Add openeo_workflow

.gitignore

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+.idea

openeo_workflow/Dockerfile

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+# docker build -t openeo_insar .
+# skopeo --insecure-policy copy --dest-tls-verify=false --multi-arch=all --format=oci docker-daemon:openeo_insar:latest docker://registry.stag.warsaw.openeo.dataspace.copernicus.eu/rand/openeo_insar:latest
+# docker run -it openeo_insar
+FROM ghcr.io/osgeo/gdal:ubuntu-small-3.10.0
+
+# Install necessary packages
+RUN apt-get update && \
+    apt-get install -y \
+        jq \
+        xmlstarlet \
+        zip \
+        default-jre \
+        bc \
+        nano \
+        wget \
+        python3-pip \
+        curl \
+        parallel \
+        dpkg && \
+    rm -rf /var/lib/apt/lists/*
+
+# Download and install jacksum and s5cmd
+RUN curl -L -O 'https://s3.waw3-2.cloudferro.com/swift/v1/jacksum/jacksum_1.7.0-4.1_all.deb' && \
+    dpkg -i jacksum_1.7.0-4.1_all.deb && rm jacksum_1.7.0-4.1_all.deb && \
+    curl -L -O 'https://github.com/peak/s5cmd/releases/download/v2.2.2/s5cmd_2.2.2_linux_amd64.deb' && \
+    dpkg -i s5cmd_2.2.2_linux_amd64.deb && rm s5cmd_2.2.2_linux_amd64.deb
+
+#COPY ./utilities /src/utilities # Copy at the end of faile to avoid slow rebuilds
+ENV PATH="${PATH}:/src/utilities/"
+
+# Set environment variables
+ENV AWS_S3_ENDPOINT=eodata.dataspace.copernicus.eu \
+    # AWS_ACCESS_KEY_ID=ACCESS \
+    # AWS_SECRET_ACCESS_KEY=DATA \
+    AWS_HTTPS=YES \
+    AWS_VIRTUAL_HOSTING=FALSE
+
+
+
+### Install esa-snap ###
+ENV DEBIAN_FRONTEND=noninteractive \
+    LC_ALL=C.UTF-8 \
+    LANG=C.UTF-8
+
+RUN apt-get update && \
+    apt-get install -y \
+      build-essential \
+      git \
+      wget \
+      python3 \
+      libgfortran5
+
+LABEL authors="Michele Claus, Emile Sonneveld"
+LABEL maintainer="[email protected], [email protected]"
+
+ENV SNAPVER=11
+
+RUN mkdir -p /src/snap
+COPY esa-snap-docker/response.varfile /src/snap/response.varfile
+
+# install and update snap
+RUN wget -q -O /src/snap/esa-snap_all_unix_${SNAPVER}_0_0.sh "https://step.esa.int/downloads/${SNAPVER}.0/installers/esa-snap_all_linux-${SNAPVER}.0.0.sh" && \
+   sh /src/snap/esa-snap_all_unix_${SNAPVER}_0_0.sh -q -varfile /src/snap/response.varfile && \
+   rm -f /src/snap/esa-snap_all_unix_${SNAPVER}_0_0.sh
+
+# update SNAP
+COPY esa-snap-docker/update_snap.sh /src/snap/update_snap.sh
+RUN sh /src/snap/update_snap.sh
+
+# add gpt to PATH
+ENV PATH="${PATH}:/usr/local/esa-snap/bin"
+
+
+ENV PATH="${PATH}:/src/"
+COPY . /src
+
+WORKDIR /src

openeo_workflow/insar.py

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+#!/usr/bin/env python3
+import base64
+import glob
+import json
+import subprocess
+import sys
+import os
+import datetime
+from pathlib import Path
+
+start_time = datetime.datetime.now()
+
+argument_list = sys.argv[1:]
+
+if len(argument_list) > 0:
+    input_dict = json.loads(base64.b64decode(argument_list[0].encode("utf8")).decode("utf8"))
+else:
+    input_dict = {
+        "message": "These are example arguments",
+        "spatial_extent": {
+            "west": 10.751,
+            "south": 46.741,
+            "east": 10.759,
+            "north": 46.749
+        },
+        "temporal_extent": [
+            "2024-08-14",
+            "2024-08-26"
+        ]
+    }
+print(input_dict)
+print("AWS_ACCESS_KEY_ID= " + str(os.environ.get("AWS_ACCESS_KEY_ID", None)))  # Don't print AWS_SECRET_ACCESS_KEY
+
+argument_list = [
+    "-s", input_dict["temporal_extent"][0],
+    "-e", input_dict["temporal_extent"][1],
+    # TODO: Specify spatial extent instead of point
+    "-x", str((input_dict["spatial_extent"]["west"] + input_dict["spatial_extent"]["east"]) / 2),
+    "-y", str((input_dict["spatial_extent"]["south"] + input_dict["spatial_extent"]["north"]) / 2),
+    "-p", "vv",
+    "-S", "IW3"  # TODO: Dynamically determine sub-swat
+]
+containing_folder = Path(os.path.dirname(__file__))
+
+# result_folder = containing_folder / "result"
+# result_folder.mkdir(parents=True, exist_ok=True)
+# result_folder = Path("/home/ubuntu")
+result_folder = Path.home()
+# tmp_insar = Path("/tmp/insar")
+# tmp_insar.mkdir(parents=True, exist_ok=True)
+tmp_insar = result_folder
+
+with open(result_folder / "output.txt", "w") as f:
+    f.write(json.dumps(input_dict))
+
+if "-o" in argument_list:
+    index_of_o = argument_list.index("-o")
+    # print("Ignoring -o parameter")
+    # argument_list = argument_list[:index_of_o] + argument_list[index_of_o + 2:]
+    if argument_list[index_of_o + 1] != "/home/ubuntu":
+        raise Exception("Only /home/ubuntu is allowed as output folder")
+else:
+    argument_list = ["-o", str(tmp_insar)] + argument_list
+
+# assert not any(tmp_insar.iterdir())
+# cmd = [str(containing_folder /"utilities/sentinel1_burst_extractor_spatiotemporal.sh")] + argument_list
+os.environ["PATH"] = os.environ["PATH"] + ":" + str(containing_folder / "utilities")
+cmd = ["sentinel1_burst_extractor_spatiotemporal.sh"] + argument_list
+print(cmd)
+# subprocess.run(cmd, check=True, cwd=containing_folder / "utilities", stderr=subprocess.STDOUT)
+
+print("seconds since start insar.py: " + str((datetime.datetime.now() - start_time).seconds))
+
+# GPT means "Graph Processing Toolkit" in this context
+glob_str = str(tmp_insar / "*/manifest.safe")
+bursts = glob.glob(glob_str)
+if len(bursts) == 0:
+    raise Exception("No files found with glob: " + glob_str)
+
+input1 = bursts[0]
+input2 = bursts[1]
+# bursts_relative = [str(Path(burst).relative_to(tmp_insar)) for burst in bursts]
+# iw_component = bursts_relative[0].split("_")[4]
+# input1 = tmp_insar / "S1A_SLC_20240814T171550_030345_IW3_VV_441043.SAFE/manifest.safe"
+# input2 = tmp_insar / "S1A_SLC_20240826T171550_030345_IW3_VV_442708.SAFE/manifest.safe"
+# input1 = tmp_insar / "S1A_SLC_20240814T171550_030345_IW3_VV_042880.SAFE/manifest.safe"
+# input2 = tmp_insar / "S1A_SLC_20240826T171550_030345_IW3_VV_043168.SAFE/manifest.safe"
+# ('-Pinput1=/home/ubuntu/S1A_SLC_20240814T171550_030345_IW3_VV_441043.SAFE/manifest.safe',
+#  '-Pinput2=/home/ubuntu/S1A_SLC_20240825T052728_359500_IW2_VV_442501.SAFE/manifest.safe',)
+
+gpt_cmd = [
+    "gpt",
+    "/src/s1-workflows/graphs/pre-processing_stackOverview_2images_GeoTiff.xml",
+    f"-Pinput1={input1}", f"-Pinput2={input2}",
+    f"-PstackOverview_filename={result_folder}/stackOverview_2images.json",
+    f"-PcoregisteredStack_filename={result_folder}/Orb_Stack_2images"
+]
+print(gpt_cmd)
+subprocess.run(gpt_cmd, check=True, stderr=subprocess.STDOUT)
+print("seconds since start insar.py: " + str((datetime.datetime.now() - start_time).seconds))
+
+# CWL Will find the result files in HOME or CD
+
+files = glob.glob(str(result_folder / "*.*"))
+print("Files in target dir: " + str(files))