data importation

[Julius Kisenyi]

hi am kisenyi julius, in kampala , uganda. we are currently using epi info to capture data for patients and we now have a high volume. we want to migrate that data to the new system thus OPENMRS. epi info data can be exported out of the program in access format,SQL and excel spreadsheets. therefore my question is: how can i safely import excel spreadsheet data into openmrs without distortion. please help. thanks 

[Tobin Greensweig]

Hi Julius,

Have you considered this module? 

https://wiki.openmrs.org/display/docs/Spreadsheet+Import+Module+Version+2

Tobin

On Wed, Jun 12, 2013 at 8:54 AM, Julius Kisenyi <juli...@gmail.com> wrote:

hi am kisenyi julius, in kampala , uganda. we are currently using epi info to capture data for patients and we now have a high volume. we want to migrate that data to the new system thus OPENMRS. epi info data can be exported out of the program in access format,SQL and excel spreadsheets. therefore my question is: how can i safely import excel spreadsheet data into openmrs without distortion. please help. thanks 

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Tobin

[Joaquín Blaya]

will this be a one time thing or something that you will do multiple times?  Sounds like a one time thing, but I wanted to check because if it's multiple times you might want to look into mirth.

Joaquín
___________________________________________________________________
Gerente de Desarrollo, eHealth Systems
Research Fellow, Escuela de Medicina de Harvard
Moderador, GHDOnline.org

[Julius Kisenyi]

its a one time thing. but you never know i might need to do it again. please let me know of all the possiblities. thanks

[Daniel Kayiwa]

Hi Julius,

I have never seen a tool that automates that. It would require knowledge of the source (epi info) and destination (openmrs) formats.
Or some sort of API that both expose for data exchange.

Do you have some developer skills in you or your organization? If yes, we could guide you in coming up with such a tool.

By the way, am also in Kampala/Uganda. :)

If we keep uppermost in our minds the unkind and unjust acts of others, we shall find it impossible to love them as Christ has loved us; but if our thoughts dwell upon the wondrous love and pity of Christ for us, the same spirit will flow out to others.

[Julius Kisenyi]

thanks for the reply daniel. 

am not that experienced with openmrs. though i would like to know, if i have a particular spread sheet format cant i map its data directly onto openmrs database?.

i was told of this module: https://modules.openmrs.org/modules/view.jsp?module=spreadsheetimport 

do u think that module could help?

thanks 

julius

[Hannan, Terry J (DHHS)]

Daniel, thanks for this. I have just designed small Hepatitis serology/immunisation data set for Nauru (pop'n ~10,000) and it will be nice to see if I can import this into OpenMRS. it will be another "homework" project for me. Terry

Sent from my iPad

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[Hannan, Terry J (DHHS)]

Daniel, is there documentation on how to use  this module? Terry

[Hannan, Terry J (DHHS)]

I have downloaded the Step by Step instructions for the Spreadsheet Import Module (Version 2) but have struck a problem in that there is no link titled Spreadsheet Import Table List on the Administration screen.

I would like some guidance please. Terry

 

 

Dr Terry J. Hannan MBBS;FRACP;FACHI;FACMI
Consultant Physician
Clinical Associate Professor  School of Human Health Sciences, University of Tasmania Department of Medicine, Launceston General Hospital
Charles Street Launceston 7250

Past President Australasian College of Health Informatics(2007-9)

Visiting Professor, Universita di Modena, e reggio emelia, Italy (Sept-Nov 2010)

 

Moderator: http://www.ghdonline.org/

 

Ph. 61 3 6348 7578
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Email terry....@dhhs.tas.gov.au

 

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From: implem...@openmrs.org [mailto:implem...@openmrs.org] On Behalf Of Julius Kisenyi
Sent: Wednesday, 12 June 2013 5:12 PM
To: implem...@openmrs.org
Subject: Re: data importation

 

thanks for the reply daniel. 

[Joaquín Blaya]

Hi Terry and Julius,

Unfortunately as Daniel mentioned, it's really hard to create a simple import system from excel to openmrs. The spreadsheet import module is an attempt at that, but it is still hard to use, and is really error prone.   I have to admit that I would suggest using Mirth to take the columns from an excel spreadsheet and place them into OpenMRS. I'm attaching here an example of a mirth channel that does exactly that and I hope to have time soon to update the OpenMRS mirth page. Actually I ended up attaching three examples.

Joaquín
___________________________________________________________________
Gerente de Desarrollo, eHealth Systems
Research Fellow, Escuela de Medicina de Harvard
Moderador, GHDOnline.org

[Hannan, Terry J (DHHS)]

Joaquin, thank you so much. With my limited “comprehension” of the nice structure of OpenMRS I wondered how “simple” it would be (or not to be) to import Excel inot the system. Terry

 

Dr Terry J. Hannan MBBS;FRACP;FACHI;FACMI
Consultant Physician
Clinical Associate Professor  School of Human Health Sciences, University of Tasmania Department of Medicine, Launceston General Hospital
Charles Street Launceston 7250

Past President Australasian College of Health Informatics(2007-9)

Visiting Professor, Universita di Modena, e reggio emelia, Italy (Sept-Nov 2010)

 

Moderator: http://www.ghdonline.org/

 

Ph. 61 3 6348 7578
Mob. 0417 144 881
Fax 61 3 6348 7577
Email terry....@dhhs.tas.gov.au

 

Web/Blog: www.austemrs.com.au

 

Skype: thehannans

 

[Julius Kisenyi]

hello joaquin 

thanks for the great insight about data importation into openmrs. i downloaded the configuracion final.zip file you attached to the last mail you sent. am not an experienced openmrs user so far(am still quiet new to openmrs). how can i use the files of the mirth channel  you sent to import data into openmrs(tutorial). am badly in need to an openmrs data importation tool at the hospital. we trying to move from the old system to openmrs and we have data in access and excel spreadsheets.

julius. k

[Joaquín Blaya]

Hi Julius,

First off where you able to install mirth and get it running? What operating system will you install mirth on? If you are using Ubuntu you can see these instructions which I've written. They are in spanish but you should be able to translate them
http://wiki.ehs.cl/display/DESARROLLO/Como+instalar+Mirth+en+Ubuntu?moved=true

Then you should do the mapping to the appropriate tables, you can see them in the openMRS data model https://wiki.openmrs.org/display/docs/Data+Model

Joaquín
___________________________________________________________________
Gerente de Desarrollo, eHealth Systems
Research Fellow, Escuela de Medicina de Harvard
Moderador, GHDOnline.org

[Julius Kisenyi]

thank you for the reply joaquin.

as i said in my previous mail. am new to openmrs, therefore i was hoping that you take me through the entire process of installing and using the mirth channel to import data from spreadsheet to openmrs database. am using windows 8 operating system. am sorry if i am burdening you so much but i really need to import this data. 

thanks 

julius

[Hannan, Terry J (DHHS)]

I am also interested in this process. Terry Hannan

Sent from my iPad

[Joaquín Blaya]

I'll do my best.

First thing is to install mirth connect (which is an open source program independent of openmrs). At www.mirthcorp.com you should find the download to install it on windows.

After installing it, run it and hit import connnector.

Here I have a 2 questions,
1. will you be creating patients or adding data to patients that already exist.
2. Have you created the concepts in your openmrs installation for all of the data you want to import?

Joaquin
____________________________________________________
Gerente Tecnológico, eHS (www.ehs.cl)
Moderador, GHDonline.org

Fellow, Escuela de Medicina de Harvard

[Julius Kisenyi]

thanks

i will be creating patients and i have created the concepts

[Hannan, Terry J (DHHS)]

Joaquin, when I go to this site they request registration and $. Also after registering they indicated that they cannot provide support so I deleted all communications. Terry

 

Dr Terry J. Hannan MBBS;FRACP;FACHI;FACMI
Consultant Physician
Clinical Associate Professor  School of Human Health Sciences, University of Tasmania Department of Medicine, Launceston General Hospital
Charles Street Launceston 7250

Past President Australasian College of Health Informatics(2007-9)

Visiting Professor, Universita di Modena, e reggio emelia, Italy (Sept-Nov 2010)

 

Moderator: http://www.ghdonline.org/

 

Ph. 61 3 6348 7578
Mob. 0417 144 881
Fax 61 3 6348 7577
Email terry....@dhhs.tas.gov.au

 

Web/Blog: www.austemrs.com.au

 

Skype: thehannans

 

From: implem...@openmrs.org [mailto:implem...@openmrs.org] On Behalf Of Joaquín Blaya
Sent: Thursday, 20 June 2013 3:29 AM
To: implem...@OPENMRS.ORG
Subject: Re: data importation

 

I'll do my best.

[Joaquín Blaya]

Ok, my apologies for taking this long to respond, it's been a bit crazy.

So what you'll want to do is in your mirth, import the channel which has the word pacientes in it. There you will see in Source tab the code to import an excel file. There you will see at the top the directory and name which the excel file must have in order for mirth to get it. The excel should be in the same computer as mirth and it must be of format 97/2003 and not 2007/2010.

Afterwards, go to Destination, then Edit Transformer. There you will see the mapping from each column (col0,col1,col2,..) to the name of the data point. Some of them are a straight mapping, others are a javascript converter (for example for dates), so you'll want to change the name of the variables to the ones that are what you want.

You'll have to save that. Then go to the destination tab and there you'll see that I"ve placed the data straight into the OpenMRS database (I would like to improve it to use the rest web services, but that'll be in a second phase). There you'll have to change the concept id to the ones that are in your database. Also, you'll have to know what datatype your concept is, if it's text, numeric, coded or date and depending on that is where you'll have to place the value in the sql statement because you'll need to insert it into value_text, value_numeric,value_coded, or value_datetime, respectively.

You'll also have to change the IP of the server, database name and password, and the location of the output file that you'd like.

Then test it on a small amount of data on a developerment server, because you'll probably have to modify it a few times to get it exactly right.  Once it works on that small amount of data you can try with the full data on your test server, and then on the production server.
You'll always want to do a mysqldump of your database before doing this, just in case something goes wrong.

Joaquín