kgatman · kgatman · May 13, 2020 · May 13, 2020 · May 13, 2020 · May 13, 2020
diff --git a/DeployingMappings.md b/DeployingMappings.md
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+# Mappings and Serialized Object auto Deployment
+
+!!! warning
+    * First start with your local instance before attempting to update the live server.
+    * When configuring the live server, please make sure that **no one** is using the system when doing Step  **1** and **2** **Removing and Creating New Container**.
+    * **Backup live server database before doing any of these steps**.
+    * It has been noticed that some of the backup services have some technical issues and therefore you are advised to double check the file size after restarting the backup service before removing and stopping the container. The other option you can manually backup facility database by yourself.
+
+
+
+### Our automated deployment for mappings and serialized object comprises 5 steps:
+
+##### 0. Preparatory Steps
+
+* SSH into the server with `ssh openmrs@_SERVER_IP_ADDRESS`
+* First check to see if your server has internet connectivity with `ping github.com`
+* If not try to check contents of resolv.conf in /etc/ by running the following command: cat /etc/resolv.conf.Normally you should see google.com nameserver pointing to its ip 8.8.8.8.Edit the file if name server is not configured in the file.
+* Nameserver(all in lowercase) 8.8.8.8.Ping 8.8.8.8 or google.com.After you may ping github.com just to make sure you are able to get packets from github.com
+
+* Then download all of the files need with `git clone https://github.com/eRegister/docs.git `
+
+* The command above will create a folder called `docs` in `/home/openmrs` if you didn't change to another directory. All of files that need to be transferred to the server are in **`docs/scripts/MappingsScript`**. Mapping folder contains the following files: <br/>
+         `concept_restore.sh`<br/>
+         `gitpull_bahmniapps.sh`<br/>
+         `gitpull_concepts.sh`<br/>
+         `gitpull_mappings.sh` <br/>
+         `gitpull_serial.sh`<br/>
+         `serializedobject_restore.sh`<br/>
+         `gitpullbahmniapps.service` <br/>
+         `gitpullconcepts.service` <br/>
+         `gitpullmappings.service`<br/>
+         `gitpullserializedobject.service`<br/>
+* Go to `/development/` and create the following directories `openmrs_reporting_release` and `openmrs_concepts_release` and grant openmrs user permissions to own the files `sudo chown -R openmrs:openmrs directory_name`.
+* Move the following files to  `/usr/local/bin/` and make them executable:
+`concept_restore.sh`,`serializedobject_restore`.
+* Move `gitpull_concepts.sh` to `/development/openmrs_concepts_release` and `gitpull_serial.sh` to `/development/openmrs_reporting_release/`, make them executable.
+
+
+!!! note
+    Files are already on the server
+
+!!! caution
+    **PLEASE ENSURE THAT YOU HAVE BACKED UP THE DB BEFORE EXECUTING THE STEPS BELOW!!!**
+
+##### 1. Removing Current Container
+
+* check the running container: `docker ps`
+* Stop the container: `docker stop openmrseregister`
+* Check that the container has stopped run `docker ps` and you should see an empty table
+* Create a new image from the stopped container: `docker commit openmrseregister omrsregrepo/bahmni_base:09082020` [*tag should be date at time of creating image*]
+* you can check the newly created image with `docker images`
+* Remove the container: `docker container rm openmrseregister`
+
+##### 2. Creating a Volumes and enabling services
+
+* Now it's time to create a new container from the image we created earlier with: `docker run -e container_name=openmrseregister -it -d --restart always -p 443:443 -p 80:80 -p 8069:8069 -p 8000:8000 --privileged --name openmrseregister -v /development/bahmni_config_release:/development/bahmni_config_release -v /development/dhisconnector_mappings:/development/dhisconnector_mappings -v /development/bahmniapps_release:/development/bahmniapps_release omrsregrepo/bahmni_base:06082020 /bin/bash
+`
+* Go to `/development/` and grant openmrs user permissions to files in `/development/dhisconnector_mappings` and `/development/bahmniapps_release`
+* Move `gitpull_bahmniapps.sh` to `/development/bahmniapps_release` and `gitpull_mappings.sh` to `/development/dhisconnector_mappings`, make them executable.
+* Create local repo's in all directories in `/development` except `/development/bahmni_config_release`, commands `git init` , `git remote add origin https://github.com:/eRegister/repo_name`
+* test that you are able to fetch files from remote repo's by `git fetch --all`
+* move all services `gitpullmappings.service`,`gitpullconcepts.serivce`,
+`gitpullbahmniapps.service` and `gitpullserializedobject.service`.
+* Nagivate into /etc/system/system/ and type the following commands to enable `gitpull_mappings.service`, `gitpullconcepts.service`, `gitpullbahmniapps.service`,`gitpullserializedobject.service`
+
+    `sudo chmod 664 service_name`   <br/>
+    `sudo systemctl daemon-reload` <br />
+    `sudo systemctl enable service_name`
+
+   ** Note:when the service has been registered successfully you should see created sym link in ** `/etc/systemd/system/default.target.wants/.`
+
+##### 3. Configuring **cronjob**
+* configure the cronjob to trigger the services everyday 7 am if our servers universal time is at UTC.
+* to edit the cronjob do: `sudo crontab -e` if it's first time running the this command it'll probably ask you to choose the default text editor, please be kind enough to choose Nano as it's the easiest editor for most administrators.
+* configure the script as shown below and then when the updates have been pulled successfully change the script to trigger services at **7:05**,**7:10**,**7:15**,**7:25** respectively.
+**Do not change the command that trigger serialized object script** <br/>
+`*/3 * * * * systemctl restart gitpullmappings.service >> /var/log gitpull_mappings.log` <br/>
+`*/4 * * * * systemctl restart gitpullserializedobject.service >> /var/log/gitpull_serial.log` <br/>
+`*/5 * * * * systemctl restart gitpullconcepts.service >> /var/log/gitpull_concepts.log` <br/>
+`*/6 * * * * sudo bash /usr/local/bin/concepts_restore.sh >> /var/log/concept_restore.log` <br/>
+`20 7 * * * sudo bash /usr/local/bin/serializedobject_restore.sh >> /var/log/serial_restore.log`
+* Wait for a while for cron job to execute the commands and check  directories in development have updates from GitHub. For failed services refer to [Automated Deployment](https://eregister.github.io/docs/ereg/automateddeployment/) **Exit Codes** to troubleshoot.
+
+
+
+##### 4. Restore database and create soft links
+
+* Go to into a container and start mysql service.
+* Connect to database server using no password `mysql -uroot -p`
+* Initialise openmrs database and users by sourcing openmsq.sql file in container root directory, `source openmrs.sql;`
+* Wait a moment for databases to be created and once the script is done quit or exit the database server and restart mysql.
+* Restore facility database using the command `mysql -uroot -ppassword openmrs;`
+* Go to `/opt/openmrs/dhisconnector`
+* Remove mappings folder and create soft link to `/development/dhisconnector_mappings/dhisconnector_mappings/mappings` <br/>
+ **command:** <br/> `sudo ln -s /development/dhisconnector_mappings/dhisconnector_mappings/mappings/ mappings` <br/>
+* Exit the container and go to `/usr/local/bin` and run `serializedobject_restore.sh`
+* Restart other services and openmrs the broswer to access openmrs admin page.
+* Go to reporting  you should see total of 36 openmrs period indicator reports. Refer to staging server to see example [eRegister Staging server](https://3.21.105.229/openmrs/)
diff --git a/Integration-DHIS2.md b/Integration-DHIS2.md
diff --git a/contacts.md b/contacts.md
diff --git a/docs/contacts.md b/docs/contacts.md
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+# Contact Information
+
+For more information, please contact below:
diff --git a/docs/covid/About-Us.md b/docs/covid/About-Us.md
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+## This is an About Page
+
+...information loading....New Version
diff --git a/docs/covid/Alerts.md b/docs/covid/Alerts.md
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+
+........content coming soon......
diff --git a/docs/covid/Capturing-Weekly-Aggregate-Data.md b/docs/covid/Capturing-Weekly-Aggregate-Data.md
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+
+........content coming soon......
diff --git a/docs/covid/How-To-Prepare-Docker-Training-Instance.md b/docs/covid/How-To-Prepare-Docker-Training-Instance.md
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+!!!note
+    we chose Docker over other many ways of installing DHIS2 because in a few minutes you can have your instance up and running
+
+
+#### Installing Docker on the host server
+
+Please refer to this [link](../ereg/intro.md) for installing Docker
+
+#### Installling Docker Compose
+
+* To install Docker Compose, please refer to the official Docker Compose site [here](https://www.docker.com)
+* To prepare the training instance, we used two images:
+    * `dhis2 core 2.33`
+    * `dmillon/postgis` (_recommended because it already has postgis which DHIS2 depends on to render maps_)
+
+#### Downloading the images
+
+    ```
+    paste contents of docker-compose.yml
+
+    ```
+
+_you can change to whichever image you want to use. But please remember to drop SQL views before creating your dump_
+
+You can go ahead and read [this](#) to prepare your instance. Within a few minutes you should by now have your DHIS2 instance running.
+
+!!!warning
+    use `postgres` as your user for the db. It poses security threats (yes) but it's easier to deal with PostgreSQL with that setup. Unless ofcourse you're a PostgreSQL ninja.
+
+
+#### Restoring Postgres Database
+
+As you saw from the previous step, your instance is running two containers with networking between them handled by Docker Compose.
+If you have a live connection to Postgres database, you can't drop and restore your db. 
+
+* Do `docker ps` to see all of the running containers. `docker-compose ps` also works fine. 
+    * _it's important to do this step first because docker-compose is going to name according to how you named the folder containing the docker-compose.yml as well as how you labeled them **inside** the file_
+* To do that, you have to kill the frontend DHIS2 container then restore the DB with `docker container kill <name_of_dhis_container>`
+* Copy DB backup file into Postgres container with `docker cp dhis_db_backup.sql <name_of_postgres_container>:/`
+* Get into the container with `docker exec -it <name_of_postgres_container> bash`
+* Switch account from `root` to `postgres` with `su postgres` and then launch the PostgreSQL interactive terminal with `psql`
+* `\l` to list all of the databases
+* `drop database dhis2;` to delete the database
+* `create database dhis2` to recreate the database. But now it's empty
+* `\q` to the interactive terminal
+* `psql --username=postgres --dbname=dhis2 < dhis_db_backup.sql` to restore all of data into the empty database. _if the command ran succefully, you should see a trail of verbosely listed SQL commands processed_
+* Then the trail is done, do `exit` to exit the container
+* Finally, start the container that we "killed" with `docker container start <name_of_dhis_container>`
diff --git a/docs/covid/Indicators.md b/docs/covid/Indicators.md
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+
+
+........content coming soon......
+
diff --git a/docs/covid/Overview.md b/docs/covid/Overview.md
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+## Welcome to the COVID19 Surviellance Tool Technical Guide
+
+#### Overview
+
+The COVID19 Surveillance system can be found here: [http://hmis.gov.ls/covid19](http://hmis.gov.ls/covid19)
+
+
+This system is built off of DHIS2's Tracker Module. All of the broader user manuals can be found [here:](https://dhis2.github.io/dhis2-docs/master/en/user/html/dhis2_user_manual_en.html)
+
+#### Table of Contents
+In addition to that, we have developed guidelines specific to our context and usecases. The document structure looks like this:
+
+```
+COVID-19
+└── Overview
+└── Data Entry Guidelines
+      ├── Registering a Case or Suspect
+      ├── Capturing Weekly Aggregate Data
+      └── Using Mobile Devices
+└── Technical
+      ├── Alerts Dataset
+      ├── Program Indicators
+      ├── Indicators
+      ├── Program Rules
+      └── How to Prepare Docker Training Instance
+```
+
+------------------------------------------------------------------------------------------------------------
+
+#### Training Instance
+We have also have a training instance which we try by all means to make it an up-to-date replica of the live system.
+It can be found here: [http://197.155.193.109:1010/](http://197.155.193.109:1010/)
diff --git a/docs/covid/Program-Indicators.md b/docs/covid/Program-Indicators.md
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+
+
+........content coming soon......
diff --git a/docs/covid/Program_Rules.md b/docs/covid/Program_Rules.md
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+
+
+........content coming soon......
diff --git a/docs/covid/Registering-a-Case-or-Suspect.md b/docs/covid/Registering-a-Case-or-Suspect.md
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+
+content loading....
diff --git a/docs/covid/Using-Mobile-Devices.md b/docs/covid/Using-Mobile-Devices.md
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+
+content loading....
diff --git a/docs/covid/Using-Mobile.md b/docs/covid/Using-Mobile.md
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+
+content loading....
diff --git a/docs/covid/Using-Web-Aggregate.md b/docs/covid/Using-Web-Aggregate.md
@@ -0,0 +1,2 @@
+
+........content coming soon......
diff --git a/docs/covid/Validation-Rules.md b/docs/covid/Validation-Rules.md
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+
+........content coming soon......
diff --git a/docs/covid/Weekly-Report.md b/docs/covid/Weekly-Report.md
diff --git a/docs/covid/registering-a-case-mobile.md b/docs/covid/registering-a-case-mobile.md
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+### User Guide
+
+........content coming soon......
+
+### Trainer Guide
+
+........content coming soon......
diff --git a/docs/covid/using-web.md b/docs/covid/using-web.md
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+
+### User Guide
+........content coming soon......
+### Trainer Guide
+........content coming soon......
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		# Contact Information

		For more information, please contact below:
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		## This is an About Page

		...information loading....New Version