[Dhis2-users] Analyze across events

[Pramil Liyanage]

Hi,

I need to analyze data across variables in two events in a program with
multiple stages.

For example, I need to find the number of patients marked as cured in
*treatment
outcome* stage,  for a cohort registered during a specified time. Can I
combine enrollment date or date from another event (e.g. *registration
event*)? Event reports will aggregate to the event, *treatment outcome*,
not registration.

I know that this is not possible to combine elements from two events in
event reports. Is it possible to do this using programme indicators? If so
what is the syntax?

Regards
Pramil
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Re: [Dhis2-users] [Dhis2-devs] Filtering Pivot Table Results (before Results Export)

[Raminosoa Rabemanantsoa, Tantely]

Hi Lars,

Thank you for this very clear instruction. It is straightforward and very
useful!

Regards,

Tantely.

Le 7 avr. 2017 6:25 PM, "Lars Helge Øverland"  a écrit :

>
> Hi Tantely,
>
> to achieve this I think you should use the "org unit group" selection
> mode. Under the organisation unit dimension section, click the gear icon
> and select "Select groups", then select the org unit group which contains
> the org units you would like to display.
>
> In the org unit tree you can leave the selected org unit at the national
> level if you would like to include facilities from the entire country.
>
>
> [image: Inline image 3]
>
>
> This will render the actual org units from that group in your pivot table.
>
> regards,
>
> Lars
>
>
>
>
>
> On Thu, Apr 6, 2017 at 5:38 PM, Raminosoa Rabemanantsoa, Tantely <
> tramino...@mikolo.org> wrote:
>
>> Dear community,
>>
>> I am trying to create a filter to be used with the pivot table results,
>> so that only the filtered OrgUnits will appear. For that I have created
>> OrgUnit groups and have used them in the pivot table. The layout is
>> illustrated in the attached file, by using the OrgUnits in the row
>> dimensions. As a result, the pivot table is only using the OrgUnit groups
>> as a categorization of the results but not filtering them as all OrgUnits
>> are still displayed. I think that an interest using a filter is to avoid
>> dumping a huge amount of data, which is sometimes freezing DHIS2 when
>> displaying the results at the lowest level of OrgUnits.
>>
>> Which way should I follow in order to filter the OrgUnits according to
>> some criteria (like using a spreadsheet filter)? Would it be possible doing
>> that in the pivot table or it would be worth creating an equivalent SQL
>> uery? One constraint with using SQL View is that we can only call
>> DataElements but not Indicators.
>>
>> I am using DHIS2 2.24.
>>
>> Thank you for your support and suggestions!
>>
>> Regards,
>>
>> Tantely.
>>
>> *This message and its attachments are confidential and solely for the
>> intended recipients. If received in error, please delete them and notify
>> the sender via reply e-mail immediately.*
>> ___
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>>
>>
>
>
> --
> Lars Helge Øverland
> Lead developer, DHIS 2
> University of Oslo
> Skype: larshelgeoverland
> l...@dhis2.org
> http://www.dhis2.org 
>
>

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Re: [Dhis2-users] [Dhis2-devs] Filtering Pivot Table Results (before Results Export)

[Lars Helge Øverland]

Hi Tantely,

to achieve this I think you should use the "org unit group" selection mode.
Under the organisation unit dimension section, click the gear icon and
select "Select groups", then select the org unit group which contains the
org units you would like to display.

In the org unit tree you can leave the selected org unit at the national
level if you would like to include facilities from the entire country.


[image: Inline image 3]


This will render the actual org units from that group in your pivot table.

regards,

Lars





On Thu, Apr 6, 2017 at 5:38 PM, Raminosoa Rabemanantsoa, Tantely <
tramino...@mikolo.org> wrote:

> Dear community,
>
> I am trying to create a filter to be used with the pivot table results, so
> that only the filtered OrgUnits will appear. For that I have created
> OrgUnit groups and have used them in the pivot table. The layout is
> illustrated in the attached file, by using the OrgUnits in the row
> dimensions. As a result, the pivot table is only using the OrgUnit groups
> as a categorization of the results but not filtering them as all OrgUnits
> are still displayed. I think that an interest using a filter is to avoid
> dumping a huge amount of data, which is sometimes freezing DHIS2 when
> displaying the results at the lowest level of OrgUnits.
>
> Which way should I follow in order to filter the OrgUnits according to
> some criteria (like using a spreadsheet filter)? Would it be possible doing
> that in the pivot table or it would be worth creating an equivalent SQL
> uery? One constraint with using SQL View is that we can only call
> DataElements but not Indicators.
>
> I am using DHIS2 2.24.
>
> Thank you for your support and suggestions!
>
> Regards,
>
> Tantely.
>
> *This message and its attachments are confidential and solely for the
> intended recipients. If received in error, please delete them and notify
> the sender via reply e-mail immediately.*
> ___
> Mailing list: https://launchpad.net/~dhis2-devs
> Post to : dhis2-d...@lists.launchpad.net
> Unsubscribe : https://launchpad.net/~dhis2-devs
> More help   : https://help.launchpad.net/ListHelp
>
>


-- 
Lars Helge Øverland
Lead developer, DHIS 2
University of Oslo
Skype: larshelgeoverland
l...@dhis2.org
http://www.dhis2.org 
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Re: [Dhis2-users] storing/linking sequence metadata in DHIS2

[Jason Pickering]

Hi Andres.

There may be some overlap here with some other scripts we have written to
syncronize category options.

Looking at this file

https://github.com/nextstrain/fauna/blob/master/source-data/flu_strain_name_fix.tsv

is seems to be a bunch of flu strains. I guess something similar exists
 for Ebola?

The approach we have taken with another system is to transform and import
these into DHIS2 through an ETL process. I think something similar might be
possible. It might be worth looking into and I would be happy to discuss
further with you about our approach.

Regards,
Jason


On Fri, Apr 7, 2017 at 2:55 PM, Andres Colubri 
wrote:

> Hi Johan,
>
> Many thanks for your kind reply. Yes, that's correct, we would like to
> associate pathogen sequence data to clinical cases. It sounds like storing
> the link to the NCBI records in a metadata attribute would be the simplest
> solution, as long as the sequences are already deposited publicly somewhere
> else. Then the app would pull the links from the DHIS2 DB and retrieve the
> full sequences. We will look into it, and will get back with more questions.
>
> Best,
>
> Andres
>
> On Fri, Apr 7, 2017 at 4:00 AM, Johan Ivar Sæbø 
> wrote:
>
>> Hi Andres,
>>
>> Welcome to the list! From what I understand, you want to associate a
>> given strain, such as MK13013 or the longer version Ebola
>> virus/H.sapiens-wt/SLE/2015/Makona-1309_C2_MK13013, with a clinical
>> case? That should be possible in several ways, either as a free text data
>> element, an option set, or as metadata attribute
>>
>> Take a look at some of the options in the manual:
>> Metadata attributes: https://docs.dhis2.org/master/
>> en/user/html/manage_attribute.html#about_attribute
>> Option sets: https://docs.dhis2.org/master/en/user/html/manage_option_set
>> .html
>>
>> If you want more of the meta-data such as the complete sequence, it
>> should in theory be possible, but a link to the ncbi would perhaps be the
>> best.
>>
>> Regards,
>> Johan Ivar Sæbø
>>
>> >-Original Message-
>> >From: Dhis2-users [mailto:dhis2-users-
>> >bounces+johansa=ifi.uio...@lists.launchpad.net] On Behalf Of Andres
>> >Colubri
>> >Sent: Thursday, April 06, 2017 3:40 PM
>> >To: dhis2-users@lists.launchpad.net
>> >Subject: [Dhis2-users] storing/linking sequence metadata in DHIS2
>> >
>> >I'm new to this mailing list, and to DHIS2 in general, so would like to
>> start by
>> >saying hi to everyone!
>> >
>> >
>> >I'm looking to create an DHIS2-based app that displays viral sequencing
>> >information on top of clinical cases (something along the lines of
>> NextStrain
>> > ). Is this
>> possible?
>> >Would I need to modify the underlying DataElement in dhis2-core to
>> support
>> >genetic metadata? Or would it be enough to add a reference to sequences
>> >stored elsewhere, for example in GenBank?
>> >
>> >Best,
>> >
>> >Andres
>>
>
>
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>
>


-- 
Jason P. Pickering
email: jason.p.picker...@gmail.com
tel:+46764147049
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Re: [Dhis2-users] storing/linking sequence metadata in DHIS2

[Andres Colubri]

Hi Johan,

Many thanks for your kind reply. Yes, that's correct, we would like to
associate pathogen sequence data to clinical cases. It sounds like storing
the link to the NCBI records in a metadata attribute would be the simplest
solution, as long as the sequences are already deposited publicly somewhere
else. Then the app would pull the links from the DHIS2 DB and retrieve the
full sequences. We will look into it, and will get back with more questions.

Best,

Andres

On Fri, Apr 7, 2017 at 4:00 AM, Johan Ivar Sæbø  wrote:

> Hi Andres,
>
> Welcome to the list! From what I understand, you want to associate a given
> strain, such as MK13013 or the longer version Ebola
> virus/H.sapiens-wt/SLE/2015/Makona-1309_C2_MK13013, with a clinical case?
> That should be possible in several ways, either as a free text data
> element, an option set, or as metadata attribute
>
> Take a look at some of the options in the manual:
> Metadata attributes: https://docs.dhis2.org/master/
> en/user/html/manage_attribute.html#about_attribute
> Option sets: https://docs.dhis2.org/master/en/user/html/manage_option_
> set.html
>
> If you want more of the meta-data such as the complete sequence, it should
> in theory be possible, but a link to the ncbi would perhaps be the best.
>
> Regards,
> Johan Ivar Sæbø
>
> >-Original Message-
> >From: Dhis2-users [mailto:dhis2-users-
> >bounces+johansa=ifi.uio...@lists.launchpad.net] On Behalf Of Andres
> >Colubri
> >Sent: Thursday, April 06, 2017 3:40 PM
> >To: dhis2-users@lists.launchpad.net
> >Subject: [Dhis2-users] storing/linking sequence metadata in DHIS2
> >
> >I'm new to this mailing list, and to DHIS2 in general, so would like to
> start by
> >saying hi to everyone!
> >
> >
> >I'm looking to create an DHIS2-based app that displays viral sequencing
> >information on top of clinical cases (something along the lines of
> NextStrain
> > ). Is this
> possible?
> >Would I need to modify the underlying DataElement in dhis2-core to support
> >genetic metadata? Or would it be enough to add a reference to sequences
> >stored elsewhere, for example in GenBank?
> >
> >Best,
> >
> >Andres
>
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Re: [Dhis2-users] [Dhis2-devs] How to output all data element list with their categories option DHIS2 V2.23 using SQLview

[vunda limbe]

Hi David and Sam,

I tried, it works now after deleting one of categorycomboid.

Thanks

On Fri, Apr 7, 2017 at 11:58 AM, David Palmer 
wrote:

> Hi Vunda,
>
>
>
> I think you’re making the same mistake I first made and trying to set it
> up as an SQL view.
>
> If you select “SQL query” instead it should save and run fine.
>
> Cheers,
>
> Dave
>
>
>
> *Dave Palmer *– MIS Technical Advisor
>
> *T* +44 (0) 20 3219 8098
>
> *M* +44 (0) 7757 109777
>
> *skype* dave-MSI
>
> david.pal...@mariestopes.org.uk
>
> www.mariestopes.org
>
>
>
> Marie Stopes International
>
> 1 Conway Street
>
> Fitzroy Square
>
> London W1T 6LP
>
> United Kingdom
>
>
>
>
>
> *From:* Dhis2-devs [mailto:dhis2-devs-bounces+david.palmer=
> mariestopes.org...@lists.launchpad.net] *On Behalf Of *vunda limbe
> *Sent:* 07 April 2017 10:41
> *To:* Sam Kasozi
> *Cc:* DHIS 2 Users list; DHIS 2 Developers list
> *Subject:* Re: [Dhis2-devs] [Dhis2-users] How to output all data element
> list with their categories option DHIS2 V2.23 using SQLview
>
>
>
> Hi Sam,
>
> Thank you for the script, but It's sending back this message: ERROR*:
> column "categorycomboid" specified more than once*
>
>
>
>
>
> On Fri, Apr 7, 2017 at 9:42 AM, Sam Kasozi  wrote:
>
> Hi Vunda,
>
>
>
> Try out the attached script.
>
>
>
> regards,
>
>
> *Sam Kasozi*
> +256 788-993-565
>
> Skype: sam.kasoziug
>
>
>
> On Fri, Apr 7, 2017 at 1:00 PM, vunda limbe  wrote:
>
> Hi everybody,
>
> I'm looking for SQL code to list data element name, id, uid,
> categoryoptioncombouid, categoryoptioncomboname.
>
> I don't know exactly wich table I have to insert in my query for listing
> the content.
>
> Your supports are welcome
>
> Thanks.
>
>
>
> ___
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>
>
>
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Re: [Dhis2-users] How to output all data element list with their categories option DHIS2 V2.23 using SQLview

[Sam Kasozi]

Yes, sorry about that.

We have 'de.categorycomboid' and 'cc.categorycomboid'. You can delete one
of them.

Sam Kasozi
+256 788-993-565
Skype: sam.kasoziug

On Fri, Apr 7, 2017 at 2:10 PM, vunda limbe  wrote:

> Hi Sam,
>
> Thank you for the script, but It's sending back this message: ERROR:
> column "categorycomboid" specified more than once
>
>
>
> On Fri, Apr 7, 2017 at 9:42 AM, Sam Kasozi  wrote:
>
>> Hi Vunda,
>>
>> Try out the attached script.
>>
>> regards,
>>
>> Sam Kasozi
>> +256 788-993-565
>> Skype: sam.kasoziug
>>
>> On Fri, Apr 7, 2017 at 1:00 PM, vunda limbe  wrote:
>>
>>> Hi everybody,
>>>
>>> I'm looking for SQL code to list data element name, id, uid,
>>> categoryoptioncombouid, categoryoptioncomboname.
>>> I don't know exactly wich table I have to insert in my query for listing
>>> the content.
>>>
>>> Your supports are welcome
>>>
>>> Thanks.
>>>
>>> ___
>>> Mailing list: https://launchpad.net/~dhis2-users
>>> Post to : dhis2-users@lists.launchpad.net
>>> Unsubscribe : https://launchpad.net/~dhis2-users
>>> More help   : https://help.launchpad.net/ListHelp
>>>
>>>
>>
>
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Re: [Dhis2-users] How to output all data element list with their categories option DHIS2 V2.23 using SQLview

[vunda limbe]

Hi Sam,

Thank you for the script, but It's sending back this message: ERROR: column
"categorycomboid" specified more than once



On Fri, Apr 7, 2017 at 9:42 AM, Sam Kasozi  wrote:

> Hi Vunda,
>
> Try out the attached script.
>
> regards,
>
> Sam Kasozi
> +256 788-993-565
> Skype: sam.kasoziug
>
> On Fri, Apr 7, 2017 at 1:00 PM, vunda limbe  wrote:
>
>> Hi everybody,
>>
>> I'm looking for SQL code to list data element name, id, uid,
>> categoryoptioncombouid, categoryoptioncomboname.
>> I don't know exactly wich table I have to insert in my query for listing
>> the content.
>>
>> Your supports are welcome
>>
>> Thanks.
>>
>> ___
>> Mailing list: https://launchpad.net/~dhis2-users
>> Post to : dhis2-users@lists.launchpad.net
>> Unsubscribe : https://launchpad.net/~dhis2-users
>> More help   : https://help.launchpad.net/ListHelp
>>
>>
>
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Re: [Dhis2-users] How to output all data element list with their categories option DHIS2 V2.23 using SQLview

[Sam Kasozi]

Hi Vunda,

Try out the attached script.

regards,

Sam Kasozi
+256 788-993-565
Skype: sam.kasoziug

On Fri, Apr 7, 2017 at 1:00 PM, vunda limbe  wrote:

> Hi everybody,
>
> I'm looking for SQL code to list data element name, id, uid,
> categoryoptioncombouid, categoryoptioncomboname.
> I don't know exactly wich table I have to insert in my query for listing
> the content.
>
> Your supports are welcome
>
> Thanks.
>
> ___
> Mailing list: https://launchpad.net/~dhis2-users
> Post to : dhis2-users@lists.launchpad.net
> Unsubscribe : https://launchpad.net/~dhis2-users
> More help   : https://help.launchpad.net/ListHelp
>
>
SELECT de.name as dataelementname, de.shortname as dataelementshortname, de.uid 
as de_uid, de.dataelementid, de.categorycomboid,
coc.name as cocname, coc.uid as cocuid, coc.categoryoptioncomboid, 
cc.categorycomboid, cc.name as ccname, cc.uid as ccuid 
FROM dataelement de LEFT JOIN categorycombos_optioncombos coccc on 
de.categorycomboid = coccc.categorycomboid
LEFT JOIN categorycombo cc ON coccc.categorycomboid = cc.categorycomboid
LEFT JOIN categoryoptioncombo coc ON coccc.categoryoptioncomboid = 
coc.categoryoptioncomboid
ORDER BY de.dataelementid___
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[Dhis2-users] How to output all data element list with their categories option DHIS2 V2.23 using SQLview

[vunda limbe]

Hi everybody,

I'm looking for SQL code to list data element name, id, uid,
categoryoptioncombouid, categoryoptioncomboname.
I don't know exactly wich table I have to insert in my query for listing
the content.

Your supports are welcome

Thanks.
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Re: [Dhis2-users] storing/linking sequence metadata in DHIS2

[Johan Ivar Sæbø]

Hi Andres,

Welcome to the list! From what I understand, you want to associate a given 
strain, such as MK13013 or the longer version Ebola 
virus/H.sapiens-wt/SLE/2015/Makona-1309_C2_MK13013, with a clinical case? That 
should be possible in several ways, either as a free text data element, an 
option set, or as metadata attribute

Take a look at some of the options in the manual:
Metadata attributes: 
https://docs.dhis2.org/master/en/user/html/manage_attribute.html#about_attribute
Option sets: https://docs.dhis2.org/master/en/user/html/manage_option_set.html

If you want more of the meta-data such as the complete sequence, it should in 
theory be possible, but a link to the ncbi would perhaps be the best.

Regards,
Johan Ivar Sæbø

>-Original Message-
>From: Dhis2-users [mailto:dhis2-users-
>bounces+johansa=ifi.uio...@lists.launchpad.net] On Behalf Of Andres
>Colubri
>Sent: Thursday, April 06, 2017 3:40 PM
>To: dhis2-users@lists.launchpad.net
>Subject: [Dhis2-users] storing/linking sequence metadata in DHIS2
>
>I'm new to this mailing list, and to DHIS2 in general, so would like to start 
>by
>saying hi to everyone!
>
>
>I'm looking to create an DHIS2-based app that displays viral sequencing
>information on top of clinical cases (something along the lines of NextStrain
> ). Is this possible?
>Would I need to modify the underlying DataElement in dhis2-core to support
>genetic metadata? Or would it be enough to add a reference to sequences
>stored elsewhere, for example in GenBank?
>
>Best,
>
>Andres
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