Column footprint editor

.gitmodules

@@ -1,3 +1,6 @@
+[submodule "postgis-geologic-map"]
+	path = services/column-footprint-editor/postgis-geologic-map
+	url = https://github.com/davenquinn/postgis-geologic-map.git
 [submodule "deps/topology-manager"]
 	path = submodules/topology-manager
 	url = https://github.com/Mapboard/topology-manager.git

pyproject.toml

@@ -31,3 +31,7 @@ markers = [
     "docker: marks tests as requiring a docker container",
     "requires_gdal: marks tests as requiring GDAL",
 ]
+
+# TODO: use UV workspaces
+# https://docs.astral.sh/uv/concepts/projects/workspaces/#workspace-sources
+

services/column-footprint-editor/.gitignore

@@ -0,0 +1,8 @@
+.node_modules
+__pycache__/
+*.pyc
+*.parcel-cache
+dist
+.env
+.vscode/
+dev.yaml

services/column-footprint-editor/.python-version

@@ -0,0 +1 @@
+3.11

services/column-footprint-editor/CHANGELOG.md

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+# Changelog:
+
+## 2025 reactivation
+
+- Switch to newer version of Python
+- Start using `uv` for dependency managment (note, this is different than other packages which use `poetry`).
+
+## Older changes on `voronoi` branch (2021)
+
+You can click on a point, that has more than one vertex, and drag them together, causing the lines to also be dragged together. Deleting and creating nodes also work.
+
+Can create new polygons from scratch using the line create tool. Edits are relatively easy, except for bugs listed below.
+
+Backend is bootstrapped to postgis-geologic-map and mapboard-server. Creates topology nicely from lines and centroid identity polygons.
+
+Database persistence onClick of the `save` button.
+
+Fixed Bug of dragging two points in same feature and 1+ of another feature. My mistake was overcomplicating the logic.
+
+I have successfully isolated the fronted custom drawing modes. Now state is handled the "right" way. The `draw.update` logic is performed in the `directselect.onstop` method.
+
+It looks like these coding clean-ups have also fixed the deleting points where shared bug that was occuring. But some odd behavior is causing me to leave it on bugs.
+
+Created a `GET` endpoint on top of a view table that joins `map_face` from `map_topology` schema onto the identity polygons and then the column properties table. Renders in the frontend as a geojson layer in mapbox, shade is determined by if the column has an identity.
+
+Clicking on shaded column brings a popup that has some basic info about the column.
+
+06/03/2021:
+Fixed the identity polygon bug, instead of using centroid use `ST_PointOnSurface`. It returns the "visual center" of a polygon much like the point of unaccessability.
+
+Polygons are automatically added to map_face table without an identity polygon being set. New polygons can be created using the line tool.
+
+Enhanced frontend with blueprint components. Nav bar buttons allows for saving and toggling between property and edit modes.
+
+Property editing works! Uses `ModelEditor` component from ui-components.
+
+Frontend component for if a polygon has two identities is around. Lists them as cards and you can choose which one.
+
+07/02/21:
+
+Multiple projects exist in the database as separate schemas and linked topologies using a config file for each project and a passing the project_id and config to a database class instance. The config is also passed to the docker container through a subprocess so the map topology can resolve the correct schema.
+
+Frontend WIP, click and add polygon. For now it just adds a box. Can become much more sophisticated to sense polygons around it and attach to their vertices if they're close by.
+
+07/13/21:
+
+Can swtich between projects through navbar and open import dialog. Import dialog has more info including all of the available projects in macrostrat.
+
+`change_set_clean` function for backend works much better now.
+
+Projects table in database holds project name and description.
+
+Slightly better U.I with more info in the import overlay
+
+Helper Project class created to make passing project attributes around easier
+
+08/02/21:
+
+Frontend context has more robust architecture. A async runActions allows for side-effects like fetching data
+in an async method while also passing off the dispatch for the rest of the app reducer. Things are simplified and standardized through types as well.
+
+Backend Project and Database class have some new methods to make it easier for creating a new project.
+
+Can now successfully create blank new projects through the frontend.
+
+08/20/21:
+
+Deleting shared nodes now works and doesn't break the frontend.
+
+Backend `clean_changeset` function works much better now after some additional fixes.
+
+MAJOR FEATURE ADDITION:
+
+- The ability to view, assign, and create `col_groups` and `col_group_names`.
+
+onClick highlight of column in property view.
+
+A color coded legned for column info.
+
+feedback on create new project and import
+
+09/01/21:
+
+Can add a known geometry by pasting either geojson or wkt into text box.
+
+Map legend for column-groups
+
+09/13/21:
+
+Column-groups are now project specific.
+
+Frontend and Backend are Dockerized
+
+11/23/21:
+
+Frontend and sql queries adjusted to allow for `multilinestrings`. Dragging points
+together uses more internal Mapbox-gl-js-draw methods now, consequently dragging is
+more effecient and works better.
+
+The `SnapLineMode` creates valid multiline strings. Now when using the tool if you snap to a non-vertix point on an existing line, it creates a vertix on that line at that position. This makes creating columns easier and more effcient.
+
+12/27/21:
+
+Backend:
+
+- `clean_change_set` function is more efficient.
+
+Frontend:
+
+- U.I enhancements: Remodeled navbar and main overlay. About tab has short 'how to' section. Property dialog is draggable.
+- Increased the click-buffer when determining which features' points should be dragged, increasing drag reliability. Also,
+  when holding down the `shift` key while clicking on a vertex will ignore any dragging, allowing for un-linking vertices.
+- Draw Polygon mode is much more enhanced. OnClick a n-sided polygon (hexagon by default) is created and mousemove will change
+  size of the polgyon. Pressing 'a' (add) and 's' (subtract) allow the user to add or subtract how many sides the n-sided polygon
+  has (minimum 3).
+
+12/28/21:
+
+Minro database schema change to allow for a description field and color field in columns and column_groups
+respectively.
+
+Users can add a description to any column via the properties dialog as well as add a color to a column group.
+Column groups are now editable through the frontend.
+### Bugs:
+
+Strange console error, `Cannot read property 'getSelectedIds' of null`, on stopDragging event
+
+- This occurs during the onTouchEnd and onMouseUp in the custom direct_select
+- During the `this.fireUpdate()`
+
+### Next Steps/ Wanted Features:
+
+__POINTS MODE__: I want the functionality to see and change the location of the idenitity points. Could be a toggle.
+
+Backend workflow to remove an identity polygon when there are two for an geometry.
+
+- Rounding of points, to 4 spots
+
+- Will include all geometries and identity polygons as point
+  - for that `ST_Centroid` will work because the identity polygons are symmetrical.
+
+Maybe have the ability to teselate polygons into n internal polygons.
+
+Burwell Layer
+
+Highlight lines on snap, on Join
+
+eODP -- drill hole points, polygons aren't showing up. Perhaps render the centroid as a point.
+
+Feedback on import and create new project should catch errors and display them
+
+Download individual columns, column-groups and selected columns (multiple)

services/column-footprint-editor/Dockerfile

@@ -0,0 +1,31 @@
+FROM ghcr.io/davenquinn/geologic-map:latest 
+
+## use https://linuxize.com/post/how-to-install-python-3-9-on-debian-10/
+RUN apt update -y \
+    && apt install -y build-essential zlib1g-dev libncurses5-dev libgdbm-dev libnss3-dev libssl-dev libsqlite3-dev libreadline-dev libffi-dev curl libbz2-dev \
+    && wget https://www.python.org/ftp/python/3.9.1/Python-3.9.1.tgz \
+    && tar -xf Python-3.9.1.tgz \
+    && cd Python-3.9.1 && ./configure --enable-optimizations \
+    && make -j 2 && make altinstall \
+    && update-alternatives --install /usr/bin/python3 python3 /usr/local/bin/python3.9 1 \
+    && apt install -y python3-pip
+
+## before running pip we need to change the first line in lab_release
+## #!/usr/bin/python3.5 -Es
+RUN sed -i "1 s/3/3.5/g" /usr/bin/lsb_release
+
+COPY requirements.txt ./requirements.txt
+
+RUN python3 -m pip install -r ./requirements.txt
+
+
+COPY . /python_app
+RUN ["chmod", "+x", "/python_app/docker-scripts/run"]
+
+ENV GEOLOGIC_MAP_CONFIG=/app/docker-assets/docker-map-config.json
+
+EXPOSE 3006
+EXPOSE 8000
+
+#CMD ["cd","/python_app","&&","python3", "__init__.py"]
+CMD /python_app/docker-scripts/run

services/column-footprint-editor/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021 Casey Idzikowski
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

services/column-footprint-editor/Makefile

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+serve:
+	uv run uvicorn macrostrat.column_footprint_editor:app --host 0.0.0.0 --port 8002 --reload
+	#cd postgis-geologic-map && docker-compose up && cd .. & python3 backend/__init__.py
+
+kill:
+	kill -9 $(lsof -i TCP:8000 | grep LISTEN | awk '{print $2}')
+
+run dev:
+	docker-compose -f dev.yaml up --build
+# command to kill the app on port 8000
+

services/column-footprint-editor/README.md

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+# Topology Editing
+
+## NOTE: This now depends upon a microservice in [this](https://github.com/UW-Macrostrat/column-builder/tree/develop) repository. It will no longer run independently.
+
+### Introduction:
+
+Column-Topology is an application that is aimed at editing GeoJSON polygons **_while_** keeping topology. This application is being developed under the [UW-Macrostrat](https://macrostrat.org/) lab group.
+
+This application will hopefully be a column management system for footprint geometries for strategraphic columns.
+
+### Motivation:
+
+The Macrostrat group keeps track of sedimentary columns around the world and a U.I interface for editing and creating new columns, in the form of GeoJSON polygons, is needed. An easy to use interface that allows users to create and edit their topologies would help expand the macrostrat database and increase community unification.
+
+### Strategy:
+
+Most of the work has been done on the client side (javascript). The frontend is made using React js with vanilla javascript as well. For the map I am using [Mapbox-gl](https://github.com/mapbox/mapbox-gl-js) and for GeoJSON rendering I am using [Mapbox-gl-draw](https://github.com/mapbox/mapbox-gl-draw). Conceptually, I am thinking about it as lines instead of polygons. In a topology, polygons share sides, which is why in topojson they remove redundant coordinates. Here I think about it similiarly. All the sides of a polygon turn in lines. Then all you need to do is drag the vertices around.
+
+### Goals:
+
+Create a column version management system. Similar to git... Have a "compare" view to view two topology versions sideby side or on top. Metadata descriptions about project being edited.. Total area of polygons.
+
+Have a info panel at top: what project, total area of polygons.
+
+Some component that shows the change_set with maybe the ability to undo them.
+
+Ability to switch between different projects and maybe even different drafts of projects.

services/column-footprint-editor/conftest.py

@@ -0,0 +1,14 @@
+import logging
+
+from dotenv import load_dotenv
+
+disable_loggers = ["macrostrat.database.utils"]
+
+
+def pytest_configure():
+    # Quiet verbose logging
+    for logger_name in disable_loggers:
+        logger = logging.getLogger(logger_name)
+        logger.disabled = True
+
+    load_dotenv()

services/column-footprint-editor/docker-compose.yaml

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+version: "3.7"
+services:
+  db:
+    # PostgreSQL 13 is needed in order to allow force-dropping the database
+    # (in testing mode)
+    image: postgis/postgis:13-3.1
+    environment:
+      - POSTGRES_DB=geologic_map
+      # This allows connections without a password, which is expedient but insecure...
+      - POSTGRES_HOST_AUTH_METHOD=trust
+    ports:
+      - "5432:5432"
+    expose:
+      - 5432
+    volumes:
+      - db_cluster:/var/lib/postgresql/data
+  frontend:
+    build: ./frontend
+    ports:
+      - "1234:3000"
+  backend:
+    build: "column_footprint_editor"
+    entrypoint: "/python_app/docker-scripts/run"
+    environment:
+      - GEOLOGIC_MAP_CONFIG=/app/docker-assets/docker-map-config.json
+    ports:
+      - "40053:8000"
+    expose:
+      - "8000"
+volumes:
+  db_cluster:

services/column-footprint-editor/docker-scripts/run

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+#!/bin/bash
+
+python3 ../python_app/__init__.py

services/column-footprint-editor/macrostrat/column_footprint_editor/.gitignore

@@ -0,0 +1,2 @@
+__pychache__/
+*.pyc

services/column-footprint-editor/macrostrat/column_footprint_editor/__init__.py

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+from .api import app  # noqa
+from .database import Database  # noqa