Merge pull request #197 from hytechimaging/dev

Dev

CHANGELOG.md

@@ -4,10 +4,32 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+-----
+## [v1.4.0] - 2023-12-08
+
+### Add
+
+- Transect management (import, selection in environment table)
+- Action to open csv data folder
+
+
+### Modified
+
+- `End` environment entities are only created for export
+- Merge processes in background
+- Keep only one side gps entities during Merge process
+- Fixes `speed` and `course` attributes in gps layer
+- Add some fields in species table
+- Fixes relation between boat and survey table
+- Fixes `state` field into `StrateType`
+- Add field `session` and `routeType` in sighting and follower export
+- Merge behaviour fields into one behaviourSpecies field
+- Prevent crash on `stretchLastSection` option
+
 -----
 ## [v1.3.2] - 2023-05-09
 
-## Modified
+### Modified
 
 - EffortGroup became a complex id and it is copied into Sighting/Followers entities during export
 - EffortLeg added and copied in Sighting entities export
@@ -22,7 +44,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [v1.3.1] - 2023-01-04
 
-## Modified
+### Modified
 
 - Remove gps shortcut
 - Fix typographic error in documentation
@@ -46,7 +68,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Unvalidated filter to help validation
 - Boat layer
 
-## Modified
+### Modified
 
 - GPS can be enable/disable (button + shortcut). Disable GPS also finishes effort
 - Merge : dateCheckbox checked by default
@@ -63,7 +85,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [v1.2.3] - 2022-07-06
 
-## Modified
+### Modified
 
 - Plateform (environment table) is not a read-only column anymore.
 
@@ -206,6 +228,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 
 
+[v1.4.0]: https://github.com/hytechimaging/sammo-boat/releases/tag/v1.4.0
 [v1.3.2]: https://github.com/hytechimaging/sammo-boat/releases/tag/v1.3.2
 [v1.3.1]: https://github.com/hytechimaging/sammo-boat/releases/tag/v1.3.1
 [v1.3.0]: https://github.com/hytechimaging/sammo-boat/releases/tag/v1.3.0

Makefile

@@ -1,4 +1,4 @@
-VERSION := "1.3.2"
+VERSION := "1.4.0"
 TMPDIR := "/tmp/sammo-boat-$(VERSION)"
 
 venv:

README.md

@@ -9,4 +9,4 @@ In particular, this tool is used by the [Megascope](https://www.observatoire-pel
 
 SAMMO-Boat is a QGIS extension that redesigns interface and handles GPS and microphone support. The GPS trace, the effort data and observations are directly seen on the map. Observers focus on animal detection and can quickly fulfill this detection by relying on audio record. This record can be used afterwards to add the missing information and to validate observations according defined standards.
 
-![](https://github.com/hytechimaging/sammo-boat/blob/main/images/interface.png?raw=true) 
+![](https://github.com/hytechimaging/sammo-boat/blob/main/doc/source/images/interface.png?raw=true)

data/behav.csv

@@ -0,0 +1,17 @@
+behav,behav_cat
+attacked,behavBird
+with_prey,behavBird
+klepto,behavBird
+diving,behavBird
+follow_boat,behavBird
+random_flight,behavBird
+circular_flight,behavBird
+straight_flight,behavBird
+bow,behavMam
+milling,behavMam
+fast_swimming,behavMam
+slow_swimming,behavMam
+diving,behavMam
+breaching,behavMam
+fishing,behavShip
+route,behavShip

data/boat.csv

@@ -1,4 +1,5 @@
 name
 Thalassa
 Europe
-PourquoiPas
+PourquoiPas
+MiguelOliver

data/observers.csv

@@ -0,0 +1 @@
+observer,firstName,lastName,organisation,contact

data/plateform.csv

@@ -1,9 +1,11 @@
 ship,plateform,plateformHeight
 Thalassa,deck,8
-Thalassa,bridge,14
-Thalassa,upper_bridge,16.5
+Thalassa,bridge_inside,14
+Thalassa,upper_bridge_outside,16.5
 Europe,deck,4
-Europe,bridge,4
+Europe,bridge_inside,4
 PourquoiPas,deck,16.3
-PourquoiPas,bridge,18.6
-PourquoiPas,upper_bridge,21.6
+PourquoiPas,bridge_inside,18.6
+PourquoiPas,upper_bridge_outside,21.6
+MiguelOliver,bridge_inside,8
+MiguelOliver,bridge_outside,8

data/survey.csv

@@ -0,0 +1,2 @@
+region,survey,computer,shipName,cycle,session
+NEA,IBTS,computer_1,Europe,cycle_1,LEG1

data/survey_type.csv

@@ -0,0 +1,10 @@
+name
+PELGAS
+PELACUS_springtime
+IBTS
+PELACUS_automn
+CAMANOC
+JUVENA
+CGFS
+EVHOE
+MOOSE

data/transect.csv

@@ -0,0 +1 @@
+transect;strateType;subRegion;length;wkt

doc/source/conf.py

@@ -22,7 +22,7 @@
 author = "Hytech-Imaging"
 
 # The full version, including alpha/beta/rc tags
-release = "1.3.2"
+release = "1.4.0"
 
 
 # -- General configuration ---------------------------------------------------

doc/source/index.rst

@@ -15,7 +15,7 @@ In particular, this tool is used by the `Megascope <https://www.observatoire-pel
 
 SAMMO-Boat is a QGIS extension that redesigns interface and handles GPS and microphone support. The GPS trace, the effort data and observations are directly seen on the map. Observers focus on animal detection and can quickly fulfill this detection by relying on audio record. This record can be used afterwards to add the missing information and to validate observations according defined standards.
 
-.. image:: ../../images/interface.png
+.. image:: images/interface.png
    :align: center
    :width: 800
 

doc/source/interface.rst

@@ -57,11 +57,18 @@ This button allows to open the settings dialog, to configure administrators tabl
 
 |
 
-`Survey`, `Transect` and `Strate` buttons open the single entity of their table
-which can be modified to fulfill the session metadata.
+`Survey` button opens the single entity of the table which can be modified to
+fulfill the session metadata. In the `Survey` table, `survey` attribute list
+values come from the `SurveyType` table, `shipName` attribute list values come
+from the `Boat` table.
 
-`Boat` and `Plateform` buttons open their tables dialog as each can contains more
-than one entity.
+`SurveyType`, `Transect`, `Boat` and `Plateform` buttons open their tables
+dialog as each can contains more than one entity.
+
+Especially for `Transect` table, it is possible to import a linear layer
+(EPSG:4326). The imported layer must have the same attribute names as the
+`Transect` table (transect,strateType,subRegion,length). Transect entity reference
+will be available in the `Environment` table.
 
 3 - |save| Validation button
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -113,6 +120,8 @@ data from two distinct session. The environment/sighting/follower tables will be
 merging, avoiding to copy identical entities captured on a previous day. Gps point
 will be also decimated to keep only one record per minutes.
 
+User can use the gps checkboxes to choose which session gps layer will be kept.
+
 6 - |environment| Environment button
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -201,18 +210,16 @@ A status will be assigned automatically to each entity.
 The first status will be ``Begin``, then ``Add`` status will be created for the
 next entities until user changes the ``routeType`` attribute. User creates
 ``Add`` entities if the environmental variables change during the route. When the
-user changes the ``routeType`` attributes, it duplicates the previous entity
-(``Begin`` or ``Add`` status) and assignes the ``End`` status to the duplica.
-Environment status are check before the validation. A dialog should pop-up if 
-there is a missing ``Start`` / ``End`` record to inform user. Use the duplicate
-action to fix it (cf. :ref:`duplicateaction`).
+user changes the ``routeType`` attributes, the status attribute will be updated to
+``Begin``. Entities with ``End`` status will be created only on export.
 
 .. _sightingtable:
 
 12 - Sighting table
 ~~~~~~~~~~~~~~~~~~~~
 
-The sighting table is used to modify sighting entity attributes. Sighting entity describes an observation made by the operator.
+The sighting table is used to modify sighting entity attributes.
+Sighting entity describes an observation made by the operator.
 
 13 - Map canvas
 ~~~~~~~~~~~~~~~
@@ -223,6 +230,8 @@ displayed:
 .. |gps_symbol| image:: images/gps.svg
   :width: 18
 
+.. |transect_symbol| image:: images/transect.svg
+
 .. |environment_symbol| image:: ../../images/environment_symbol.svg
   :width: 18
 
@@ -233,7 +242,8 @@ displayed:
   :width: 18
 
 - world (as background map)
-- |gps_symbol| gps 
+- |gps_symbol| gps
+- |transect_symbol| transect
 - |environment_symbol| environmenent 
 - |sighting_symbol| sighting 
 - |follower_symbol| follower 

doc/source/session.rst

@@ -1,5 +1,3 @@
-.. _session:
-
 Session
 =======
 
@@ -8,9 +6,22 @@ Session
 
 Sammo-boat integrates a session system to works properly. To create a new session
 or load a existing session, user clicks on the |session| button in the
-Sammo-boat toolbar (cf. :ref:`sessionbutton`). User will select a folder in the dialog. If there is already
-a `sammo-boat.gpkg` database in the folder, this session will be opened.
+Sammo-boat toolbar (cf. :ref:`sessionbutton`). User will select a folder in the
+dialog.
+
+If there is already a `sammo-boat.gpkg` database in the folder, this session
+will be opened.
+
 Otherwise a new database will be created in the folder with the needed table.
+Notice that administrator and auxiliary tables can be populated by csv files,
+if there are located in the data folder.
+
+.. image:: init_data_folder_action.png
+   :align: center
+
+|
+
+This action opens the folder where csv files are located
 
 Database
 --------
@@ -24,22 +35,42 @@ to look at the database tables.
 
 |
 
-Some tables are administrator tables and should be populated with the survey information
-by an administrator :
+Some tables are administrator tables and should be populated with the survey
+information by an administrator. These tables can be fulfilled using the
+settings interface (cf. :ref:`settingsbutton`) or with csv files during the
+database initialization :
 
-- survey
-- boat
-- plateform
-- strate
-- transect
-- observers
-- species
+.. list-table:: Administrator tables
+
+  * - **Table**
+    - **csv file**
+  * - survey
+    - survey.csv 
+  * - survey_type
+    - survey_type.csv
+  * - transect
+    - transect.csv   
+  * - boat
+    - boat.csv
+  * - plateform
+    - plateform.csv
+
+There is also three auxiliary tables that can be fulfilled with csv files :
+
+.. list-table:: Auxiliary tables
+
+  * - **Table**
+    - **csv file**
+  * - observers
+    - observers.csv
+  * - species
+    - species.csv
+  * - behaviour_species
+    - behav.csv
 
 .. |settings| image:: ../../images/settings.png
   :height: 18
 
-Most of these tables can be configured in the settings dialog (cf. :ref:`settingsbutton`)
-
 The main tables used by operator will be the following:
 
 - environment
@@ -51,4 +82,9 @@ and the world table is only here to provide a map background.
 
 .. warning::
   Do not alter tables by removing fields or your database may become 
-  unusable in the Sammo-boat plugin.
+  unusable in the Sammo-boat plugin.
+
+
+Here is the full UML diagram of the database:
+
+.. image:: images/uml_diagram.png

metadata.txt

@@ -2,8 +2,8 @@
 name=Sammo-Boat
 description=Tool for megafauna observations from halieutic boats
 about=Tool for megafauna observations
-version=1.3.2
-qgisMinimumVersion=3.16
+version=1.4.0
+qgisMinimumVersion=3.28
 author=Paul Blottière
 [email protected]
 repository=https://github.com/hytechimaging/sammo-boat/