ontodev-cogs 0.0.1

COGS Operates Google Sheets

COGS Operates Google Sheets

WARNING This project is work in progress.

COGS takes a set of TSV files on your local file system and allows you to edit them using Google Sheets.

Overview

Since COGS is designed to synchronize local and remote sets of tables, we try to follow the familiar git interface and workflow:

• cogs init creates a .cogs/ directory to store configuration data and creates a spreadsheet for the project
• cogs add foo.tsv starts tracking the foo.tsv table as a sheet
• cogs rm foo.tsv stops tracking the foo.tsv table as a sheet
• cogs push pushes changes to local sheets to the project spreadsheet
• cogs fetch fetches the data from the spreadsheet and stores it in .cogs/
• cogs ls shows a list of currently-tracked sheet names and their local names
• cogs status summarizes the differences between tracked files and their copies in .cogs/
• cogs diff shows detailed differences between local files and the spreadsheet
• cogs pull overwrites local files with the data from the spreadsheet, if they have changed

There are some other commands that do not correspond to any git actions:

• cogs apply applys formatting & notes to the spreadsheet from a standardized table
• cogs delete destroys the spreadsheet and configuration data, but leaves local files alone
• cogs mv foo.tsv bar.tsv updates the path to the local version of a spreadsheet from foo.tsv to bar.tsv
• cogs open displays the URL of the spreadsheet
• cogs share shares the spreadsheet with specified users

There is no step corresponding to git commit.

We recommend running cogs push after updating a local tracked sheet to keep the remote sheets in sync.

When updating a remote sheet, we recommend the following to keep the local sheets in sync:

cogs fetch
cogs pull

Logging

To print info-level logging messages (error and critical level messages are always printed), run any command with the -v/--verbose flag:

cogs [command & opts] -v

Otherwise, most commands succeed silently.

Definitions

• Spreadsheet: the remote Google Sheets spreadsheet - each COGS project corresponds to one spreadsheet
• Sheet: a tab in the spreadsheet - each sheet corresponds to one local TSV or CSV table
• Remote: data from Google Sheets
• Local: data from your local working directory
• Cached: data stored in .cogs/ which is fetched from the remote spreadsheet
• Format: the format applied to a cell in a sheet (e.g., background color, font family, etc.)
• Note: a note (a.k.a. comment) on a cell that appears when hovered over in the sheet

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Development

Until we distribute COGS with Pypi, and for local development on Unix (Linux or macOS), we suggest these install instructions:

$ python3 -m venv .venv
$ source .venv/bin/activate
$ pip install -r requirements.txt
$ pip install -e .
$ cogs --help

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Commands

add

Running add will begin tracking a local TSV or CSV table. The table details (path, name/title, and description) get added to .cogs/sheet.tsv and all headers are added to .cogs/field.tsv, if they do not already exist with the default datatype of cogs:text (text string).

cogs add [path] -d "[description]"

The -d/--description is optional.

The sheet title is created from the path (e.g., tables/foo.tsv will be named foo). If a sheet with this title already exists in the project, the task will fail. The sheet/file name cannot be one of the COGS reserved names: config, field, sheet, renamed, or user.

This does not add the table to the spreadsheet as a sheet - use cogs push to push all tracked local tables to the project spreadsheet.

apply

Running apply applies the details of one or more standardized problems tables to the spreadsheet as cell formatting and notes.

cogs apply [problems1.tsv problems2.tsv ...]

The three levels of problems will be formatted with a black border and the following backgrounds:

• error: light red background
• warn/warning: light yellow background
• info: light blue background

The notes and formats will be added to any existing, but will take priority over the existing notes and formats.

Running apply again will remove any "applied" formats and notes from the last time apply was run and add new details from the current problems table(s). To erase all "applied" formats and notes, run cogs apply with no additional arguments. Existing formats and notes added by the user will not be removed.

Standardized Problems Tables

Standardized problems tables provide a standard table output that can be converted into formatting and notes in the spreadsheet using apply. As long as the table follows the format described below, any type of problem can be applied to the sheets. One example is the errors from ROBOT template.

These tables must have the following headers:

• ID: local numeric identifier starting at 1 and counting up
• table: name of the table that the problem occurs in
• cell: A1 format of problematic cell location
• level: severity of the problem; error, warn, or info - this determines the background color of the cell
• rule ID: an IRI or CURIE to uniquely identify the problem
• rule name: descriptive name of the problem - this is converted to the cell note
• value: value of the cell causing problem
• fix: can be left blank; a suggested value to replace the problematic value
• instructions: can be left blank; detailed instructions on how to fix the problem

delete

Running delete reads the configuration data in .cogs/config.tsv to retrieve the spreadsheet ID. This spreadsheet is deleted in Google Sheets and the .cogs directory containing all project data is also removed. Any local TSV/CSV tables specified as sheets in the spreadsheet are left untouched.

cogs delete

diff

Running diff will display all file changes between local and remote sheets after running cogs fetch or after updating a local sheet (before pushing or pulling those changes).

cogs diff

By default, this will display all files with changes. If you wish to just see the changes for one or more paths, you can provide those paths:

cogs diff path1.tsv path2.tsv ...

diff opens a responsive scrolling window. To scroll down, press the down arrow. To scroll up, press the up arrow (see all navigation below). For large files with many columns, you can also scroll to the right with the right arrow and back to the left with the left arrow.

The start of a diff for a sheet begins in bold with the file name (local and remote versions).

The displayed text below has formatting for changes between the local and remote sheets:

• Lines that have been removed from the remote version of the sheet are in red text and begin with ---.
• Lines that have been added to the local version of the sheet are in green text and begin with +++.
• Lines that have been changed between the remote and local versions are in blue text and begin with ->.

In cells with changed values, the cell is formatted as so:

old text -> new text

If a sheet has been newly created or deleted, these changes will not appear in diff. Instead, use cogs status.

To navigate the diff:

• ↑: move one line up
• ↓: move one line down
• →: move 20 characters right
• ←: move 20 characters left
• q: quit
• t: go to top (first line)
• b: go to bottom (last line)
• r: go to rightmost characters (last column)
• l: to to leftmost characters (first column)

fetch

Running fetch will sync the local .cogs/ directory with all remote spreadsheet changes.

cogs fetch

This will download all sheets in the spreadsheet to that directory as {sheet-title}.tsv - this will overwrite the existing sheets in .cogs/, but will not overwrite the local versions specified by their path. As the sheets are downloaded, the fields are checked against existing fields in .cogs/field.tsv and any new fields are added with the default datatype of cogs:text (text string). Any sheets that have been added with add and then pushed to the remote sheet with push will be given their IDs in .cogs/sheet.tsv.

.cogs/format.tsv and .cogs/note.tsv are also updated for any cell formatting or notes on cells, respectively. Each unique format is given a numerical ID and is stored as CellFormat JSON.

If a new sheet has been added to the Google spreadsheet, this sheet will be downloaded and added to .cogs/sheet.tsv. The default path for pulling changes will be the current working directory (the same directory as .cogs/ is in). This path can be updated with cogs mv.

To sync the local version of sheets with the data in .cogs/, run cogs pull.

Note that if a sheet has been renamed remotely, the old sheet title will be replaced with the new sheet title. Any changes made to the local file corresponding to the old title will not be synced with the remote spreadsheet. Instead, once you run cogs pull, a new sheet {new-sheet-title}.tsv will appear in the current working directory (the same as if a new sheet were created). It is the same as if you were to delete the old sheet remotely and create a new sheet remotely with the same contents. Use cogs pull to write the new path - the old local file will not be deleted.

init

Running init creates a .cogs directory containing configuration data. This also creates a new Google Sheets spreadsheet and stores the ID. Optionally, this new sheet may be shared with users.

cogs init -c [path-to-credentials] -t [project-title] -u [email] -r [role]

Options:

• -c/--credentials: required, path to Google API credentials in JSON format
• -t/--title: required, title of the project which will be used as the title of the Google spreadsheet
• -u/--user: email of the user to share the sheet with (if a --role is not specified, this user will be a writer)
• -r/--role: role of the user specified by --user: writer or reader
• -U/--users: path to TSV containing emails and roles for multiple users (header optional)

Three files are created in the .cogs/ directory when running init:

• config.tsv: COGS configuration, including the spreadsheet details
• field.tsv: Field names used in sheets (contains default COGS fields)
• format.tsv: Sheet ID, cell location or range, and format IDs (the format for each format ID is stored as a JSON dictionary in .cogs/formats.json)
• note.tsv: Sheet ID, cell location, and note for all notes
• sheet.tsv: Sheet names in spreadsheet and details (empty) - the sheets correspond to local tables

All other tasks will fail if a COGS project has not been initialized in the working directory.

ls

Running ls displays a list of tracked sheet names and their local paths, even if the local path does not yet exist.

cogs ls

open

Running open displays the URL of the spreadsheet.

cogs open

pull

Running pull will sync local sheets with remote sheets after running cogs fetch.

cogs pull

Note that if you make changes to a local sheet without running cogs push, then run cogs fetch and cogs pull, the local changes will be overwritten.

push

Running push will sync the spreadsheet with your local changes. This includes creating new sheets for any added tables (cogs add) and deleting sheets for any removed tables (cogs rm). Any changes to the local tables are also pushed to the corresponding sheets.

cogs push

This will also push all notes and formatting from .cogs/format.tsv and .cogs/note.tsv.

mv

Running mv will update the path of a local sheet.

cogs mv [old_path] [new_path]

The old path must exist as a local file. It will be renamed to the new path during this process. If the basename of the new path (e.g., tables/foo.tsv -> foo) is already a tracked sheet, this command will fail as you cannot have two sheets with the same name.

We recommend running cogs push after cogs mv to keep the remote spreadsheet in sync.

rm

Running rm will stop tracking one or more local sheets. They are removed from .cogs/sheet.tsv, and the .cogs/field.tsv is updated to remove the fields that were unique to those sheets. Additionally, this does not delete any local copies of sheets specified by their paths.

cogs rm [paths]

This does not delete the sheet(s) from the spreadsheet - use cogs push to push all local changes to the remote spreadsheet and remove cached data about the sheet.

share

Running share shares the spreadsheet with the specified user(s).

cogs share -r [reader-email] -w [writer-email]

There are three options:

• -r/--reader: email of the user to give read access to
• -w/--writer: email of the user to give write access to
• -o/--owner: email of the user to transfer ownership to

We do not recommend transferring ownership of the COGS project spreadsheet, as this will prevent COGS from performing any administrative actions (e.g., cogs delete). If you do transfer ownership and wish to delete the project, you should simply remove the .cogs/ directory and then go online to Google Sheets and manually delete the project.

status

Running status shows the difference between local and remote copies of tracked sheets.

cogs status

There are five kinds of statuses (note that any changes to the remote spreadsheet will not be accounted for until you run cogs fetch)

• Modified locally: the sheet exists both locally and remotely (cached), but the local version has been edited since the last time cogs fetch or cogs push were run
  • use cogs diff [path] to see details
  • use cogs push to sync local changes to remote version (overwriting any changes to remote not yet pulled)
• Modified remotely: the sheet exists both locally and remotely, but cogs fetch has been run and returned a modified sheet since the last time the local version was edited
  • use cogs diff [path] to see details
  • use cogs pull to sync remote changes to local version (overwriting any changes to local not yet pushed)
• Added locally: the sheet exists locally and has been added to tracking, but is not yet pushed to the remote spreadsheet
  • use cogs push to add the sheet to the remote spreadsheet
• Added remotely: the sheet exists remotely and has been added to tracking, but is not yet pulled to a local copy
  • use cogs pull to add the sheet to locally
• Removed locally: the sheet exists remotely but has been removed from tracking using cogs rm
  • use cogs push to remove the sheet from the remote spreadsheet
• Removed remotely: the sheet exists locally but has been removed from remote spreadsheet
  • use cogs pull to remove the sheet locally