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| * [:RankerProgram:Ranker Program] -- The ranker program is used to develop and input Baboon social ranks. * [:BabaseVPN:The Babase VPN] -- The Babase Virtual Private Network is available to those people who have a Unix Login on Papio. It is primarly used to run the ranker program. * [:PsionFormat:The Psion Data Format] -- The Psions are handheld data collection devices. They output their data in a custom format. * [:BabaseChangelog:Babase 2.0 Changelog] |
* [[RankerProgram|Ranker Program]] -- The ranker program is used to develop and input Baboon social ranks. * [[BabaseVPN|The Babase VPN]] -- The Babase Virtual Private Network is available to those people who have a Unix Login on Papio. It is primarly used to run the ranker program. * [[PsionFormat|The Psion Data Format]] -- The Psions are handheld data collection devices. They output their data in a custom format. * [[UserManagement|User Management]] * [[DukeOITTools|Duke OIT Tools]] * [[FirewallTools|Firewall Tools]] * [[BabaseChangelog|Babase 2.0 Changelog]] |
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| * [:ProgramLinks:Generic Programs] * [:ProgramLinks:Babase's Bespoke Programs] |
* [[ProgramLinks|Babase's Bespoke Programs]] |
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| * [:DukeDMP:Duke's Data Management Protocol] -- Data Maintenance and Demography Update Protocols * attachment:Princeton%20Data%20Management%20Protocol%20Babase%201.0 -- Data Maintenance and Demography Update Protocols. The attached protocol is for Babase 1.0. The revised protocol for Babase 2.0 is still under construction. The basis of data decisions (such as maturedates and dispersedates) will not change with Babase 2.0, but the table input order and upload procedure will differ. |
* [[attachment:2023_07_03 Behav_GrpMovement Data Management Protocols.pdf|Behavioral and Group Movement Data Management Protocol]] (last updated 2023-07-03) -- Protocol for maintenance of interaction data, focal sampling data, GPS/SWERB data, male ranks, dartings, and predation and human disturbance data. Also known as the "Duke Protocol". * [[attachment:Census_and_Reproductive_Data_Management_Protocol.pdf|Census and Reproductive Data Management Protocol]] (last updated 2023-03-31) -- Protocol for Data Checking and the Demography/Reproduction Update * [[attachment:Data Storage.pdf]] -- See attachment for information on how data that come from the field are stored * [[attachment:Electronic Data Handling.pdf]] -- See attachment for information on how electronic data are processed * [[attachment:Paper Data Handling.pdf]] -- See attachment for information on how paper data are processed * [[GeneticTableForms|Forms for adding new data to the genetics tables]] |
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| * [:DukeIDEP:Duke's Interaction Data Entry Protocol] -- Specific to Grooming, MCE, and Agonisms | |
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| * [:TabbyTest:Tabby's test page] | * [[TabbyTest|Tabby's test page]] |
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| * [:WritingAComplexQuery] | * [[WritingAComplexQuery]] |
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[[Anchor(usermanagement)]] === User Management === [[Anchor(newuser)]] ==== Adding a User to Babase ==== Users can be added to babase, as well as a schema created, and permissions set, by completing the following steps using a SSH client. {{{ PGPASSWORD='*********' babase-user-add USERNAME babase_readers}}} * The ********* here would be the babase_admin password * The Username selected will become not only the babase username and temporary password but also the schema name. * It is very important that the user immediately change their password using PPA's password change option. [[Anchor(deleteuser)]] ==== Deleting a User from Babase ==== ---- WARNING: The process described in this section deletes the user's personal schemas. Be sure to examine the tables in these schemas before deletion to be sure that nothing should be saved. A table may be transferred to another schema by the babase administrator with the following SQL command: {{{ ALTER TABLE oldschema.sometable SET SCHEMA newschema;}}} ---- Users can be deleted from babase, and their personal schemas deleted as well, by running the following command on papio using a SSH client: {{{ babase-user-delete USERNAME}}} The password requested is that of the babase administrator. Be sure to peruse the output as it not only displays all the tables and other database objects deleted but may also contain error messages and descriptions of why the operation failed. Lines containing error messages and further information are are prefixed with 'ERROR:' and 'DETAIL:'. Errors are generally due to the user having explicit permissions to or ownership of objects that are not in their personal schema. These issues are resolved by connecting to the database in question (usually babase) as the database administrator and either using PPA's management features or directly issuing SQL commands. The SQL command to remove permissions from, say, a table is: {{{ REVOKE ALL ON TABLE sometable FROM someuser;}}} If the database object in question is not a table then change the word {{{TABLE}}} in the above command to kind of object in question. To reassign ownership of, say, a table to another user use the following SQL command: {{{ AlTER TABLE sometable OWNER TO anotheruser;}}} Again, if the database object in question is not a table then change the word {{{TABLE}}} in the above command to kind of object in question. Note that each user has a personal schema in each database, {{{babase}}}, {{{babase_test}}}, and {{{babase_copy}}}. The {{{babase-user-delete}}} command can succeed in deleting schemas from some databases and not others. If this occurs the command can be re-run once the situation which prevents schema deletion is rectified. In this case you may receive errors which say that schemas do not exist. These can be safely ignored. |
* [[attachment:Historic Agonism Summary.xls]] |
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| PGPASSWORD='*********' babase-copy-babase-schema babase babase_test}}} * The ********* here would be the babase_admin password |
PGPASSWORD='*********' babase-copy-babase-schema YOURADMINNAME babase babase_test }}} * The ********* here would be the password of YOURADMINNAME |
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| PGPASSWORD='*********' babase-copy-babase-schema -f babase_test babase}}} | PGPASSWORD='*********' babase-copy-babase-schema -f YOURADMINNAME babase_test babase }}} * When Backing up the DB, the 'help' directory can offer some direction |
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* When Backing up the DB, the 'help' directory can offer some direction |
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| [YOU@papio ~]$ pg_dump --help}}} |
[YOU@papio ~]$ pg_dump --help }}} |
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| After you have logged into the database as the administrator, select the babase database. | Log in to phpPgAdmin as an administrator, then select the babase database. |
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| You may have to click cancel on the process you are killing a couple of times. It will tell you that the function has failed, its just kidding! | You will see a list of ongoing processes (queries, usually). Click the "Cancel" button next to whichever process you want to kill. You may have to click cancel on the process you are killing a couple of times. It might tell you that the function has failed, but you can ignore that; it's an error in phpPgAdmin, not with Postgres. |
This page is used to store codes, protocols, and procedures for use by the Data Managers.
Babase Technical Information
These links are primarly of interest to the Babase support staff.
Ranker Program -- The ranker program is used to develop and input Baboon social ranks.
The Babase VPN -- The Babase Virtual Private Network is available to those people who have a Unix Login on Papio. It is primarly used to run the ranker program.
The Psion Data Format -- The Psions are handheld data collection devices. They output their data in a custom format.
Programs
Protocols
Behavioral and Group Movement Data Management Protocol (last updated 2023-07-03) -- Protocol for maintenance of interaction data, focal sampling data, GPS/SWERB data, male ranks, dartings, and predation and human disturbance data. Also known as the "Duke Protocol".
Census and Reproductive Data Management Protocol (last updated 2023-03-31) -- Protocol for Data Checking and the Demography/Reproduction Update
Data Storage.pdf -- See attachment for information on how data that come from the field are stored
Electronic Data Handling.pdf -- See attachment for information on how electronic data are processed
Paper Data Handling.pdf -- See attachment for information on how paper data are processed
Wiki Administration
Misc Links
SandboxPage -- Sandbox page for sharing code remotely
Copying the Babase Schema
The babase-copy-babase-schema Unix program copies the entire babase schema, including data, table definitions, validation, and everything else, from one database to another. All existing data, table definitions, validation, etc is deleted from the babase schema in the target database. You must be logged in to papio and at the Unix prompt to run the program.
The following example copies the babase schema from the babase database to the babase_test database. The first database (babase) is the database to copy from, the second (babase_test) the database to copy into.
PGPASSWORD='*********' babase-copy-babase-schema YOURADMINNAME babase babase_test
- The ********* here would be the password of YOURADMINNAME
The next example copies the babase scheme from the babase_test database to the babase_database. The program will not copy into the babase database unless the -f (force) flag is given.
PGPASSWORD='*********' babase-copy-babase-schema -f YOURADMINNAME babase_test babase
- When Backing up the DB, the 'help' directory can offer some direction
[YOU@papio ~]$ pg_dump --help
Killing a Process in PPA
Log in to phpPgAdmin as an administrator, then select the babase database.
There is a tab along the top of the browser window with a button for Processes. Click this button.
You will see a list of ongoing processes (queries, usually). Click the "Cancel" button next to whichever process you want to kill. You may have to click cancel on the process you are killing a couple of times. It might tell you that the function has failed, but you can ignore that; it's an error in phpPgAdmin, not with Postgres.