cbeier-studio/xolmis

A free, open source, and multi-platform ornithological data manager, written in Lazarus/FPC.

Xolmis

A free, open source, multi-platform ornithological data manager, built using Lazarus/FPC.

Important

Xolmis is in the early stages of development and is subject to some breaking changes. As soon as possible, a stable version will be made available to anyone who intends to use the app in production.

Xolmis is an ornithological data management system intended for researchers and birdwatchers. It was designed to aggregate separated data files (e.g. CSV files and Excel spreadsheets), which may end up being lost over time. In addition to the objective of aggregating different types of data collected in research and observations, it also aims to facilitate the curation, crossing and sharing of data, while increasing its consistency and security.

🕊️ Xolmis is a genus of Neotropical passerines. Today it is represented by two species: Xolmis irupero and Xolmis velatus.

Features

Here is a list of the main features:

• Management of database connections.
• Start page with dashboard.
• Management of expeditions and samplings.
• Lists of sightings and samples collection.
• Bands and markings management (Brazilian system/CEMAVE).
• Management of known individuals and captures (including molt data).
• Record of breeding biology data.
• Record of institutions, researchers, and projects.
• Management of permits.
• Record of toponyms (gazetteer) and sampling plots.
• Updated bird taxonomies (Clements/eBird, IOC, and CBRO).
• Geographical coordinates converter (WGS84) from/to Decimal Degrees, DMS, and UTM formats.
• Import eBird records (CSV file).
• Import banding journals (CSV file).
• Import captures (CSV file).
• Attachment of images, audio recording, documents and links to the field records.

See the Milestones for more information on planned features.

Download and installation

See the Wiki for options and instructions of how to install.

Note

Linux and MacOS versions are not released yet. They need more work. Let me know if you are interested in helping.

How to contribute

Giving feedback

You can create pull requests directly and give feedback using the GitHub Issues. All suggestions, bugs reported and general issues are much appreciated.

Coding

If you want to help in Xolmis development, please send me a message to [email protected].

For requirements and packages needed, see the Wiki.

License

Xolmis is available under the GPL-3.0 license.

Icons used in Xolmis were adapted from Fluent UI System Icons and Fluent Emoji. Both were made available by Microsoft Corporation under the MIT license.

xolmis's Issues

Audio recordings list

List of audio recordings with basic playback controls.
Used to view, navigate, and select audio recordings.

• #15

Import nest journals

Import nests data from files with fixed schema (CSV format).
A file for description and measurements of the nest, a file for nest visits, and a file for eggs measurements.

• #51

Generator of combinations of colored bands

Using the colors informed by the user, generates all the possible combinations os colors for bird bands, indicating the combinations already used.

Reset combinations for distinct species and localities? Or just warn the user of the possibility of duplicated combinations?

Automatic software update

Download and update Xolmis automatically.

R/Python scripts integration

Generate R/Python scripts that use the database to get the data?
Static scripts to run some tasks?

Literature references

Citations of books, papers, websites, and other literary types.

Link between the references and the data records (source of data)?

Unified search bar

Search for:

• Records.
• Attachments.
• Settings.
• Commands.

New filetype to update taxonomies

Filetype based on JSON with data schema comprising:

• Taxonomy
• Version
• Type of update
• Taxon
• Property
• Value

Image viewer

Simple image viewer with features like zoom, rotate, flip, save, open in external editor, etc.
Depends on #15

Geographical coordinates editor

Dialog to help edit geographical coordinates in different formats.
With a list of imported coordinates to select. #10

Remember the window and panels size/position

Save the windows size and position.
Save the panels sizes proportional to the window.

Save other properties?

Export data to common file formats

Export data of the grid to common file formats as CSV, XML, and JSON.
Check a checkbox to export using the Darwin Core schema.

Better treatment of partial dates

Better search and validation of partial dates (only year or month/year).

Better management of eBird special taxa

Manage eBird special taxa (subspecific groups, spuh, slashes, hybrids, intergrades, forms, domestics) separately from traditional taxa (orders, families, genera, species).

Separated fields for each case?

• Subspecies and subspecific groups.
• Domestics and forms.
• Spuh and slashes.
• Hybrids and intergrades (two or three taxa).

Management of inactive records (recycle bin)

Panel containing a list of inactive records and buttons to restore or delete permanently.

Genealogical trees for individuals and nests

Draw genealogical tree of an individual with/without nests in it

Search and insert data from online databases

Search and get records from online databases, like GBIF, iNaturalist, eBird, VertNet, etc.

• #19

Taxa data sheets

Window to view taxon data.
Includes summary and statistics.

Show in a HtmlViewer?

Auto update taxonomies

Download and update taxonomies using simple files.

• #24

Export data to eBird format

Export using the eBird format allowing the user to import the data to eBird.org.

Attach files to a record

Attach images, audio recordings, documents, and links to data records.
Option to drop the files to add/link to the record.

• #19

Column summaries

Panel showing a summary of the data from the selected column.
The summary may contain diverse types of info:

• Simple statistics (average, min, max, standard deviation/error).
• Count of each distinct value.
• Map of geographical coordinates, etc.

Search taxa in the Web

Search taxa in various websites, like Google, Google Images, Birds of the World, Wiki Aves, iNaturalist, GBIF, VertNet, etc.
Open in the default web browser.

Copy record data to the clipboard

Copy record data (as text) to the clipboard to be pasted in other applications.

Define the format of field/accession number

Define the format of field/accession number to assemble it automatically.

Automatic database backup

Create a backup of the user database periodically.
Let the user set the backup interval?

Undo data changes from the record history

The user could undo the data changes in the record history.

Import files with varied schemas

Create a wizard to help to import files in other schemas.
It must:

• Select and open the file.
• Set the fields correspondence.
• Determine what to do with missing values.
• Finally, import the file.

Source of data and license notes

Fields to specify source and license of the data.

Editable lookup lists

Change the static lists (e.g. types of specimens, types of preparations) to editable lookup lists.

Import and export geographical coordinates from/to GPX and GeoJSON files

As in #10, but other file formats.

Record verifications

List of researcher verification events for each data record.
It adds the level of reliability to the records.

Import and export geographical coordinates

Import and export geographical coordinates from CSV and KML files.
The imported coordinates will be available to use in records.

Create CITES and IUCN fields in taxa records

Create the fields for CITES and IUCN categories for each taxon.
And import this data from the respective databases.

Phonetic search

Use phonetic search to maximize the chance of finding what it is looking for.

Image album

Simple grid of images with some labels to describe each image.
Used to view, navigate, and select images.

• #15
• #16

Better treatment of data conflicts

Enhance the management of data conflicts when editing and importing.
Includes duplicated and missing records, etc.

Summary popup on mouse hover for some linked records

When mouse hover a link to a record (e.g. capture, survey, individual, band, sighting, taxon, etc) show a popup window containing a summary of it.

Search multiple values at once

Search for multiple values of the same type at once.

Map viewer

Simple map viewer to show the geolocated records.

Advanced filters dialog

Simplified UI to create SQL queries.

Import from Darwin Core files

Import files in Darwin Core (DwC) format.
It requires to determine the correspondence of the fields in the database and the DwC file.

Group records using categorical columns

Display the records grouped by a categorical column in the grid.

Merge records

Merge duplicated records into one record.

Click on the map to get the geographical coordinate

Dialog with a map to get a geographical coordinate clicking on it.

Print and export basic reports

System to preview and print data reports.
Export to PDF.

Insert batch of specimens from a capture

Inform the types and quantities of specimens collected and inserts the records using the capture data.

Export to Darwin Core format

Use the Darwin Core schema to export data.

Dark mode

Create dark mode.
Setting to select light or dark mode.

Select which columns are visible

Let the user select the grid columns to display.
Save this in the settings.