CSV to Docs

Seeding data with medic-conf

Seeding data with medic-conf

Users, contacts, and report data can be specified in comma-separated value (CSV) files, then converted to JavaScript Object Notation (JSON) files and uploaded into your instance using medic-conf. This documentation will cover the CSV notation used, fetching CSV files from Google Sheets, converting the CSV files into JSON docs, and then uploading the data from the JSON files to your instance.

Converting CSVs

Running medic-conf with the csv-to-docs action converts CSV files from the csv folder into JSON docs to be uploaded to your instance. The JSON files are stored in the json_docs folder. Instructions for creating the CSV files are in sections below.

Uploading CSVs

Running medic-conf with the upload-docs action will upload the JSON docs that were generated from the CSV files to your instance. For example, running medic-conf --local upload-docs will upload the converted docs into your local instance. The target location --local can be replaced with an instance or URL. See medic-conf for detailed instructions.

Creating CSV files for Contacts, Reports

A separate CSV file is needed for each type of place, person, or report in your project’s local csv folder. 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. By default, the place types are one of clinic, health_center, or district_hospital. As of 3.7 of the Core Framework, the number of place types and their names can be configured — the {place_type} should match with the hierarchy names used.
  • person.{parent_place_type}.csv: where {parent_place_type} is the type of place to which the people in the file will belong.
  • 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"

In each of these files a header row is used to specify the JSON field names, and each subsequent row specifies the corresponding values for a doc. A _id field is automatically generated with a universally unique identifier.

Here is an example of a csv/person.clinic.csv file for people belonging to clinics:

name,sex,date_of_birth
Adriana Akiyama,female,1985-12-31
Becky Backlund,female,1987-10-17
Carson Crane,male,2015-01-23

Here is the table representation of the CSV:

namesexdate_of_birth
Adriana Akiyamafemale1985-12-31
Becky Backlundfemale1987-10-17
Carson Cranemale2015-01-23

Converting that CSV file to JSON docs with the csv-to-docs action would generate three files, one for each person. Here is one of the corresponding JSON files, json_docs/dbfbc0f0-117a-59ec-9542-3313fb10ef25.doc.json, which was created from the CSV data above:

{
  "type": "person",
  "name": "Adriana Akiyama",
  "sex": "female",
  "date_of_birth": "1985-12-31",
  "_id": "dbfbc0f0-117a-59ec-9542-3313fb10ef25"
}

Special notations

Specifying property type

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

column_one,column_two:bool,column_three:int,column_four:float,column_five:date,column_six:timestamp
some string,true,1,2.3,2017-12-31,1513255007072

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
}
Excluding column

A special column type, excluded, is used for excluding a column from the final JSON data:

my_column_that_will_not_be_a_property:excluded

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

Including another doc

Often times database documents need to include or refer to other documents in the database. This can be achieved with queries across CSV files, which is done by specifying a query in the column header. The query specifies the doc type (person or place) and matching condition.

For instance, to include the parent district’s doc in a health center’s doc, the parent:place WHERE reference_id=COL_VAL column header is used. The COL_VAL is a special notation for that column’s value for the row, and it will be used to match against the reference_id field in all other places. Given these example CSVs, you can see the corresponding JSON structure:

place.district.csv:

reference_id:excludedis_name_generatednamereported_date:timestamp
district_1falseD11544031155715
district_2falseD21544031155715
district_3falseD31544031155715

place.health_center.csv:

reference_id:excludedparent:place WHERE reference_id=COL_VALis_name_generatednamereported_date:timestamp
health_center_1district_1falseHC11544031155715
health_center_2district_2falseHC21544031155715
health_center_3district_3falseHC31544031155715

480d0cd0-c021-5d55-8c63-d86576d592fc.doc.json:

{
  "type": "health_center",
  "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"
}
Including value from another doc

Similar to including another doc, it is also possible to get the value of a specific field in another doc. For instance, if parent:GET _id OF place WHERE reference_id=COL_VAL were used in the example above, the parent field’s value would have been set to the _id of the refered to doc instead of including the whole doc. Note that _id is a generated value included in all generated docs.

reference_id:excludedparent:GET _id OF place WHERE reference_id=COL_VALis_name_generatednamereported_date:timestamp
health_center_1district_1falseHC11544031155715
health_center_2district_2falseHC21544031155715
health_center_3district_3falseHC31544031155715

The resulting doc would be as follows, with the _id from district_1 as the parent value:

{
  "type": "health_center",
  "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"
}

Creating CSV files for users

To create user accounts from CSV files, a users.csv file will be needed in the csv folder. The users.csv file requires columns for username and password. Additional columns can be used for any additional fields needed on the user’s doc, for example roles, phone. Running the csv-to-docs upload-docs create-users actions in that order will generate the necessary JSON docs with a users.csv file in your working directory, and then create the people, places, and users.

The following sections describe the different ways to associate the new users to contacts.

Creating new users with existing contacts

When creating users that are associated to existing contacts, contact and place columns should be created. Each row should have the UUID of an existing person for contact, and an existing place for place.

Creating new users with new contacts

To create new contacts for each new user provide values for contact.name, place.name, and place.parent (can be existing place), as seen in this example CSV:

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

The username, password, contact.name, place.type, place.name columns are required to have functional users with new places.

Creating new users linked to contacts in CSV files

To associate the new users to contacts that will also be created with the csv-to-docs action, use reference queries to the contacts. For instance, the column header for the person would be contact:person WHERE reference_id=COL_VAL, and for the place would be place:GET _id OF place WHERE reference_id=COL_VAL.

Here is a example of how the three CSV files 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"

Using CSV files on Google Drive

Individual Google Sheets can be used for each CSV file, which can be exported manually to CSV file format, or linked to your project to be downloaded by medic-conf.

To fetch the files from Google Drive run the fetch-csvs-from-google-drive action in medic-conf. This will download the CSV files specified in the csvs-on-google-drive.json file, and place them into the csv folder.

Linking to Google Drive

The file csvs-on-google-drive.json in your project’s home directory will consist of a key value pair for each CSV file. The keys must be the filename where the CSV will be stored locally — see the CSV file documentation for the notation. The value of each key must be the ID of the corresponding file in Google Drive — the ID can be obtained from the URL eg https://docs.google.com/spreadsheets/d/{FILE_ID}/edit.

{
    "person.clinic.csv":"google_drive_ID",
}

Google Drive authentication

Medic-conf leverages Google authentication to access Google Drive. You will need to create a client_secrets file named .gdrive.secrets.json and place it in your working directory, and create a token.

Create the .gdrive.secrets.json file by downloading the client_secrets.json from Google. You will need a CLIENT_ID, CLIENT_SECRET and REDIRECT_URL. You can find these pieces of information by going to the Developer Console, clicking your project –> APIs & auth –> credentials –> Download JSON. This will download the credentials but will need modified to be in this structure.

{
		"client_id": "<client_id>.apps.googleusercontent.com",
		"project_id": "proj_id",
		"auth_uri": "https://accounts.google.com/o/oauth2/auth",
		"token_uri": "https://accounts.google.com/o/oauth2/token",
		"auth_provider_x509_cert_url": "https://www.googleapis.com/oauth2/v1/certs",
		"client_secret": "client_secret",
		"redirect_uris": ["urn:ietf:wg:oauth:2.0:oob","http://localhost"]
}

See Google’s docs here on Oauth2


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