the collection was deleted, the user could not access the rules
that were not deleted, without going directly to the database and 
understand the problem.
We don't know why all the rules were not deleted, probably there was
a timeout on the connection between the php code and the database?

What version of the product are you using? On what operating system?
S3DB   3.5.7

Please provide any additional information below.
if the problem was the one described above, here is a possible 
solution:
Isolate the "delete collection and all dependencies"
in a transaction this means:
(pseudo code)
begin transaction 1
  get collection by id
  get all dependecies by id(items,rules,statements)
  delete collection
  delete all dependencies
close transaction 1
if(transaction error ) rollback transaction 1

This will ensure that if some error occurs that there won't
be data inconsistencies in the database and therefore 
on the API and Interface functionalities.

Regards.

What is the URL of your deployment?
http://biodata.mdanderson.org/s3db
or
http://dqsbcb01.mdanderson.edu/s3db

What steps will reproduce the problem?
1. Enter URL into browser (with a valid KEY)

http://biodata.mdanderson.org/s3db/S3QL.php?key=KEY&<S3QL><select>*</select><fro
m>projects</from></S3QL>&format=xml

2. Check the output against the documentation at http://s3db.org

What is the expected output? What do you see instead?

The following fields are returned from the query and are not documented
[i] project_name (duplicates 'name')
[ii] project_description (duplicates 'description')
[iii] project_owner
[iv] permission_level
[v] assigned_permission
[vi] effective_permission
[vii] uid
[viii] uri

If the duplicates are there for backwards compatibility, then they should
be documented as "deprecated'.

The meanings of the various permission fields need to be clearly documented.

Similarly,the uid and uri should be documented.

What version of the product are you using? On what operating system?
biodata: 3.5.2
dqsbcb01: 3.5.7

Please provide any additional information below.

What is the URL of your deployment?

http://aleph.inesc-id.pt/s3db/

What steps will reproduce the problem?
1.Login
2.Select Project Pneumopath
3.Select Project Files Collection
4.List Project Files
5.Add file to any statement

What is the expected output? 
statement saved, file added to statement

What do you see instead?
the message in the attachet file
"Filesize cannot be null"

What version of the product are you using? 
S3DB   3.5.7
D1313779
Update status From Admin Menu:
"Last code update was on Sunday, 01st November, 2009 @ 06:55pm. Updating
only affects minor bugs, it will not affect major functionality. Before
reporting a bug, please update your code, the bug might have been fixed."

On what operating system?
Linux slackware 12.0

Please provide any additional information below.
This does not allow pneumopath users to insert files on 
the project file ontology, which is crucial to this project.

* What is the URL of your deployment?
<http://biodata.mdanderson.org/s3db/>

* What steps will reproduce the problem?
1. Pick an item somewhere and edit it.
2. Put an ampersand in the Notes textfield of the item
3.

* What is the expected output? What do you see instead?
Expected to see '&amp;' if this same item is requested via S3QL.
The current response from S3DB contains invalid HTML due to
the ampersand not having been escaped.

* What version of the product are you using? On what operating system?
S3DB 3.5.2 (D1356676)
Redhat 5.2

Please provide any additional information below.

[NOTE] Data entered has been patched manually already.

These were my troubleshooting steps:

$ curl 'http://biodata.mdanderson.org/s3db/S3QL.php?key= 
KEYNAME&query=<S3QL><from>statements</from><where><project_id>80192</project_id
><rule_id>3472</rule_id></where></S3QL>' | tidy

This was the response:
'<TABLE><TR><TD>statement_id</TD><TD>value</TD><TD>notes</TD><TD>file_name<
/TD><TD>file_size</TD><TD>rule_id</TD><TD>resource_id</TD><TD>project_id</TD><
TD>created_on</TD><TD>created_by</TD><TD>subject</TD><TD>verb</TD><TD>object
</TD><TD>description</TD><TD>instance_id</TD><TD>item_id</TD><TD>permission_le
vel</TD><TD>assigned_permission</TD><TD>effective_permission</TD><TD>uid</TD><T
D>uri</TD></TR><TR><TD>3477</TD><TD>Affymetrix 
U133A</TD><TD></TD><TD></TD><TD></TD><TD>3472</TD><TD>3474</TD><TD>
80192</TD><TD>2009-02-09 
16:12:21.580683</TD><TD>13</TD><TD>Platform</TD><TD>called</TD><TD>name</T
D><TD></TD><TD>3474</TD><TD>3474</TD><TD>222</TD><TD>---
</TD><TD>222</TD><TD>D1356676U3229S3477</TD><TD>http://biodata.mdanderson.o
rg/s3db/S3477</TD></TR><TR><TD>3486</TD><TD>Reverse Phase Protein 
Array</TD><TD></TD><TD></TD><TD></TD><TD>3472</TD><TD>3483</TD><TD>8
0192</TD><TD>2009-02-09 
16:14:42.431864</TD><TD>13</TD><TD>Platform</TD><TD>called</TD><TD>name</T
D><TD></TD><TD>3483</TD><TD>3483</TD><TD>222</TD><TD>---
</TD><TD>222</TD><TD>D1356676U3229S3486</TD><TD>http://biodata.mdanderson.o
rg/s3db/S3486</TD></TR><TR><TD>3494</TD><TD>Sequenom INT05 
Set</TD><TD></TD><TD></TD><TD></TD><TD>3472</TD><TD>3491</TD><TD>801
92</TD><TD>2009-02-09 
16:16:23.521709</TD><TD>13</TD><TD>Platform</TD><TD>called</TD><TD>name</T
D><TD></TD><TD>3491</TD><TD>3491</TD><TD>222</TD><TD>---
</TD><TD>222</TD><TD>D1356676U3229S3494</TD><TD>http://biodata.mdanderson.o
rg/s3db/S3494</TD></TR><TR><TD>3503</TD><TD>Illumina Human WG-6 
v.3.0</TD><TD></TD><TD></TD><TD></TD><TD>3472</TD><TD>3500</TD><TD>8
0192</TD><TD>2009-02-09 
16:17:40.710258</TD><TD>13</TD><TD>Platform</TD><TD>called</TD><TD>name</T
D><TD></TD><TD>3500</TD><TD>3500</TD><TD>222</TD><TD>---
</TD><TD>222</TD><TD>D1356676U3229S3503</TD><TD>http://biodata.mdanderson.o
rg/s3db/S3503</TD></TR><TR><TD>4533</TD><TD>None</TD><TD></TD><TD></TD
><TD></TD><TD>3472</TD><TD>4527</TD><TD>80192</TD><TD>2009-02-27 
17:39:03.054361</TD><TD>3229</TD><TD>Platform</TD><TD>called</TD><TD>name<
/TD><TD></TD><TD>4527</TD><TD>4527</TD><TD>222</TD><TD>---
</TD><TD>222</TD><TD>D1356676U3229S4533</TD><TD>http://biodata.mdanderson.o
rg/s3db/S4533</TD></TR><TR><TD>6006</TD><TD>miRCURY LNA 
v11.0</TD><TD>v.11.0 - hsa; mmu & 
rno;</TD><TD></TD><TD></TD><TD>3472</TD><TD>5980</TD><TD>80192</TD><T
D>2009-03-16 
15:28:52.496267</TD><TD>15</TD><TD>Platform</TD><TD>called</TD><TD>name</T
D><TD>v.11.0 - hsa; mmu & 
rno;</TD><TD>5980</TD><TD>5980</TD><TD>222</TD><TD>---
</TD><TD>222</TD><TD>D1356676U3229S6006</TD><TD>http://biodata.mdanderson.o
rg/s3db/S6006</TD></TR><TR><TD>6024</TD><TD>SMARTpool whole 
genome</TD><TD></TD><TD></TD><TD></TD><TD>3472</TD><TD>6017</TD><TD
>80192</TD><TD>2009-03-16 
15:36:33.035634</TD><TD>15</TD><TD>Platform</TD><TD>called</TD><TD>name</T
D><TD></TD><TD>6017</TD><TD>6017</TD><TD>222</TD><TD>---
</TD><TD>222</TD><TD>D1356676U3229S6024</TD><TD>http://biodata.mdanderson.o
rg/s3db/S6024</TD></TR></TABLE>'

Running the response through 'Tidy' gives:
line 1 column 1 - Warning: missing <!DOCTYPE> declaration
line 1 column 2783 - Warning: unescaped & which should be written as &amp;
line 1 column 3010 - Warning: unescaped & which should be written as &amp;
line 1 column 1 - Warning: inserting missing 'title' element
line 1 column 1 - Warning: <table> lacks "summary" attribute
Info: Document content looks like HTML 3.2
5 warnings, 0 errors were found!

[SNIP irrelevant output]
<tr>
<td>6006</td>
<td>miRCURY LNA v11.0</td>
<td>v.11.0 - hsa; mmu & rno;</td>
<td></td>
<td></td>
<td>3472</td>
<td>5980</td>
<td>80192</td>
<td>2009-03-16 15:28:52.496267</td>
<td>15</td>
<td>Platform</td>
<td>called</td>
<td>name</td>
<td>v.11.0 - hsa; mmu & rno;</td>
<td>5980</td>
<td>5980</td>
<td>222</td>
<td>---</td>
<td>222</td>
<td>D1356676U3229S6006</td>
<td>http://biodata.mdanderson.org/s3db/S6006</td>
</tr>
[SNIP remaining output]

What is the URL of your deployment?
http://mdadqss3db05/s3db

What steps will reproduce the problem?
1. Run the following query:
http://mdadqss3db05/s3db/S3QL.php?
query=<S3QL><key>Q5vSzS4YrFyQuCX</key><delete>project</delete><where><user_
id>3203</user_id><flag>all</flag><project_id>179701</project_id></where></S
3QL>

ps.: this key will be valid until March 13, 2009

What is the URL of your deployment?

ibl.mdanderson.org

What steps will reproduce the problem?
1. create collection in the s3db.php tool

What is the expected output? What do you see instead?

it works fine - it creates the collection, but it also issues the error 
message "account_lid cannot be empty. For syntax instructions refer to S3DB 
Documentation"

What is the URL of your deployment?
http://biodata.mdanderson.org/s3db/S3QL.php

What steps will reproduce the problem?

Run the following query:
http://biodata.mdanderson.org/s3db/S3QL.php?query=<s3ql><key>sVsQDlcCFT1YK9u</ke
y><select>*</select><from>statements</from><where><rule_id>~'47011|47029'</rule_
id></where><format>xml</format></s3ql>

(Note that the specified key will disappear very soon....) 

What is the expected output? 
Just the statements belonging to the two specified rule IDs. 

What do you see instead?
Gazoodles of statemets from different rules and different projects.

What version of the product are you using? On what operating system?
S3DB 3.5.2, D1356676

Please provide any additional information below.

If you specify the project_id as well, then the query appear to fail in a
different way (even though project_id is not documented as a valid field
for selecting statements...), which I will file as a second bug repotr

What is the URL of your deployment?

What steps will reproduce the problem?
1.
2.
3.

What is the expected output? What do you see instead?


What version of the product are you using? On what operating system?


Please provide any additional information below.

What is the URL of your deployment?
http://aleph.inesc-id.pt/s3db/

What steps will reproduce the problem?
1.Install s3db in linux supported by postgres 
2. insert a statement
3.

What is the expected output? What do you see instead?
Expected s3db_statement_log table to be updated.
I see in postgresql error log:
ERROR:  invalid input syntax for integer: ""
STATEMENT:  insert into s3db_statement_log (statement_log_id, statement_id,
old_rule_id, old_resource_id, old_project_id, old_value, old_notes, action,
modified_by, modified_on, created_on, created_by) values ('', '34649',
'29048','34636','3628','NUMBER','','create','3510', now(), '', '3510')


What version of the product are you using? On what operating system?
3.5.7 on the last beta update (see pic). linux.

Please provide any additional information below.

The field type "timestamp" in postgres, does not except strings.
in the error log, the field created_on is being filled with '',
which represents a string.

Further I think the problem is conceptual. the audit trail table only
has to accept "modified date". the first modified date of a statement,
that appears in s3db_statement_log is actually the created_on date...
 therefore created_on and created_by are redundant fields in this table,
in my opinion.

What is the URL of your deployment?
cannot create deployment

What steps will reproduce the problem?
1.deploy s3db code in an apache served folder
2.access application the 1st time through the browser
3.try to configure the host of database connection

What is the expected output? 
There should be a field "Database location"
to set the ip/domain of the database host

What do you see instead?
there isn't such field, the application assumes the database
will always be localhost.

What version of the product are you using? 
S3DB   3.5.7
On what operating system?
linux debian 5 (lenny)

Please provide any additional information below.
it is not possible to optimized the application by distributing 
cpu processing on a web-server and on a database-server from 
a different machine, without changing the php code.

Thanks.

Mauro

[deleted issue]

What is the URL of your deployment?

http://biodata.mdanderson.org

What steps will reproduce the problem?
1. http://biodata.mdanderson.org/s3db/S3QL.php?
key=[your_key_here]&query=<S3QL><from>statements</from><where><rule_id>3705
</rule_id></where></S3QL>
2. http://biodata.mdanderson.org/s3db/S3QL.php?
key=[your_key_here]&query=<S3QL><from>statements</from><where><project_id>8
0192</project_id><rule_id>3705</rule_id></where></S3QL>
3.

What is the expected output? What do you see instead?

One should get the same output for both queries

What version of the product are you using? On what operating system?

Code time stamp February 2009

Please provide any additional information below.

Since the project_id is correct it shouldn't make any difference if it is 
there or not

What is the URL of your deployment?

ibl.mdanderson.org/gcc

What steps will reproduce the problem?

successful S3QL delete of a statement will produce redundant message, 
something like: 'S2199 removed from S2199.'

What is the expected output? What do you see instead?

something like: 'Sxxx removed from Iyyy, Rzzz.'

What is the URL of your deployment?
https://biodata.mdanderson.org/s3db/
What steps will reproduce the problem?
In this query,
https://biodata.mdanderson.org/s3db/S3QL.php?query=<S3QL><key>yourkey</key><sele
ct>*</select><from>statements</from><where><value>%7E%5E.*this.*</value><subject
>Project</subject><object>title</object></where></S3QL>&format=xml
I got a return result where the <object> is "abstract" instead of the
"title" as specified in the query

What is the expected output? What do you see instead?
should not get the result with the object as "abstract"

What version of the product are you using? On what operating system?


Please provide any additional information below.

What is the URL of your deployment?
http://biodata.mdanderson.org/s3db/

What steps will reproduce the problem?
Try the following three queries:
1.
http://biodata.mdanderson.org/s3db/S3QL.php?query=<s3ql><key>sVsQDlcCFT1YK9u</ke
y><select>*</select><from>statements</from><where><rule_id>47011</rule_id><proje
ct_id>23813</project_id></where><format>xml</format></s3ql>

2.
http://biodata.mdanderson.org/s3db/S3QL.php?query=<s3ql><key>sVsQDlcCFT1YK9u</ke
y><select>*</select><from>statements</from><where><rule_id>47029</rule_id><proje
ct_id>23813</project_id></where><format>xml</format></s3ql>

3.
http://biodata.mdanderson.org/s3db/S3QL.php?query=<s3ql><key>sVsQDlcCFT1YK9u</ke
y><select>*</select><from>statements</from><where><rule_id>~'47011|47029'</rule_
id><project_id>23813</project_id></where><format>xml</format></s3ql>


What is the expected output? What do you see instead?

Query 1 returns 13 statements
Query 2 returns 18 statements
Query 3 is expected to return 13+18=31 statements, but actually returns 0
statements.

What version of the product are you using? On what operating system?
S3DB 3.5.2,  D1356676

Please provide any additional information below.

What is the URL of your deployment?
http://mdadqss3db02/s3db
What steps will reproduce the problem?
1.One user doing the same query at the same time using different browsers
(firefox and internet explorer, as exemple),at the same project.

What is the expected output? What do you see instead?
A list of patients, but a query fail and the other get the imcomplete result. 
I expected a list with 1119 patients, but I get 6.

What is the URL of your deployment?
http://biodata.mdanderson.org/s3db/S3QL.php?
query=<S3QL><key>jD24zubLlHUVH6t</key><select>value</select><from>statement
s</from><where><item_id>10484</item_id><verb>refers%20to</verb></where></S3
QL>

What steps will reproduce the problem?
1.Digit the follow URL: http://biodata.mdanderson.org/s3db/S3QL.php?
query=<S3QL><key>jD24zubLlHUVH6t</key><select>value</select><from>statement
s</from><where><item_id>10484</item_id><verb>refers%20to</verb></where></S3
QL>
2.The URL above return anything.
3.But if you digit the follow URL http://biodata.mdanderson.org/s3db/S3QL.php?
query=<S3QL><key>jD24zubLlHUVH6t</key><select>*</select><from>statements</f
rom><where><item_id>10484</item_id><verb>refers%20to</verb></where></S3QL>,
where <select>value</select> was replaced by <select>*<select> the column 
value return one value.

What is the URL of your deployment?

http://dqsbcb01.mdanderson.edu/s3db

What steps will reproduce the problem?
1. Login as MDACC user.
2. Click on Project tab

What is the expected output? What do you see instead?

Should have displayed list of projects.
Instead, you are logged out.

What version of the product are you using? On what operating system?

S3DB 3.5.7 (D1378171)
RHEL 5.3

Please provide any additional information below.

Logging back in again afterwards will function normally.