Recent changes to Home

Home modified by mkhushi

mkhushi — Wed, 08 Feb 2017 22:31:36 -0000

--- v12
+++ v13
@@ -4,6 +4,12 @@

 **BiSA for Linux/Mac Documentation**
+*Restore database with SQL*
+
+RESTORE DATABASE bisa FROM DISK='c:\temp\BiSA_SQL_Server_database_backup0.95.bak'  WITH NORECOVERY,
+MOVE 'bisa_data' TO  'C:\Program Files\Microsoft SQL Server\MSSQL12.SQLEXPRESS\MSSQL\Data\bisa.mdf',   
+      MOVE 'bisa_Log'   TO 'C:\Program Files\Microsoft SQL Server\MSSQL12.SQLEXPRESS\MSSQL\Data\bisa_log.ldf' ;
+

 *Importing datasets*

Home modified by mkhushi

mkhushi — Fri, 03 May 2013 01:27:39 -0000

--- v11
+++ v12
@@ -5,13 +5,14 @@

 **BiSA for Linux/Mac Documentation**

-*Importing datasets into BiSA Knowledge Base could be slow*
+*Importing datasets*

-Windows BiSA's import function for SQL Server is much faster than the PostgreSQL equivalent, for the reason that SQL Server supports Table Valued Parameters (TVP) which is an efficient way of inserting multiple records into a database no matter if database server resides on the same physical machine as that of the user front or deployed on a different networked machine. 
+Windows BiSA's import function for SQL Server is much faster than the PostgreSQL equivalent, for the reason that SQL Server supports Table Valued Parameters (TVP) which is an efficient way of inserting multiple records into a database no matter if database server resides on the same physical machine as that of the user front-end or deployed on a different networked machine. 

-BiSA for Unix like Operating Systems is written in Python that runs under Galaxy. Galaxy uses SQLAlchemy to connect to different database engines, therefore import function of BiSA is written to support various scenarios. Each line of the imported dataset file is inserted by a single *insert* statement which is a slower way of importing a large dataset into a database. However this works for both local machine databases and databases hosted on a different machine than the web front-end. 
+PostgreSQL has COPY command that moves data between PostgreSQL tables and standard file-system files efficiently. In BiSA 0.92 version COPY is default way of importing datasets into database, however COPY can only import a file from a directory that is visible to the database server, so if PostgreSQL is hosted on a different machine than the web front-end then this will not work. A workaround of this problem can be achieved by mapping web front-end machine's datasets folder to the server hosting PostgreSQL. Then inject the COPY command by correcting the path of the file to be imported. Therefore the code in step1importkb.py needs to be modified to a user's specific environment.

-This could be speed-up by un-commenting the 'copy' command code in step1importkb.py file. However *copy* can only import a file from a directory that is visible to database server, so if PostgreSQL is hosted on a different machine than the web front-end then this will not work. A workaround of this problem can be achieved by mapping web front-end machine's datasets folder to the server hosting PostgreSQL. Then pass the *copy* command by correcting the path of the file to be imported. Therefore the code in step1importkb.py needs to be modified to a user's environment.
+Or comment out copySQL function and enable insertSQL function which is written to support various scenarios. Each line of the imported dataset file is inserted by a single *insert* statement which is a slower way of importing a large dataset into a database. However this works for both local machine databases and databases hosted on a different machine than the web front-end. 
+

Home modified by mkhushi

mkhushi — Mon, 22 Apr 2013 03:46:32 -0000

--- v10
+++ v11
@@ -11,7 +11,7 @@

 BiSA for Unix like Operating Systems is written in Python that runs under Galaxy. Galaxy uses SQLAlchemy to connect to different database engines, therefore import function of BiSA is written to support various scenarios. Each line of the imported dataset file is inserted by a single *insert* statement which is a slower way of importing a large dataset into a database. However this works for both local machine databases and databases hosted on a different machine than the web front-end. 

-This could be speed-up by un-commenting the 'copy' commend code in step1importkb.py file. However *copy* can only import a file from a directory that is visible to database server, so if PostgreSQL is hosted on a different machine than the web front-end then this will not work. A workaround of this problem can be achieved by mapping web front-end machine's datasets folder to the server hosting PostgreSQL. Then pass the *copy* command by correcting the path of the file to be imported. Therefore the code in step1importkb.py needs to be modified to a user's environment.
+This could be speed-up by un-commenting the 'copy' command code in step1importkb.py file. However *copy* can only import a file from a directory that is visible to database server, so if PostgreSQL is hosted on a different machine than the web front-end then this will not work. A workaround of this problem can be achieved by mapping web front-end machine's datasets folder to the server hosting PostgreSQL. Then pass the *copy* command by correcting the path of the file to be imported. Therefore the code in step1importkb.py needs to be modified to a user's environment.

Home modified by mkhushi

mkhushi — Mon, 22 Apr 2013 03:46:03 -0000

--- v9
+++ v10
@@ -7,13 +7,11 @@

 *Importing datasets into BiSA Knowledge Base could be slow*

-Windows BiSA's import function for SQL Server is much faster than the PostgreSQL equivalent, for the reason that SQL Server supports Table Valued Parameters (TVP) which is an efficient way of inserting multiple records into a database no matter if database server resides on the same physical machine as that of user front or deployed on a different networked machine. 
+Windows BiSA's import function for SQL Server is much faster than the PostgreSQL equivalent, for the reason that SQL Server supports Table Valued Parameters (TVP) which is an efficient way of inserting multiple records into a database no matter if database server resides on the same physical machine as that of the user front or deployed on a different networked machine. 

-BiSA for Unix like Operating Systems is writte in Python that runs under Galaxy. Galaxy uses SQLAlchemy to connect to different database engines, therefore import function of BiSA is written to support various scenarios. Each line of the imported dataset file is inserted by a single *insert* statement which is a slower way of importing large a dataset into a database. However this works for both local machine databases and databases hosted on a different machine than web front-end. 
+BiSA for Unix like Operating Systems is written in Python that runs under Galaxy. Galaxy uses SQLAlchemy to connect to different database engines, therefore import function of BiSA is written to support various scenarios. Each line of the imported dataset file is inserted by a single *insert* statement which is a slower way of importing a large dataset into a database. However this works for both local machine databases and databases hosted on a different machine than the web front-end. 

-This could be speed-up by by un-commenting the 'copy' commend code in step1importkb.py file. However this will only work if PostgreSQL is hosted on a local machine. Another workaround of this problem can be achieved by mapping web front-end machine's datasets folder to the server hosting PostgreSQL. Then pass the *copy* command by correcting the path of the file to be imported.
-
-
+This could be speed-up by un-commenting the 'copy' commend code in step1importkb.py file. However *copy* can only import a file from a directory that is visible to database server, so if PostgreSQL is hosted on a different machine than the web front-end then this will not work. A workaround of this problem can be achieved by mapping web front-end machine's datasets folder to the server hosting PostgreSQL. Then pass the *copy* command by correcting the path of the file to be imported. Therefore the code in step1importkb.py needs to be modified to a user's environment.

Home modified by mkhushi

mkhushi — Mon, 22 Apr 2013 02:57:56 -0000

--- v8
+++ v9
@@ -1,6 +1,6 @@
 **BiSA for Windows Documentation**

-Follow installation guide lines on http://bisa.sourcefore.net
+Follow installation guide lines on http://bisa.sourceforge.net

 **BiSA for Linux/Mac Documentation**

Home modified by mkhushi

mkhushi — Mon, 22 Apr 2013 02:56:38 -0000

--- v7
+++ v8
@@ -1,46 +1,22 @@
-BiSA is a database driven software and stores all of its data in a relational database management system (RDBMS) such as SQL Server in Windows or Postgres on Linux.
+**BiSA for Windows Documentation**

-**BiSA for Windows**
+Follow installation guide lines on http://bisa.sourcefore.net

-It is required that you install SQL Server before you [install BiSA](https://sourceforge.net/p/bisa/wiki/Installing%20Microsoft%20SQL%20Server/). So there are three steps:

-1. Download the BiSA package and unzip. 
-2. [Install Microsoft SQL Server](https://sourceforge.net/p/bisa/wiki/Installing%20Microsoft%20SQL%20Server/) and restore BiSA database.
-3. Run BiSA.exe
-3. If you have previously installed BiSA database, then delete the database and restore from the new version.
+**BiSA for Linux/Mac Documentation**

-**BiSA for Linux runs under Galaxy (Alpha Version)**
+*Importing datasets into BiSA Knowledge Base could be slow*

-BiSA for MacOS/Linux/Unix is written in Python and PosgreSQL, and is designed to run under Galaxy. Galaxy is a web-based platform which is designed for intensive biomedical research. 
+Windows BiSA's import function for SQL Server is much faster than the PostgreSQL equivalent, for the reason that SQL Server supports Table Valued Parameters (TVP) which is an efficient way of inserting multiple records into a database no matter if database server resides on the same physical machine as that of user front or deployed on a different networked machine. 

-1. Follow the Galaxy's official guidelines to install Galaxy then install PostgreSQL.
-2. If your database server is on different machine than your web front-end then you would have to configure pg_hba.conf to allow connections from your web front-end machine. Make sure that your firewall is open for PostgreSQL port (default is 5432),  if PostgreSQL is installed on Windows 7 machine then allow incoming connections to the port 5432 using Windows Firewall with Advanced Security under Control Panel.
-3. Download BiSA Linux package from this site.
-4. Create a new database say bisa0.9.
-5. Restore database by following command: 
-pg_restore --host=localhost --port=5432 --username=your_db_username --password  --dbname=bisa0.9  /backup_location/bisa_pg_0.xxx.backup 
-6. Create a directory named bisa in tools directory of galaxy installation typically /galaxy-dist/tools/bisa/
-7. Copy all (*.py and *.xml) files in /galaxy-dis/tools/bisa/
-8. Add a new section in /galaxy-dist/tools_conf.xml by dropping the following lines:
-  
-        
-           
-         
-            
-         
-    
- 
-9. Restart Galaxy by sh run.sh and open Galaxy in a browser. A new section BiSA should appear on the left column.
+BiSA for Unix like Operating Systems is writte in Python that runs under Galaxy. Galaxy uses SQLAlchemy to connect to different database engines, therefore import function of BiSA is written to support various scenarios. Each line of the imported dataset file is inserted by a single *insert* statement which is a slower way of importing large a dataset into a database. However this works for both local machine databases and databases hosted on a different machine than web front-end. 
+
+This could be speed-up by by un-commenting the 'copy' commend code in step1importkb.py file. However this will only work if PostgreSQL is hosted on a local machine. Another workaround of this problem can be achieved by mapping web front-end machine's datasets folder to the server hosting PostgreSQL. Then pass the *copy* command by correcting the path of the file to be imported.

-Welcome to your wiki!

-This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].

-[Installing Microsoft SQL Server]
-
-The wiki uses [Markdown](/p/bisa/wiki/markdown_syntax/) syntax.

 [[project_admins]]
 [[download_button]]

Home modified by mkhushi

mkhushi — Sat, 13 Apr 2013 13:13:30 -0000

--- v6
+++ v7
@@ -2,10 +2,10 @@

 **BiSA for Windows**

-It is required that you install SQL Server before you install BiSA. So there are three steps:
+It is required that you install SQL Server before you [install BiSA](https://sourceforge.net/p/bisa/wiki/Installing%20Microsoft%20SQL%20Server/). So there are three steps:

 1. Download the BiSA package and unzip. 
-2. Install Microsoft SQL Server and restore BiSA database.
+2. [Install Microsoft SQL Server](https://sourceforge.net/p/bisa/wiki/Installing%20Microsoft%20SQL%20Server/) and restore BiSA database.
 3. Run BiSA.exe
 3. If you have previously installed BiSA database, then delete the database and restore from the new version.

Home modified by mkhushi

mkhushi — Sat, 13 Apr 2013 13:11:56 -0000

--- v5
+++ v6
@@ -4,24 +4,24 @@

 It is required that you install SQL Server before you install BiSA. So there are three steps:

-Download the BiSA package and unzip. The package is ultra compressed so un-compression will be slow on slow machines.
-Install Microsoft SQL Server and restore BiSA database.
-Run BiSA.exe
-If you have previously installed BiSA database, then delete the database and restore from the new version.
+1. Download the BiSA package and unzip. 
+2. Install Microsoft SQL Server and restore BiSA database.
+3. Run BiSA.exe
+3. If you have previously installed BiSA database, then delete the database and restore from the new version.

 **BiSA for Linux runs under Galaxy (Alpha Version)**

 BiSA for MacOS/Linux/Unix is written in Python and PosgreSQL, and is designed to run under Galaxy. Galaxy is a web-based platform which is designed for intensive biomedical research. 

-Follow the Galaxy's official guidelines to install Galaxy then install PostgreSQL.
-If your database server is on different machine than your web front-end then you would have to configure pg_hba.conf to allow connections from your web front-end machine. Make sure that your firewall is open for PostgreSQL port (default is 5432),  if PostgreSQL is installed on Windows 7 machine then allow incoming connections to the port 5432 using Windows Firewall with Advanced Security under Control Panel.
-Download BiSA Linux package from this site.
-Create a new database say bisa0.9.
-Restore database by following command: 
+1. Follow the Galaxy's official guidelines to install Galaxy then install PostgreSQL.
+2. If your database server is on different machine than your web front-end then you would have to configure pg_hba.conf to allow connections from your web front-end machine. Make sure that your firewall is open for PostgreSQL port (default is 5432),  if PostgreSQL is installed on Windows 7 machine then allow incoming connections to the port 5432 using Windows Firewall with Advanced Security under Control Panel.
+3. Download BiSA Linux package from this site.
+4. Create a new database say bisa0.9.
+5. Restore database by following command: 
 pg_restore --host=localhost --port=5432 --username=your_db_username --password  --dbname=bisa0.9  /backup_location/bisa_pg_0.xxx.backup 
-Create a directory named bisa in tools directory of galaxy installation typically /galaxy-dist/tools/bisa/
-Copy all (*.py and *.xml) files in /galaxy-dis/tools/bisa/
-Add a new section in /galaxy-dist/tools_conf.xml by dropping the following lines:
+6. Create a directory named bisa in tools directory of galaxy installation typically /galaxy-dist/tools/bisa/
+7. Copy all (*.py and *.xml) files in /galaxy-dis/tools/bisa/
+8. Add a new section in /galaxy-dist/tools_conf.xml by dropping the following lines:
   
         
            
@@ -30,7 +30,7 @@
          
     

-Restart Galaxy by sh run.sh and open Galaxy in a browser. A new section BiSA should appear on the left column.
+9. Restart Galaxy by sh run.sh and open Galaxy in a browser. A new section BiSA should appear on the left column.

Home modified by mkhushi

mkhushi — Sat, 13 Apr 2013 12:40:03 -0000

--- v4
+++ v5
@@ -1,3 +1,39 @@
+BiSA is a database driven software and stores all of its data in a relational database management system (RDBMS) such as SQL Server in Windows or Postgres on Linux.
+
+**BiSA for Windows**
+
+It is required that you install SQL Server before you install BiSA. So there are three steps:
+
+Download the BiSA package and unzip. The package is ultra compressed so un-compression will be slow on slow machines.
+Install Microsoft SQL Server and restore BiSA database.
+Run BiSA.exe
+If you have previously installed BiSA database, then delete the database and restore from the new version.
+
+**BiSA for Linux runs under Galaxy (Alpha Version)**
+
+BiSA for MacOS/Linux/Unix is written in Python and PosgreSQL, and is designed to run under Galaxy. Galaxy is a web-based platform which is designed for intensive biomedical research. 
+
+Follow the Galaxy's official guidelines to install Galaxy then install PostgreSQL.
+If your database server is on different machine than your web front-end then you would have to configure pg_hba.conf to allow connections from your web front-end machine. Make sure that your firewall is open for PostgreSQL port (default is 5432),  if PostgreSQL is installed on Windows 7 machine then allow incoming connections to the port 5432 using Windows Firewall with Advanced Security under Control Panel.
+Download BiSA Linux package from this site.
+Create a new database say bisa0.9.
+Restore database by following command: 
+pg_restore --host=localhost --port=5432 --username=your_db_username --password  --dbname=bisa0.9  /backup_location/bisa_pg_0.xxx.backup 
+Create a directory named bisa in tools directory of galaxy installation typically /galaxy-dist/tools/bisa/
+Copy all (*.py and *.xml) files in /galaxy-dis/tools/bisa/
+Add a new section in /galaxy-dist/tools_conf.xml by dropping the following lines:
+  
+        
+           
+         
+            
+         
+    
+ 
+Restart Galaxy by sh run.sh and open Galaxy in a browser. A new section BiSA should appear on the left column.
+
+
+
 Welcome to your wiki!

 This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].

Home modified by mkhushi

mkhushi — Sat, 13 Apr 2013 12:32:24 -0000

--- v3
+++ v4
@@ -2,7 +2,7 @@

 This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].

-Installing Microsoft SQL Server
+[Installing Microsoft SQL Server]

 The wiki uses [Markdown](/p/bisa/wiki/markdown_syntax/) syntax.