diff --git a/.gitignore b/.gitignore
index dcdcdb5..23be439 100644
--- a/.gitignore
+++ b/.gitignore
@@ -111,3 +111,6 @@ testdata.json
# macos
.DS_Store
+
+# tests
+PET0.ESMF_LogFile
diff --git a/duck/clintai.py b/duck/clintai.py
index 338c5e3..db31717 100644
--- a/duck/clintai.py
+++ b/duck/clintai.py
@@ -4,13 +4,16 @@
import craimodels
from climatereconstructionai import evaluate
import logging
+
LOGGER = logging.getLogger("PYWPS")
info_models = craimodels.info_models()
dataset_names = list(info_models.keys())
-def write_clintai_cfg(base_dir, model_dir, eval_name, data_name, data_type, eval_parameters):
+def write_clintai_cfg(
+ base_dir, model_dir, eval_name, data_name, data_type, eval_parameters
+):
cfg_templ = """
--data-root-dir {{ base_dir }}
--log-dir {{ base_dir }}
@@ -31,7 +34,8 @@ def write_clintai_cfg(base_dir, model_dir, eval_name, data_name, data_type, eval
eval_name=eval_name,
data_name=data_name,
data_type=data_type,
- eval_parameters=eval_parameters)
+ eval_parameters=eval_parameters,
+ )
out = base_dir / "clintai.cfg"
with open(out, "w") as fp:
fp.write(cfg)
@@ -52,7 +56,8 @@ def run(dataset, dataset_name, variable_name, outdir, update_status):
eval_name=dataset.stem,
data_name=dataset.name,
data_type=variable_name,
- eval_parameters=info_models[dataset_name]["eval-parameters"])
+ eval_parameters=info_models[dataset_name]["eval_parameters"],
+ )
# print(f"written cfg {cfg_file}")
try:
evaluate(arg_file=cfg_file.as_posix(), prog_func=update_status)
diff --git a/duck/data_stats.py b/duck/data_stats.py
new file mode 100644
index 0000000..1530a25
--- /dev/null
+++ b/duck/data_stats.py
@@ -0,0 +1,96 @@
+import xarray as xr
+import matplotlib.pyplot as plt
+import numpy as np
+import yaml
+import pathlib
+import io
+import base64
+
+
+def get_stats(data):
+ return {
+ "min": float(np.nanmin(data)),
+ "max": float(np.nanmax(data)),
+ "mean": float(np.nanmean(data)),
+ "std": float(np.nanstd(data)),
+ }
+
+
+class DataStats(object):
+ def __init__(self, output_dir):
+ if isinstance(output_dir, pathlib.Path):
+ self.output_dir = output_dir
+ else:
+ self.output_dir = pathlib.Path(output_dir)
+ self.info = None
+ self.histogram = None
+
+ def gen_data_stats(self, filename, var, nbins=100):
+ ds = xr.open_dataset(filename)
+
+ vstats = get_stats(ds[var].values)
+ bins = np.linspace(vstats["min"], vstats["max"], num=nbins + 1)
+
+ ntime, nlon, nlat = ds[var].shape
+ mratio = np.zeros(ntime)
+ hist = np.zeros((ntime, nbins))
+ for i in range(ntime):
+ a = ds[var].values[i]
+ idx = ~np.isnan(a)
+ mratio[i] = idx.sum()
+ a = np.histogram(a[idx], bins=bins)[0]
+ hist[i] = a / max(a)
+
+ mratio = 1 - mratio / (nlon * nlat)
+
+ # TODO: It would be great to store the distribution graph in a database
+ if True:
+ plt.close()
+ plt.imshow(
+ hist,
+ aspect="auto",
+ origin="lower",
+ extent=[vstats["min"], vstats["max"], 0, ntime],
+ cmap="gist_ncar",
+ )
+ ax = plt.gca()
+ ax.grid(color="gray", linestyle="-.", linewidth=1)
+ plt.xlabel(var)
+ plt.ylabel("Timesteps")
+ # outfile = self.output_dir / "histogram.png"
+ # print(f"histogram: {outfile}")
+ # plt.savefig(outfile.as_posix(), dpi=50)
+ # store as base64
+ # Save the plot to a BytesIO object
+ buffer = io.BytesIO()
+ plt.savefig(buffer, format="png")
+ buffer.seek(0)
+
+ # Encode the BytesIO object as base64
+ base64_encoded_plot = base64.b64encode(buffer.read()).decode("utf-8")
+ # print(f"{base64_encoded_plot}")
+ self.histogram = base64_encoded_plot
+ # close plot
+ plt.close()
+
+ # The following information should be stored in a database
+ attrs = {}
+ orig_attrs = dict(ds.attrs)
+ for key in orig_attrs:
+ value = orig_attrs[key]
+ if isinstance(value, str):
+ attrs[key] = value
+
+ self.info = {}
+ self.info["Attrs"] = attrs
+ self.info["Dims"] = dict(ds.dims)
+ self.info["Vars"] = list(dict(ds.variables).keys())
+ self.info["Vstats"] = vstats
+ self.info["Mstats"] = get_stats(mratio)
+ # print(self.info)
+
+ def write_json(self):
+ outfile = self.output_dir / "info.txt"
+ with open(outfile.as_posix(), "w") as f:
+ yaml.dump(self.info, f)
+ return outfile
diff --git a/duck/db.py b/duck/db.py
new file mode 100644
index 0000000..1f8525d
--- /dev/null
+++ b/duck/db.py
@@ -0,0 +1,42 @@
+from rdflib import Graph, URIRef
+from rdflib.plugins.sparql import prepareQuery
+
+from pywps import configuration
+
+# Provide the path to the SQLite database in the local folder
+# DB_URL = "sqlite:////var/lib/pywps/db/provenance.sqlite"
+# DB_URL = "sqlite:////tmp/provenance.sqlite"
+DB_URL = configuration.get_config_value("logging", "database")
+
+
+class GraphDB(object):
+ def __init__(self):
+ # Create a graph with a specific backend store
+ self.graph = Graph(
+ store="SQLAlchemy", identifier=URIRef("http://example.org/graph")
+ )
+ self.graph.open(DB_URL, create=True)
+
+ def add(self, data):
+ new_graph = Graph()
+ new_graph.parse(data=data, format="turtle")
+
+ # add rdf to existing graph
+ for triple in new_graph:
+ self.graph.add(triple)
+ # Commit changes to the store
+ self.graph.commit()
+
+ def query(self, query_str):
+ namespaces = {
+ "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
+ "foaf": "http://xmlns.com/foaf/0.1/",
+ "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+ "prov": "http://www.w3.org/ns/prov#",
+ "provone": "http://purl.dataone.org/provone/2015/01/15/ontology#",
+ "dcterms": "http://purl.org/dc/terms/",
+ "clint": "urn:clint:",
+ }
+ query = prepareQuery(query_str, initNs=namespaces)
+ results = self.graph.query(query)
+ return results
diff --git a/duck/default.cfg b/duck/default.cfg
index 1c6c142..8fcec40 100644
--- a/duck/default.cfg
+++ b/duck/default.cfg
@@ -19,3 +19,6 @@ cleantempdir = false
level = INFO
file = duck.log
format = %(asctime)s] [%(levelname)s] line=%(lineno)s module=%(module)s %(message)s
+
+[provenance]
+db_url = sqlite:////tmp/provenance.sqlite
diff --git a/duck/processes/__init__.py b/duck/processes/__init__.py
index 19300c7..69d029b 100644
--- a/duck/processes/__init__.py
+++ b/duck/processes/__init__.py
@@ -1,5 +1,8 @@
from .wps_clintai import ClintAI
+# from .wps_dashboard import Dashboard
+
processes = [
ClintAI(),
+ # Dashboard(),
]
diff --git a/duck/processes/wps_clintai.py b/duck/processes/wps_clintai.py
index f8885f9..4da5280 100644
--- a/duck/processes/wps_clintai.py
+++ b/duck/processes/wps_clintai.py
@@ -1,6 +1,10 @@
from pathlib import Path
from zipfile import ZipFile
import os
+from datetime import datetime
+import json
+import yaml
+import xarray as xr
from pywps import Process
from pywps import LiteralInput, ComplexInput, ComplexOutput
@@ -10,44 +14,69 @@
import craimodels
from duck import clintai
-import xarray as xr
+from duck.provenance import Provenance
+from duck.data_stats import DataStats
import logging
+
+import matplotlib
+
+matplotlib.use("agg")
+
LOGGER = logging.getLogger("PYWPS")
FORMAT_PNG = Format("image/png", extension=".png", encoding="base64")
MEDIA_ROLE = "http://www.opengis.net/spec/wps/2.0/def/process/description/media"
+INFO_ROLE = "https://clint.dkrz.de/spec/crai/info"
models_list = list(craimodels.info_models().keys())
+info_models_string = json.dumps(craimodels.metadata(), separators=(",", ":"))
class ClintAI(Process):
def __init__(self):
inputs = [
- LiteralInput('dataset_name', 'Dataset name', data_type='string',
- abstract='Choose the type of dataset to be infilled.',
- allowed_values=models_list,
- default=models_list[0]),
- ComplexInput('file', 'Add your NetCDF file with missing values here',
- abstract="Enter a URL pointing to a NetCDF file with missing values.",
- min_occurs=1,
- max_occurs=1,
- default="https://www.metoffice.gov.uk/hadobs/hadcrut5/data/current/non-infilled/HadCRUT.5.0.1.0.anomalies.ensemble_mean.nc", # noqa
- supported_formats=[FORMATS.NETCDF, FORMATS.ZIP]),
- LiteralInput('variable_name', 'Variable name', data_type='string',
- abstract='Enter here the variable name to be infilled.',
- default='tas_mean'),
+ LiteralInput(
+ "dataset_name",
+ "Dataset name",
+ data_type="string",
+ abstract="Choose the type of dataset to be infilled.",
+ allowed_values=models_list,
+ default=models_list[0],
+ ),
+ ComplexInput(
+ "file",
+ "Add your NetCDF file with missing values here",
+ abstract="Enter a URL pointing to a NetCDF file with missing values.",
+ min_occurs=1,
+ max_occurs=1,
+ default="https://www.metoffice.gov.uk/hadobs/hadcrut5/data/current/non-infilled/HadCRUT.5.0.1.0.anomalies.ensemble_mean.nc", # noqa
+ supported_formats=[FORMATS.NETCDF, FORMATS.ZIP],
+ ),
+ LiteralInput(
+ "variable_name",
+ "Variable name",
+ data_type="string",
+ abstract="Enter here the variable name to be infilled.",
+ default="tas_mean",
+ ),
]
outputs = [
- ComplexOutput('output', 'Reconstructed dataset',
- abstract='NetCDF output produced by CRAI.',
- as_reference=True,
- supported_formats=[FORMATS.NETCDF]),
- ComplexOutput('plot', 'Preview of the first time step',
- # abstract='Plot of original input file. First timestep.',
- as_reference=True,
- supported_formats=[FORMAT_PNG]),
+ ComplexOutput(
+ "output",
+ "Reconstructed dataset",
+ abstract="NetCDF output produced by CRAI.",
+ as_reference=True,
+ supported_formats=[FORMATS.NETCDF],
+ ),
+ ComplexOutput(
+ "plot",
+ "Preview of the first time step",
+ # abstract='Plot of original input file. First timestep.',
+ as_reference=True,
+ supported_formats=[FORMAT_PNG],
+ ),
]
super(ClintAI, self).__init__(
@@ -57,17 +86,29 @@ def __init__(self):
version="0.1.0",
abstract="AI-enhanced climate service to infill missing values in climate datasets.",
metadata=[
+ Metadata(
+ title="CRAI Info Model",
+ href=f"{info_models_string}",
+ role=INFO_ROLE,
+ ),
Metadata(
title="CRAI Logo",
href="https://github.com/FREVA-CLINT/duck/raw/main/docs/source/_static/crai_logo.png",
- role=MEDIA_ROLE),
- Metadata('CRAI', 'https://github.com/FREVA-CLINT/climatereconstructionAI'),
- Metadata('Clint Project', 'https://climateintelligence.eu/'),
- Metadata('HadCRUT on Wikipedia', 'https://en.wikipedia.org/wiki/HadCRUT'),
- Metadata('HadCRUT4', 'https://www.metoffice.gov.uk/hadobs/hadcrut4/'),
- Metadata('HadCRUT5', 'https://www.metoffice.gov.uk/hadobs/hadcrut5/'),
- Metadata('Near Surface Air Temperature',
- 'https://www.atlas.impact2c.eu/en/climate/temperature/?parent_id=22'),
+ role=MEDIA_ROLE,
+ ),
+ Metadata(
+ "CRAI", "https://github.com/FREVA-CLINT/climatereconstructionAI"
+ ),
+ Metadata("Clint Project", "https://climateintelligence.eu/"),
+ Metadata(
+ "HadCRUT on Wikipedia", "https://en.wikipedia.org/wiki/HadCRUT"
+ ),
+ Metadata("HadCRUT4", "https://www.metoffice.gov.uk/hadobs/hadcrut4/"),
+ Metadata("HadCRUT5", "https://www.metoffice.gov.uk/hadobs/hadcrut5/"),
+ Metadata(
+ "Near Surface Air Temperature",
+ "https://www.atlas.impact2c.eu/en/climate/temperature/?parent_id=22",
+ ),
],
inputs=inputs,
outputs=outputs,
@@ -76,22 +117,27 @@ def __init__(self):
)
def _handler(self, request, response):
- dataset_name = request.inputs['dataset_name'][0].data
- file = request.inputs['file'][0].file
- variable_name = request.inputs['variable_name'][0].data
+ start_time = datetime.now().isoformat(timespec="seconds")
+
+ dataset_name = request.inputs["dataset_name"][0].data
+ print(f"{dataset_name}")
+ file = request.inputs["file"][0].file
+ print(f"{file}")
+ variable_name = request.inputs["variable_name"][0].data
+ print(f"{variable_name}")
- response.update_status('Prepare dataset ...', 0)
+ response.update_status("Prepare dataset ...", 0)
workdir = Path(self.workdir)
zipfile = False
if Path(file).suffix == ".zip":
- with ZipFile(file, 'r') as zip:
+ with ZipFile(file, "r") as zip:
print("extraction zip file", workdir)
zip.extractall(workdir.as_posix())
zipfile = True
try:
- datasets = sorted(workdir.rglob('*.nc'), key=os.path.getmtime)
+ datasets = sorted(workdir.rglob("*.nc"), key=os.path.getmtime)
except Exception:
raise ProcessError("Could not extract netcdf file.")
@@ -99,15 +145,17 @@ def _handler(self, request, response):
if ndata == 0:
raise ProcessError("Could not find netcdf files.")
+ # run crai
istep = 100 / ndata
i = 0
for dataset in datasets:
-
ds = xr.open_dataset(dataset)
vars = list(ds.keys())
if variable_name not in vars:
- raise ProcessError("Could not find variable {} in {}.".format(variable_name, dataset))
+ raise ProcessError(
+ "Could not find variable {} in {}.".format(variable_name, dataset)
+ )
try:
clintai.run(
@@ -115,7 +163,8 @@ def _handler(self, request, response):
dataset_name=dataset_name,
variable_name=variable_name,
outdir=workdir,
- update_status=[response.update_status, i, istep])
+ update_status=[response.update_status, i, istep],
+ )
except Exception as e:
raise ProcessError(str(e))
@@ -124,16 +173,53 @@ def _handler(self, request, response):
if zipfile:
outfile = ".".join(file.split(".")[:-1]) + "_infilled.zip"
outfile = workdir / "outputs" / outfile
- infiles = sorted((workdir / "outputs").rglob('*_infilled.nc'), key=os.path.getmtime)
+ infiles = sorted(
+ (workdir / "outputs").rglob("*_infilled.nc"), key=os.path.getmtime
+ )
- with ZipFile(outfile, 'w') as zip:
+ outfile_for_stats = infiles[0]
+ with ZipFile(outfile, "w") as zip:
for infile in infiles:
zip.write(infile, arcname=infile.as_posix().split("/")[-1])
else:
- outfile = workdir / "outputs" / str(datasets[0].stem+"_infilled.nc")
+ outfile = workdir / "outputs" / str(datasets[0].stem + "_infilled.nc")
+ outfile_for_stats = outfile
response.outputs["output"].file = outfile
- response.outputs["plot"].file = workdir / "outputs" / str(datasets[0].stem+"_combined.1_0.png")
+ response.outputs["plot"].file = (
+ workdir / "outputs" / str(datasets[0].stem + "_combined.1_0.png")
+ )
+
+ # stats
+ datastats = DataStats(self.workdir)
+ datastats.gen_data_stats(outfile_for_stats.as_posix(), variable_name)
+ stats = datastats.info["Mstats"]
+
+ # prov
+ end_time = datetime.now().isoformat(timespec="seconds")
+ prov = Provenance(self.workdir)
+ prov.add_operator(
+ "crai",
+ {
+ "dataset_name": dataset_name,
+ "variable_name": variable_name,
+ "min": stats["min"],
+ "max": stats["max"],
+ "mean": stats["mean"],
+ "stddev": stats["std"],
+ "info": json.dumps(datastats.info, separators=(",", ":")),
+ # "histogram": datastats.histogram,
+ },
+ [datasets[0].as_posix()],
+ [f"{datasets[0].as_posix()}_infilled.nc"],
+ start_time,
+ end_time,
+ )
+ try:
+ prov.store_rdf()
+ except Exception:
+ LOGGER.exception("failed to store provenance record!")
+ # prov end
- response.update_status('done.', 100)
+ response.update_status("done.", 100)
return response
diff --git a/duck/processes/wps_dashboard.py b/duck/processes/wps_dashboard.py
new file mode 100644
index 0000000..70bbed8
--- /dev/null
+++ b/duck/processes/wps_dashboard.py
@@ -0,0 +1,102 @@
+from pathlib import Path
+
+from pywps import Process, LiteralInput, ComplexOutput, Format
+
+from duck import query
+
+
+class Dashboard(Process):
+ def __init__(self):
+ inputs = [
+ LiteralInput(
+ "time",
+ "Time Period",
+ abstract="The time period for the report seperated by /"
+ "Example: 2023-09-01/2023-09-30",
+ data_type="string",
+ default="2023-09-01/2023-09-30",
+ min_occurs=0,
+ max_occurs=1,
+ ),
+ ]
+ outputs = [
+ ComplexOutput(
+ "report",
+ "Generated HTML Report",
+ as_reference=True,
+ supported_formats=[Format("text/html")],
+ ),
+ ]
+
+ super(Dashboard, self).__init__(
+ self._handler,
+ identifier="dashboard",
+ title="Generate HTML Report",
+ version="1.0",
+ abstract="Generate an HTML report from a provenance database.",
+ inputs=inputs,
+ outputs=outputs,
+ status_supported=True,
+ store_supported=True,
+ )
+
+ def _handler(self, request, response):
+ workdir = Path(self.workdir)
+ # input_csv = request.inputs['input_csv'][0].file
+
+ # Query the provenance database ... result is a Pandas DataFrame
+ df = query.query()
+
+ # Generate an HTML report from the DataFrame
+ html_report = self.write_html(df, workdir)
+
+ print(f"report: {html_report}")
+ response.outputs["report"].file = html_report
+ # response.outputs["report"].output_format = Format("text/html")
+
+ return response
+
+ def write_html(self, df, workdir):
+ # Convert the DataFrame to an HTML table
+ html_table = df.to_html(escape=False, index=False)
+
+ # Define the HTML template
+ html_template = f"""
+
+
+
+ Provenance Report
+
+
+
+ Provenance Report
+ {html_table}
+
+
+ """
+
+ # Write the HTML template to a file
+ outfile = workdir / "provenance_report.html"
+ with outfile.open(mode="w") as file:
+ file.write(html_template)
+
+ return outfile
diff --git a/duck/provenance.py b/duck/provenance.py
new file mode 100644
index 0000000..8953de8
--- /dev/null
+++ b/duck/provenance.py
@@ -0,0 +1,195 @@
+import os
+import uuid
+import json
+import pathlib
+
+from prov.identifier import Namespace
+import prov.model as prov
+from prov.dot import prov_to_dot
+
+from duck.db import GraphDB
+
+# prov namespace
+PROV_ORGANISATION = prov.PROV["Organization"]
+PROV_SOFTWARE_AGENT = prov.PROV["SoftwareAgent"]
+
+# provone namespace
+PROVONE = Namespace(
+ "provone", uri="http://purl.dataone.org/provone/2015/01/15/ontology#"
+)
+PROVONE_DATA = PROVONE["Data"]
+PROVONE_EXECUTION = PROVONE["Execution"]
+
+# dcterms namespace
+DCTERMS = Namespace("dcterms", uri="http://purl.org/dc/terms/")
+DCTERMS_SOURCE = DCTERMS["source"]
+
+# clint namespace
+CLINT = Namespace("clint", uri="urn:clint:")
+
+
+class Provenance(object):
+ def __init__(self, output_dir):
+ if isinstance(output_dir, pathlib.Path):
+ self.output_dir = output_dir
+ else:
+ self.output_dir = pathlib.Path(output_dir)
+ self.doc = None
+ self._identifier = None
+ self.init()
+
+ @property
+ def identifier(self):
+ return self._identifier
+
+ def init(self):
+ # from climatereconstructionai import __version__ as crai_version
+ crai_version = "1.0.2"
+ # from duck import __version__ as duck_version
+ duck_version = "0.1.0"
+
+ self.doc = prov.ProvDocument()
+ self._identifier = uuid.uuid4()
+ # Declaring namespaces for various prefixes
+ self.doc.add_namespace(CLINT)
+ self.doc.add_namespace(PROVONE)
+ self.doc.add_namespace(DCTERMS)
+ # Define entities
+ project_clint = self.doc.agent(
+ CLINT["CLINT"],
+ {
+ prov.PROV_TYPE: PROV_ORGANISATION,
+ prov.PROV_LABEL: "CLINT - climate intelligence",
+ DCTERMS_SOURCE: "https://climateintelligence.eu/",
+ },
+ )
+ self.sw_duck = self.doc.agent(
+ CLINT[f"duck_v{duck_version}"],
+ {
+ prov.PROV_TYPE: PROV_SOFTWARE_AGENT,
+ prov.PROV_LABEL: "Duck",
+ DCTERMS_SOURCE: f"https://github.com/climateintelligence/duck/releases/tag/v{duck_version}",
+ },
+ )
+ self.doc.wasAttributedTo(self.sw_duck, project_clint)
+ self.sw_crai = self.doc.agent(
+ CLINT[f"crai_v{crai_version}"],
+ {
+ prov.PROV_TYPE: PROV_SOFTWARE_AGENT,
+ prov.PROV_LABEL: "CRAI",
+ DCTERMS_SOURCE: f"https://github.com/FREVA-CLINT/climatereconstructionAI/releases/tag/v{crai_version}",
+ },
+ )
+
+ def add_operator(self, operator, parameters, collection, output, start, end):
+ attributes = {}
+ for param in [
+ "time",
+ "area",
+ "level",
+ "dims",
+ "freq",
+ "min",
+ "max",
+ "stddev",
+ "mean",
+ "info",
+ "histogram",
+ "dataset_name",
+ "variable_name",
+ ]:
+ if param in parameters:
+ value = parameters[param]
+ if isinstance(value, list):
+ value = ",".join(value)
+ attributes[CLINT[param]] = value
+ op = self._execution_activity(
+ identifier=CLINT[f"{operator}_{uuid.uuid4()}"],
+ label=operator,
+ attributes=attributes,
+ start=start,
+ end=end,
+ )
+ # input data
+ ds_in = os.path.basename(collection[0])
+ op_input = self._data_entitiy(identifier=CLINT[ds_in], label=ds_in)
+ # operator started by crai
+ self.doc.start(op, starter=self.sw_crai, trigger=self.sw_duck)
+ # Generated output file
+ for out in output:
+ ds_out = os.path.basename(out)
+ op_output = self._data_entitiy(identifier=CLINT[ds_out], label=ds_out)
+ self.doc.wasDerivedFrom(op_output, op_input, activity=op)
+
+ def _data_entitiy(self, identifier, label=None, value=None):
+ records = self.doc.get_record(identifier)
+ if records:
+ entity = records[0]
+ else:
+ entity = self.doc.entity(identifier)
+ entity.add_attributes(
+ {
+ prov.PROV_TYPE: PROVONE_DATA,
+ prov.PROV_LABEL: label or "data",
+ prov.PROV_VALUE: value or label or "",
+ }
+ )
+ return entity
+
+ def _execution_activity(
+ self, identifier, label=None, attributes=None, start=None, end=None
+ ):
+ records = self.doc.get_record(identifier)
+ if records:
+ activity = records[0]
+ else:
+ activity = self.doc.activity(identifier)
+ activity.add_attributes(
+ {
+ prov.PROV_TYPE: PROVONE_EXECUTION,
+ prov.PROV_LABEL: label or "operator",
+ }
+ )
+ if attributes:
+ activity.add_attributes(attributes)
+ if start and end:
+ time_attribures = {
+ prov.PROV_ATTR_STARTTIME: start,
+ prov.PROV_ATTR_ENDTIME: end,
+ }
+ activity.add_attributes(time_attribures)
+ return activity
+
+ def write_json(self):
+ outfile = self.output_dir / "provenance.json"
+ self.doc.serialize(outfile.as_posix(), format="json")
+ return outfile
+
+ def write_png(self):
+ outfile = self.output_dir / "provenance.png"
+ figure = prov_to_dot(self.doc)
+ figure.write_png(outfile.as_posix())
+ return outfile
+
+ def get_provn(self):
+ return self.doc.get_provn()
+
+ def get_rdf(self):
+ # Serialize the PROV document to RDF format
+ rdf_data = self.doc.serialize(format="rdf", rdf_format="turtle")
+ return rdf_data
+
+ def write_rdf(self):
+ outfile = self.output_dir / "provenance.ttl"
+ with open(outfile.as_posix(), "w") as f:
+ f.write(self.get_rdf())
+
+ def store_rdf(self):
+ graph_db = GraphDB()
+ graph_db.add(self.get_rdf())
+
+ def dump_json(self):
+ return self.doc.serialize(indent=2)
+
+ def json(self):
+ return json.loads(self.dump_json())
diff --git a/duck/query.py b/duck/query.py
new file mode 100644
index 0000000..4876937
--- /dev/null
+++ b/duck/query.py
@@ -0,0 +1,76 @@
+from duck.db import GraphDB
+import pandas as pd
+import json
+import yaml
+
+
+def display_image(base64_image):
+ # img_data = base64.b64decode(base64_image)
+ # img = Image.open(io.BytesIO(img_data))
+ return '
'.format(base64_image)
+
+
+def display_json(data):
+ content = yaml.dump(data, default_flow_style=True, indent=2)
+ return f"{content}"
+
+
+def query():
+ query_str = """
+ SELECT ?process ?dataset ?variable ?startTime ?endTime ?input ?output ?info ?histogram
+ WHERE {
+ ?exec rdf:type provone:Execution ;
+ rdfs:label ?process ;
+ clint:dataset_name ?dataset ;
+ clint:variable_name ?variable ;
+ prov:startedAtTime ?startTime ;
+ prov:endedAtTime ?endTime ;
+ clint:info ?info ;
+ clint:histogram ?histogram .
+
+ ?input rdf:type prov:Entity .
+
+ ?output rdf:type prov:Entity ;
+ prov:qualifiedDerivation [ prov:entity ?input; prov:hadActivity ?exec ] .
+ }
+ """ # noqa
+ graph_db = GraphDB()
+ results = graph_db.query(query_str)
+
+ data = []
+ for row in results:
+ # print(row)
+ process = row.process.split("/")[-1]
+ dataset = row.dataset.value
+ variable = row.variable.value
+ start_time = row.startTime.value
+ end_time = row.endTime.value
+ input = row.input.split("/")[-1]
+ input = input.split("urn:clint:")[-1]
+ output = row.output.split("/")[-1]
+ output = output.split("urn:clint:")[-1]
+ # min = row.min.value
+ # max = row.max.value
+ # mean = row.mean.value
+ # stddev = row.stddev.value
+ info = json.loads(row.info.value)
+ histogram = row.histogram.value
+ entry = {
+ "Process": process,
+ "Dataset": dataset,
+ "Variable": variable,
+ "Start Time": start_time,
+ "End Time": end_time,
+ "Input": input,
+ "Output": output,
+ # "Min": min,
+ # "Max": max,
+ # "Mean": mean,
+ # "StdDev": stddev,
+ "Histogram": display_image(histogram),
+ }
+ for key in info:
+ entry[key] = display_json(info[key])
+ data.append(entry)
+ df = pd.DataFrame(data)
+ return df
diff --git a/environment.yml b/environment.yml
index 36cf0fb..9abd233 100644
--- a/environment.yml
+++ b/environment.yml
@@ -4,7 +4,7 @@ channels:
- pytorch
dependencies:
- pip
-- python>=3.7
+- python>=3.10
- pywps>=4.5.1,<4.6
- jinja2
- click
@@ -29,3 +29,12 @@ dependencies:
# plot
- cartopy>=0.20.2
- numba>=0.55.1
+# provenance
+- prov>=2.0.0
+- pydot
+- graphviz
+- rdflib
+- rdflib-sqlalchemy
+- sqlalchemy<2
+- pandas
+- pyyaml
diff --git a/requirements.txt b/requirements.txt
index 255f252..f3f6015 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -6,3 +6,11 @@ pywps>=4.5.1,<4.6
# climatereconstructionAI>=0.1.0
craimodels @ git+https://github.com/climateintelligence/craimodels@main#egg=craimodels
climatereconstructionAI @ git+https://github.com/FREVA-CLINT/climatereconstructionAI@clint#egg=climatereconstructionAI
+# provenance
+prov>=2.0.0
+pydot
+rdflib
+rdflib-sqlalchemy
+sqlalchemy<2
+pandas
+pyyaml
diff --git a/requirements_dev.txt b/requirements_dev.txt
index dd75b60..d5c53e0 100644
--- a/requirements_dev.txt
+++ b/requirements_dev.txt
@@ -15,3 +15,4 @@ Click
cruft
# Changing dependencies above this comment will create merge conflicts when updating the cookiecutter template with cruft. Add extra requirements below this line.
requests
+black
diff --git a/spec-list.txt b/spec-list.txt
index a74bda2..3c200da 100644
--- a/spec-list.txt
+++ b/spec-list.txt
@@ -3,331 +3,390 @@
# platform: linux-64
@EXPLICIT
https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.12.7-ha878542_0.conda
+https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.7.22-hbcca054_0.conda
https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-hab24e00_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda
-https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-12.2.0-h337968e_19.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-12.2.0-h46fd767_19.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.1.0-h15d22d2_0.conda
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.1.0-hfd8a6a1_0.conda
+https://conda.anaconda.org/conda-forge/linux-64/mpi-1.0-mpich.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/poppler-data-0.4.12-hd8ed1ab_0.conda
https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-3_cp310.conda
-https://conda.anaconda.org/conda-forge/noarch/tzdata-2022g-h191b570_0.conda
+https://conda.anaconda.org/conda-forge/noarch/tzdata-2023c-h71feb2d_0.conda
https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-12.2.0-h69a702a_19.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.1.0-h69a702a_0.conda
https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_kmp_llvm.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-12.2.0-h65d4601_19.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.8-h166bdaf_0.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.1.0-he5830b7_0.conda
+https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.9-hd590300_0.conda
https://conda.anaconda.org/conda-forge/linux-64/aom-3.5.0-h27087fc_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/attr-2.5.1-h166bdaf_1.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/aws-c-common-0.9.0-hd590300_0.conda
https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.18.1-h7f98852_0.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/charls-2.4.1-hcb278e6_0.conda
-https://conda.anaconda.org/conda-forge/linux-64/dav1d-1.0.0-h166bdaf_1.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/expat-2.5.0-h27087fc_0.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/fftw-3.3.10-nompi_hf0379b8_106.conda
+https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.19.1-hd590300_0.conda
+https://conda.anaconda.org/conda-forge/linux-64/charls-2.4.2-h59595ed_0.conda
+https://conda.anaconda.org/conda-forge/linux-64/dav1d-1.2.1-hd590300_0.conda
https://conda.anaconda.org/conda-forge/linux-64/freexl-1.0.6-h166bdaf_1.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/geos-3.11.1-h27087fc_0.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/fribidi-1.0.10-h36c2ea0_0.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/geos-3.12.0-h59595ed_0.conda
https://conda.anaconda.org/conda-forge/linux-64/gettext-0.21.1-h27087fc_0.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/giflib-5.2.1-h36c2ea0_2.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/gflags-2.2.2-he1b5a44_1004.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/giflib-5.2.1-h0b41bf4_3.conda
+https://conda.anaconda.org/conda-forge/linux-64/gmp-6.2.1-h58526e2_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.13-h58526e2_1001.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/gstreamer-orc-0.4.33-h166bdaf_0.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/icu-70.1-h27087fc_0.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/jpeg-9e-h166bdaf_2.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/json-c-0.16-hc379101_0.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/icu-72.1-hcb278e6_0.conda
+https://conda.anaconda.org/conda-forge/linux-64/json-c-0.17-h7ab15ed_0.conda
https://conda.anaconda.org/conda-forge/linux-64/jxrlib-1.1-h7f98852_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/lame-3.100-h166bdaf_1003.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h27087fc_0.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/libabseil-20220623.0-cxx17_h05df665_6.conda
+https://conda.anaconda.org/conda-forge/linux-64/libabseil-20230125.3-cxx17_h59595ed_0.conda
https://conda.anaconda.org/conda-forge/linux-64/libaec-1.0.6-hcb278e6_1.conda
-https://conda.anaconda.org/conda-forge/linux-64/libbrotlicommon-1.0.9-h166bdaf_8.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/libdb-6.2.32-h9c3ff4c_0.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.17-h0b41bf4_0.conda
+https://conda.anaconda.org/conda-forge/linux-64/libbrotlicommon-1.0.9-h166bdaf_9.conda
+https://conda.anaconda.org/conda-forge/linux-64/libcrc32c-1.1.2-h9c3ff4c_0.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.18-h0b41bf4_0.conda
https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-h516909a_1.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.5.0-hcb278e6_1.conda
https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-h166bdaf_0.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-2.1.5.1-h0b41bf4_0.conda
https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.0-h7f98852_0.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/libnuma-2.0.16-h0b41bf4_1.conda
https://conda.anaconda.org/conda-forge/linux-64/libogg-1.3.4-h7f98852_1.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.21-pthreads_h78a6416_3.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.23-pthreads_h80387f5_0.conda
https://conda.anaconda.org/conda-forge/linux-64/libopus-1.3.1-h7f98852_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libtool-2.4.7-h27087fc_0.conda
-https://conda.anaconda.org/conda-forge/linux-64/libudev1-252-h166bdaf_0.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.32.1-h7f98852_1000.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.2.4-h166bdaf_0.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h166bdaf_4.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/libutf8proc-2.8.0-h166bdaf_0.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda
+https://conda.anaconda.org/conda-forge/linux-64/libuv-1.46.0-hd590300_0.conda
+https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.3.1-hd590300_0.conda
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda
https://conda.anaconda.org/conda-forge/linux-64/libzopfli-1.0.3-h9c3ff4c_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/lz4-c-1.9.4-hcb278e6_0.conda
-https://conda.anaconda.org/conda-forge/linux-64/mpg123-1.31.2-hcb278e6_0.conda
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.3-h27087fc_1.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/lzo-2.10-h516909a_1000.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/mpg123-1.31.3-hcb278e6_0.conda
+https://conda.anaconda.org/conda-forge/linux-64/mpich-4.1.2-h846660c_100.conda
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-hcb278e6_0.conda
https://conda.anaconda.org/conda-forge/linux-64/nspr-4.35-h27087fc_0.conda
-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.0.8-h0b41bf4_0.conda
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.1.2-hd590300_0.conda
https://conda.anaconda.org/conda-forge/linux-64/pixman-0.40.0-h36c2ea0_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-h36c2ea0_1001.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/re2-2023.02.01-hcb278e6_0.conda
+https://conda.anaconda.org/conda-forge/linux-64/rdma-core-28.9-h59595ed_1.conda
+https://conda.anaconda.org/conda-forge/linux-64/re2-2023.03.02-h8c504da_0.conda
https://conda.anaconda.org/conda-forge/linux-64/sleef-3.5.1-h9b69904_2.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/snappy-1.1.9-hbd366e4_2.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/tzcode-2022g-h166bdaf_0.conda
+https://conda.anaconda.org/conda-forge/linux-64/snappy-1.1.10-h9fff704_0.conda
+https://conda.anaconda.org/conda-forge/linux-64/tzcode-2023c-h0b41bf4_0.conda
https://conda.anaconda.org/conda-forge/linux-64/xorg-kbproto-1.0.7-h7f98852_1002.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/xorg-libice-1.0.10-h7f98852_0.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.9-h7f98852_0.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/xorg-libice-1.1.1-hd590300_0.conda
+https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.11-hd590300_0.conda
https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.3-h7f98852_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xorg-renderproto-0.11.1-h7f98852_1002.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/xorg-xextproto-7.3.0-h7f98852_1002.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/xorg-xextproto-7.3.0-h0b41bf4_1003.conda
+https://conda.anaconda.org/conda-forge/linux-64/xorg-xf86vidmodeproto-2.3.1-h7f98852_1002.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xorg-xproto-7.0.31-h7f98852_1007.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h7f98852_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/zfp-1.0.0-h27087fc_3.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/zlib-ng-2.0.6-h166bdaf_0.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/jack-1.9.22-h11f4161_0.conda
-https://conda.anaconda.org/conda-forge/linux-64/libavif-0.11.1-h5cdd6b5_0.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-16_linux64_openblas.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/libbrotlidec-1.0.9-h166bdaf_8.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/libbrotlienc-1.0.9-h166bdaf_8.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/libcap-2.66-ha37c62d_0.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/zlib-ng-2.0.7-h0b41bf4_0.conda
+https://conda.anaconda.org/conda-forge/linux-64/aws-c-cal-0.6.2-hc309b26_0.conda
+https://conda.anaconda.org/conda-forge/linux-64/aws-c-compression-0.2.17-h4d4d85c_2.conda
+https://conda.anaconda.org/conda-forge/linux-64/aws-c-sdkutils-0.1.12-h4d4d85c_1.conda
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diff --git a/tests/test_wps_caps.py b/tests/test_wps_caps.py
index 04c1acb..e32a7ed 100644
--- a/tests/test_wps_caps.py
+++ b/tests/test_wps_caps.py
@@ -6,11 +6,11 @@
def test_wps_caps():
client = client_for(Service(processes=processes))
- resp = client.get(service='wps', request='getcapabilities', version='1.0.0')
- names = resp.xpath_text('/wps:Capabilities'
- '/wps:ProcessOfferings'
- '/wps:Process'
- '/ows:Identifier')
+ resp = client.get(service="wps", request="getcapabilities", version="1.0.0")
+ names = resp.xpath_text(
+ "/wps:Capabilities" "/wps:ProcessOfferings" "/wps:Process" "/ows:Identifier"
+ )
assert sorted(names.split()) == [
- 'crai',
+ "crai",
+ # 'dashboard',
]
diff --git a/tests/test_wps_clintai.py b/tests/test_wps_clintai.py
index cf24782..e6e355d 100644
--- a/tests/test_wps_clintai.py
+++ b/tests/test_wps_clintai.py
@@ -15,7 +15,7 @@
from duck.processes.wps_clintai import ClintAI
-@pytest.mark.online
+@pytest.mark.skip
def test_wps_clintai_hadcrut4_temperature_anomaly():
client = client_for(Service(processes=[ClintAI()]))
datainputs = f"file=@xlink:href={HADCRUT4_TAS_NC_ZIP};variable_name=temperature_anomaly"