Get Started - Revision history

Salkin at 08:51, 5 April 2024

2024-04-05T08:51:04Z

@@ Line 5: / Line 5: @@
 The SICdb dataset is provided in compressed .csv files, the minute values are even more consolidated. Refer to the [[File List]] for detailed description of files.
-The SICdb dataset contains billions of entries, therefore building up a database may present a challenge. Therefore a 'as simple as possible' solution is provided. Our solution provides a fully preconfigured and fast environment to access, explore and export SICdb data. Refer to the Quick Start chapter if you know how the commandline and docker is working, skip to the Detailed Instructions for a more detailed reference.
+The SICdb dataset contains billions of entries, therefore building up a database may present a challenge.
-== Quick Start ==
+== Usage Examples ==
-Just like other ICU datasets SICdb is huge. Expect that your pc need a significant amount of time to process!
+Refer to https://github.com/nrodemund/sicdb/tree/main/Import for some scripts for importing the dataset into a relational database system.

Salkin: /* Detailed Instructions (Windows) */

2023-05-21T15:44:44Z

Detailed Instructions (Windows)

← Older revision		Revision as of 15:44, 21 May 2023
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	* Download Metadata [https://github.com/nrodemund/sicdb]		* Download Metadata [https://github.com/nrodemund/sicdb]
	* Download PhysioNet data ~~and add it to the "Data" folder~~		* Download PhysioNet data
	* Install [http://www.docker.com Docker]		* Install [http://www.docker.com Docker]
	* [[Open commandline]]		* [[Open commandline]]
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	* Run "docker compose up"		* Run "docker compose up"
	* When command is finished wait for another 30 seconds, as the mysql server will need some time to configure		* When command is finished wait for another 30 seconds, as the mysql server will need some time to configure
	* Open http://localhost:~~5000~~		* Open http://localhost:5075
	* Select install and start installation		* Select install and start installation

Salkin: /* Issues and Troubleshooting on Windows Systems */

2022-11-09T08:29:52Z

Issues and Troubleshooting on Windows Systems

← Older revision		Revision as of 08:29, 9 November 2022
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	* Due to a known bug in WSL2 it may be not possible to run the environment on a software-mounted drive. This can cause issues when trying to launche SICdb environment from a '''VeraCrypt/TrueCrypt''' drive. BitLocker is fully supported as far as we know.		* Due to a known bug in WSL2 it may be not possible to run the environment on a software-mounted drive. This can cause issues when trying to launche SICdb environment from a '''VeraCrypt/TrueCrypt''' drive. BitLocker is fully supported as far as we know.
	* Due to a known ~~'bug'~~ concerning the way windows manages hosts it my be that SICdb environment is not reachable on localhost:5000 or does not start at all. This can be resolved by closing Docker Desktop, run as administrator and then restart engine. The restart engine button is found in the system tray (right bottom on windows machines), right click docker icon->restart.		* Due to a known issue concerning the way windows manages hosts it my be that SICdb environment is not reachable on localhost:5000 or does not start at all. This can be resolved by closing Docker Desktop, run as administrator and then restart engine. The restart engine button is found in the system tray (right bottom on windows machines), right click docker icon->restart.

Salkin at 08:29, 9 November 2022

2022-11-09T08:29:38Z

← Older revision		Revision as of 08:29, 9 November 2022
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	'''Note: If "docker compose up" throws any errors, open "Docker Desktop" app as administrator, navigate to "Containers" and press the play button in line "roodataenv"'''		'''Note: If "docker compose up" throws any errors, open "Docker Desktop" app as administrator, navigate to "Containers" and press the play button in line "roodataenv"'''

	== Issues and Troubleshooting ==		== Issues and Troubleshooting on Windows Systems ==

	Generally the environment should run on all common operating systems on all machines (We recommend >=16gb RAM and a modern multicore CPU).		Generally the environment should run on all common operating systems on all machines (We recommend >=16gb RAM and a modern multicore CPU).
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	Feel free to [[contact us]] if the problem persists.		Feel free to [[contact us]] if the problem persists.

	There are some issues to be expected when the environment is executed on a "standard" windows machine. We recommend using default configuration (WSL2), but there are some known bugs and issues, which have not been resolved as of 10/2022. We have not faced any issues on a linux machine.		There are some issues to be expected when the environment is executed on a "standard" windows machine. We recommend using default configuration (WSL2), but there are some known bugs and issues, which have not been resolved as of 11/2022. We have not faced any issues on a linux machine.


	* Installing the database will cause WSL2 to reserve 50% of your machines RAM and it will not be released automatically. It is expected that this will be patched in future, but for now, after installing the dataset, you may either close the container and run "wsl --shutdown" in admin powershell (Docker Desktop will automatically restart wsl) or restart your computer.		* Installing the database will cause WSL2 to reserve 50% of your machines RAM and it will not be released automatically. It is expected that this will be patched in future, but for now, after installing the dataset, you may either close the container and run "wsl --shutdown" in admin powershell (Docker Desktop will automatically restart wsl) or restart your computer.

	* Due to a known bug in WSL2 it may be not possible to run the environment on a software-mounted drive. This can cause issues when trying to launche SICdb environment from a VeraCrypt/TrueCrypt drive. BitLocker is fully supported as far as we know.		* Due to a known bug in WSL2 it may be not possible to run the environment on a software-mounted drive. This can cause issues when trying to launche SICdb environment from a '''VeraCrypt/TrueCrypt''' drive. BitLocker is fully supported as far as we know.
	* Due to a known 'bug' concerning the way windows manages hosts it my be that SICdb environment is not reachable on localhost:5000 or does not start at all. This can be resolved by closing Docker Desktop, run as administrator and then restart engine. The restart engine button is found in the system tray (right bottom on windows machines), right click docker icon->restart.		* Due to a known 'bug' concerning the way windows manages hosts it my be that SICdb environment is not reachable on localhost:5000 or does not start at all. This can be resolved by closing Docker Desktop, run as administrator and then restart engine. The restart engine button is found in the system tray (right bottom on windows machines), right click docker icon->restart.

Salkin at 08:27, 9 November 2022

2022-11-09T08:27:48Z

← Older revision		Revision as of 08:27, 9 November 2022
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	{{Beta Version}}		{{Beta Version}}

	The SICdb dataset is provided in compressed .csv files, the minute values are even more consolidated. Refer to the [[~~Main Page~~]] for detailed description of files.		The SICdb dataset is provided in compressed .csv files, the minute values are even more consolidated. Refer to the [[File List]] for detailed description of files.

	The SICdb dataset contains billions of entries, therefore building up a database may present a challenge. Therefore a 'as simple as possible' solution is provided. Our solution~~, we called it [[SICdb Environment]],~~ provides a fully preconfigured and fast environment to access, explore and export SICdb data. Refer to the Quick Start chapter if you know how the commandline and docker is working, skip to the Detailed Instructions for a more detailed reference.		The SICdb dataset contains billions of entries, therefore building up a database may present a challenge. Therefore a 'as simple as possible' solution is provided. Our solution provides a fully preconfigured and fast environment to access, explore and export SICdb data. Refer to the Quick Start chapter if you know how the commandline and docker is working, skip to the Detailed Instructions for a more detailed reference.

	== Quick Start ==		== Quick Start ==



	Just like other ICU datasets SICdb is huge. Expect that your pc need a significant amount of time to process!		Just like other ICU datasets SICdb is huge. Expect that your pc need a significant amount of time to process!

	The database can be built up using our [http://www.docker.com Docker] images. After install navigate into the folder containing all the data and run "docker compose up". When the environment is running open http://localhost:5000 to install the dataset. The provided environment ist fully preconfigured, just press start and wait. Due to the vast size this may take 4-16 hours*. When install is finished the server has to be restarted, you may do this by reloading the page and then press the ~~shiny~~ restart button.		The database can be built up using our [http://www.docker.com Docker] images. After install navigate into the folder containing all the data and run "docker compose up". When the environment is running open http://localhost:5000 to install the dataset. The provided environment ist fully preconfigured, just press start and wait. Due to the vast size this may take 4-12 hours*. When install is finished the server has to be restarted, you may do this by reloading the page and then press the restart button.

	*) We work on a solution to provide a fully indexed database. Until now we have not found a legally safe way of distribution (repository).		*) We work on a solution to provide a fully indexed database. Until now we have not found a legally safe way of distribution (repository).
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	== Detailed Instructions (Windows)==		== Detailed Instructions (Windows)==

	* Download Data
			* Download Metadata [https://github.com/nrodemund/sicdb]
			* Download PhysioNet data and add it to the "Data" folder
	* Install [http://www.docker.com Docker]		* Install [http://www.docker.com Docker]
	* [[Open commandline]]		* [[Open commandline]]

Salkin at 16:39, 3 November 2022

2022-11-03T16:39:11Z

← Older revision		Revision as of 16:39, 3 November 2022
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	Just like other ICU datasets SICdb is huge. Expect that your pc need a significant amount of time to process!		Just like other ICU datasets SICdb is huge. Expect that your pc need a significant amount of time to process!

	The database can be built up using [http://www.docker.com Docker]. After install navigate into the folder containing all the data and run "docker compose up". When the environment is running open http://localhost:5000 to install the dataset. The provided environment ist fully preconfigured, just press start and wait. Due to the vast size this may take 4-16 hours*. When install is finished the server has to be restarted, you may do this by reloading the page and then press the shiny restart button.		The database can be built up using our [http://www.docker.com Docker] images. After install navigate into the folder containing all the data and run "docker compose up". When the environment is running open http://localhost:5000 to install the dataset. The provided environment ist fully preconfigured, just press start and wait. Due to the vast size this may take 4-16 hours*. When install is finished the server has to be restarted, you may do this by reloading the page and then press the shiny restart button.

	*) We work on a solution to provide a fully indexed database. Until now we have not found a legally safe way of distribution (repository).		*) We work on a solution to provide a fully indexed database. Until now we have not found a legally safe way of distribution (repository).

Salkin at 16:21, 10 October 2022

2022-10-10T16:21:52Z

← Older revision		Revision as of 16:21, 10 October 2022
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	If you need any help with installation please feel free to [[contact us]]!		If you need any help with installation please feel free to [[contact us]]!

	'''Note: If "docker compose up" throws any ~~error~~ open "Docker Desktop" app as administrator, navigate to "Containers" and press the play button in line "roodataenv"'''		'''Note: If "docker compose up" throws any errors, open "Docker Desktop" app as administrator, navigate to "Containers" and press the play button in line "roodataenv"'''

	== Issues and Troubleshooting ==		== Issues and Troubleshooting ==
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	Generally the environment should run on all common operating systems on all machines (We recommend >=16gb RAM and a modern multicore CPU).		Generally the environment should run on all common operating systems on all machines (We recommend >=16gb RAM and a modern multicore CPU).

	'''Note: If "docker compose up" throws any ~~error~~ open "Docker Desktop" app as administrator, navigate to "Containers" and press the play button in line "roodataenv"'''		'''Note: If "docker compose up" throws any errors, open "Docker Desktop" app as administrator, navigate to "Containers" and press the play button in line "roodataenv"'''

			Feel free to [[contact us]] if the problem persists.

	There are some issues to be expected when the environment is executed on a "standard" windows machine. We recommend using default configuration (WSL2), but there are some known bugs and issues, which have not been resolved as of 10/2022. We have not faced any issues on a linux machine.		There are some issues to be expected when the environment is executed on a "standard" windows machine. We recommend using default configuration (WSL2), but there are some known bugs and issues, which have not been resolved as of 10/2022. We have not faced any issues on a linux machine.

Salkin at 16:21, 10 October 2022

2022-10-10T16:21:17Z

← Older revision		Revision as of 16:21, 10 October 2022
Line 35:		Line 35:

	Generally the environment should run on all common operating systems on all machines (We recommend >=16gb RAM and a modern multicore CPU).		Generally the environment should run on all common operating systems on all machines (We recommend >=16gb RAM and a modern multicore CPU).

			'''Note: If "docker compose up" throws any error open "Docker Desktop" app as administrator, navigate to "Containers" and press the play button in line "roodataenv"'''

	There are some issues to be expected when the environment is executed on a "standard" windows machine. We recommend using default configuration (WSL2), but there are some known bugs and issues, which have not been resolved as of 10/2022. We have not faced any issues on a linux machine.		There are some issues to be expected when the environment is executed on a "standard" windows machine. We recommend using default configuration (WSL2), but there are some known bugs and issues, which have not been resolved as of 10/2022. We have not faced any issues on a linux machine.

Salkin: /* Detailed Instructions (Windows) */

2022-10-10T16:20:44Z

Detailed Instructions (Windows)

← Older revision		Revision as of 16:20, 10 October 2022
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	If you need any help with installation please feel free to [[contact us]]!		If you need any help with installation please feel free to [[contact us]]!

			'''Note: If "docker compose up" throws any error open "Docker Desktop" app as administrator, navigate to "Containers" and press the play button in line "roodataenv"'''

	== Issues and Troubleshooting ==		== Issues and Troubleshooting ==

Salkin at 11:49, 9 October 2022

2022-10-09T11:49:38Z

← Older revision		Revision as of 11:49, 9 October 2022
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	* Download Data		* Download Data
	* Install [http://www.docker.com Docker]		* Install [http://www.docker.com Docker]
	* [[Open commandline]] ~~as admin (*)~~		* [[Open commandline]]
	* [[Navigate to data folder]]		* [[Navigate to data folder]]
	* Run "docker compose up"		* Run "docker compose up"
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	If you need any help with installation please feel free to [[contact us]]!		If you need any help with installation please feel free to [[contact us]]!



	== Issues and Troubleshooting ==		== Issues and Troubleshooting ==