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Medic Project Configurer

Requirements

  • nodejs 8 or later
  • python 2.7
  • or Docker

Installation

Docker

docker build -t medic-conf:v0 .
docker run medic-conf:v0
docker exec -it <container_name> /bin/bash

Ubuntu

npm install -g medic-conf
sudo python -m pip install git+https://github.com/medic/pyxform.git@medic-conf-1.17#egg=pyxform-medic

OSX

npm install -g medic-conf
pip install git+https://github.com/medic/pyxform.git@medic-conf-1.17#egg=pyxform-medic

Windows

As Administrator:

npm install -g medic-conf
python -m pip install git+https://github.com/medic/pyxform.git@medic-conf-1.17#egg=pyxform-medic --upgrade

Bash completion

To enable tab completion in bash, add the following to your .bashrc/.bash_profile:

eval "$(medic-conf --shell-completion bash)"

Upgrading

To upgrade to the latest version

npm install -g medic-conf

Usage

medic-conf will upload the configuration from your current directory.

Specifying the server to configure

localhost

medic-conf --local

A specific Medic instance

medic-conf --instance=instance-name.dev

Username admin is used. A prompt is shown for entering password.

If a different username is required, add the --user switch:

--user user-name --instance=instance-name.dev

An arbitrary URL

medic-conf --url=https://username:password@example.com:12345

Into an archive to be uploaded later

medic-conf --archive

The resulting archive is consumable by Medic's API >v3.7 to create default configurations.

Perform specific action(s)

medic-conf <--archive|--local|--instance=instance-name|--url=url> <...action>

The list of available actions can be seen via medic-conf --help.

Perform actions for specific forms

medic-conf <--local|--instance=instance-name|--url=url> <...action> -- <...form>

Currently supported

App Settings

  • compile from:
    • tasks
    • rules
    • schedules
    • contact-summary
    • purge
  • backup from server
  • upload to server

Forms

  • fetch from google docs/google sheets/google drive and save locally as .xlsx
  • backup from server
  • delete all forms from server
  • delete specific form from server
  • upload to server

Resources

  • upload to server

Translations

  • upload of custom translations to the server

csv-to-docs

To convert CSV to JSON docs, use the csv-to-docs action.

CSV File Name

The name of the file determines the type of doc created for rows contained in the file. The possible types are: report, person, and place. Each of these has a further specifier provided in the filename:

  • place.{place_type}.csv: where {place_type} is the type of place specified in the file, one of: clinic, health_center, district_hospital
  • person.{parent_place_type}.csv: where {parent_place_type} is the parent for the person, one of: clinic, health_center, district_hospital
  • report.{form_id}.csv: where {form_id} is the form ID for all the reports in the file. You will need one file per form ID

Here are some examples:

File named place.district_hospital.csv adds the property "type":"district_hospital"
File named person.clinic.csv add the property "type":"person"
File named report.immunization_visit.csv add the property "type":"report", "form":"immunization_visit"

Property Types

By default, values are parsed as strings. To parse a CSV column as a JSON type, suffix a data type to the column definition, e.g.

column_one,column_two:bool,column_three:int,column_four:float,column_five:date,column_six:timestamp

This would create a structure such as:

{
	"_id": "09efb53f-9cd8-524c-9dfd-f62c242f1817",
	"column_one": "some string",
	"column_two": true,
	"column_three": 1,
	"column_four": 2.3,
	"column_five": "2017-12-31T00:00:00.000Z",
	"column_six": 1513255007072
}

Excluded Columns

To exclude a column from the final object structure, give it the type excluded:

my_column_that_will_not_be_a_property:excluded

This can be useful if using a column for doc references.

Doc References

In the reference example below. A property on the JSON doc will be populated with the doc that matches the WHERE statement. The CSV example below using the reference will find the doc with district_1 and create a parent property with the value of the district_1 doc

To reference other docs, replace the type suffix with a matching clause:

parent:place WHERE reference_id=COL_VAL

Refered to CSV Example:

reference_id:excluded is_name_generated name reported_date:timestamp
district_1 false D1 1544031155715
district_2 false D2 1544031155715
district_3 false D3 1544031155715

CSV Using Reference

reference_id:excluded parent:place WHERE reference_id=COL_VAL is_name_generated name reported_date:timestamp
health_center_1 district_1 false HC1 1544031155715
health_center_2 district_2 false HC2 1544031155715
health_center_3 district_3 false HC3 1544031155715

This would create a structure such as:

{
  "type": "health_center",
  //Parent Property with district_1 doc as the value
  "parent": {
    "type": "district_hospital",
    "parent": "",
    "is_name_generated": "false",
    "name": "D2",
    "external_id": "",
    "notes": "",
    "geolocation": "",
    "reported_date": 1544031155715,
    "_id": "f223f240-5d6a-5a7a-91d4-46d3c59de73e"
  },
  "is_name_generated": "false",
  "name": "HC7",
  "external_id": "",
  "notes": "",
  "geolocation": "",
  "reported_date": 1544031155715,
  "_id": "480d0cd0-c021-5d55-8c63-d86576d592fc"
}

Doc Property References

To reference specific properties of other docs:

parent:GET _id OF place WHERE reference_id=COL_VAL

In this example the health_ccenter doc will have a property of parent set to the _id of the refered to doc district_1 property of _id

NOTE: _id is a generated value that is inside the generated docs.

Refered to CSV Example:

reference_id:excluded is_name_generated name reported_date:timestamp
district_1 false D1 1544031155715
district_2 false D2 1544031155715
district_3 false D3 1544031155715

CSV Using Reference

reference_id:excluded parent:GET _id OF place WHERE reference_id=COL_VAL is_name_generated name reported_date:timestamp
health_center_1 district_1 false HC1 1544031155715
health_center_2 district_2 false HC2 1544031155715
health_center_3 district_3 false HC3 1544031155715

This would create a structure such as:

{
  "type": "health_center",
  //Parent property with the _id from district_1 as the value.
  "parent": "0c31056a-3a80-54dd-b136-46145d451a66",
  "is_name_generated": "false",
  "name": "HC3",
  "external_id": "",
  "notes": "",
  "geolocation": "",
  "reported_date": 1544031155715,
  "_id": "45293356-353c-5eb1-9a41-baa3427b4f69"
}

Note the special string COL_VAL - this matches the CSV column value for the row being processed.

create-users

Creating a new user with a new place

To create new users associated to new place and a new contact. Provide values for contact.name, place.name, and place.parent(can be existing place)

username,password,roles,name,phone,contact.name,place.c_prop,place.type,place.name,place.parent
alice,Secret_1,district-admin,Alice Example,+123456789,Alice,p_val_a,health_center,alice area, district_uuid
bob,Secret_1,district-admin,bob Example,+123456789,bob,p_val_a,health_center,bob area,disctrict_uuid

Linking users to contacts created from csv-to-docs

To create user accounts for contacts that are created while running csv-to-docs action follow these steps.

  1. Create a users.csv file in the csv folder with the rest of the csvs needed for csv-to-docs action.
  2. Add columns for username, password, roles, phone, contact, place, and any other additional fields you want to populate.
  3. Use the following query language as the header names: for contact contact:person WHERE reference_id=COL_VAL and place place:GET _id OF place WHERE reference_id=COL_VAL. This feature is also supported in the csv-to-docs csv files.
  4. Run medic-conf csv-to-docs upload-docs create-users
    1. This will generate the contacts, places, and users associated to those contacts. The users are placed into a users.csv file in your working directory. Then upload the json docs creating your data and creating users associated.

Here is a example of how the three csvs need to be configured to setup a user linked to existing place and contact.

csv/place.health_center.csv

reference_id:excluded,parent:place WHERE reference_id=COL_VAL,is_name_generated,name,reported_date:timestamp
health_center_1,district_1,FALSE,HC1,1544031155715

Generated json doc for the health center

{
  "type": "health_center",
  "parent": {
    "type": "district_hospital",
    "parent": "",
    "is_name_generated": "false",
    "name": "District1",
    "external_id": "",
    "notes": "",
    "geolocation": "",
    "reported_date": 1544031155715,
    "_id": "e8f9739a-5d37-5b1e-be3c-a571b2c2409b"
  },
  "is_name_generated": "FALSE",
  "name": "HC1",
  "reported_date": 1544031155715,
  "_id": "8606a91a-f454-56e3-a089-0b686af3c6b7"
}

csv/person.csv

reference_id:excluded,parent:place WHERE reference_id=COL_VAL,name,phone,sex,role,reported_date,patient_id
p_hc1,health_center_1,Bob Johnson 1,+16143291527,male,manager,1552494835669,60951
p_hc2,health_center_1,Bob Johnson 2,+16143291528,male,manager,1552494835669,60951

Generated json doc for the person

{
  "type": "person",
  "parent": {
    "type": "health_center",
    "parent": {
      "type": "district_hospital",
      "parent": "",
      "is_name_generated": "false",
      "name": "District1",
      "external_id": "",
      "notes": "",
      "geolocation": "",
      "reported_date": 1544031155715,
      "_id": "e8f9739a-5d37-5b1e-be3c-a571b2c2409b"
    },
    "is_name_generated": "FALSE",
    "name": "HC1",
    "reported_date": 1544031155715,
    "_id": "8606a91a-f454-56e3-a089-0b686af3c6b7"
  },
  "name": "Bob Johnson 1",
  "phone": "+16143291527",
  "sex": "male",
  "role": "manager",
  "reported_date": "1552494835669",
  "patient_id": "60951",
  "_id": "65c52076-84c5-53a2-baca-88e6ec6e0875"
}

csv/users.csv

username,password,roles,phone,contact:person WHERE reference_id=COL_VAL,place:GET _id OF place WHERE reference_id=COL_VAL
ac1,Secret_1,district_admin:red1,+123456789,p_hc1,health_center_1
ac2,Secret_1,district_admin:supervisor,+123456789,p_hc2,health_center_1
ac3,Secret_1,district_admin,+123456789,p_hc3,health_center_1
ac4,Secret_1,district_admin,+123456789,p_hc4,health_center_1

This will generate the users.csv file in the working directory which is used by the create-users action. The contact and place fields should be resolved to the actual UUIDs.

p_hc1"username","password","roles","contact","phone","place"
"ac1","Secret_1","district_admin:red1","65c52076-84c5-53a2-baca-88e6ec6e0875","+123456789","8606a91a-f454-56e3-a089-0b686af3c6b7"
"ac2","Secret_1","district_admin:supervisor","b7d0dbd5-beeb-52a8-8e4c-513d0baece8e","+123456789","8606a91a-f454-56e3-a089-0b686af3c6b7"

Moving Contacts within the Hierarchy

Contacts are organized into a hierarchy. It is not straight-forward to move contacts from one position in the hierarchy to another because many copies of this hierarchy exist. Use the move-contacts action to assign a new parent to contacts. This command will move the specified contact, all the contacts under that contact, and all reports created by any of those contacts. This action will download all documents that need to be updated, update the lineages within those documents, and then save the updated documents on your local disk. To commit those changes to the database, run the upload-docs action.

Offline users who have contacts removed from their visible hierarchy will not automatically see those contacts disappear. The contact remains on the user's device. Any updates made to the contact (or any reports created for that contact) will silently fail to sync (medic/medic/#5701). These users must be encouraged to clear cache and resync! Also impactful, but less serious - this script can cause significant amounts of changes to the database and offline users who have contacts moved into their visible hierarchy may experience lengthy and bandwidth-intensive synchronizations.

Parameter Description Required
contacts Comma delimited list of contact IDs which will be moved Yes
parent ID of the new parent which will be assigned to the provided contacts Yes
docDirectoryPath This action outputs files to local disk at this destination No. Default json-docs

Some constraints when moving contacts:

  • Allowed Parents - When moving contacts on WebApp >v3.7, your chosen parent must be listed as a valid parent for the contact as defined in the configuration for place hierarchy. For WebApp <v3.7, the default hierarchy is enforced.
  • Circular Hierarchy - Nobody's parent can ever be themself or their child.
  • Primary Contacts - Primary contacts must be a descendant of the place for which they are the primary contact. You may need to select a new primary contact for a place through the WebApp if you'd like to move a primary contact to a new place in the hierarchy.
  • Minification - Due to contact "minification" (#2635) which was implemented in v2.13, this script should not be used for versions prior to v2.13.

Examples

Move the contacts with the id contact_1 and contact_2 to have the parent parent_id. The changes will be in the local folder my_folder only for review. Run the second command to upload the changes after review.

medic-conf --instance= move-contacts -- --contacts=contact_1,contact_2 --parent=parent_id --docDirectoryPath=my_folder
medic-conf --local upload-docs -- --docDirectoryPath=my_folder

Move the contact with the id contact_1 to the top of the hierarchy (no parent).

medic-conf --local move-contacts upload-docs -- --contacts=contact_1 --parent=root

Project Layout

This tool expects a project to be structured as follows:

example-project/
	.eslintrc
	app_settings.json
	contact-summary.js
	purge.js
	resources.json
	resources/
		icon-one.png
		…
	targets.js
	tasks.js
	task-schedules.json
	forms/
		app/
			my_project_form.xlsx
			my_project_form.xml
			my_project_form.properties.json
			my_project_form-media/
				[extra files]
				…
		contact/
			person-create.xlsx
			person-create.xml
			person-create-media/
				[extra files]
				…
		…
		…
	translations/
		messages-xx.properties
		…

If you are starting from scratch you can initialise the file layout using the initialise-project-layout action:

medic-conf initialise-project-layout

Derived configs

Configuration can be inherited from another project, and then modified. This allows the app_settings.json and contained files (task-schedules.json, targets.json etc.) to be imported, and then modified.

To achieve this, create a file called settings.inherit.json in your project's root directory with the following format:

{
	"inherit": "../path/to/other/project",
	"replace": {
		"keys.to.replace": "value-to-replace-it-with"
	},
	"merge": {
		"complex.objects": {
			"will_be_merged": true
		}
	},
	"delete": [
		"all.keys.listed.here",
		"will.be.deleted"
	],
	"filter": {
		"object.at.this.key": [
			"will",
			"keep",
			"only",
			"these",
			"properties"
		]
	}
}

medic-logs

Fetch logs from a production server.

This is a standalone command installed alongside medic-conf. For usage information, run medic-logs --help.

Usage

medic-logs <instance-name> <log-types...>

Accepted log types:

api
couchdb
gardener
nginx
sentinel

Testing Locally

  1. Clone the project locally
  2. Make changes to medic-conf or checkout a branch for testing
  3. Test changes
    1. To test CLI changes locally you can run node <project_dir>/src/bin/medic-conf.js. This will run as if you installed via npm.
    2. To test changes that are imported in code run npm install <project_dir> to use the local version of medic-conf.

compress images

To compress PNGs and SVGs in the current directory and its subdirectories, two commands are available:

compress-pngs
compress-svgs

Wishlist

  • only upload things which have changed (this could be a separate mode - e.g. update vs configure)

Releasing

  1. Create a pull request. Get it reviewed and approved.
  2. Run npm version patch, npm version minor, or npm version major as appropriate.
  3. Merge the pull request.

Copyright

Copyright 2013-2018 Medic Mobile, Inc. hello@medicmobile.org

License

The software is provided under AGPL-3.0. Contributions to this project are accepted under the same license.