3929938005

Build Type

push

github

Committed by GitHub

Commit Message

Merge #713

Run Details

84930 of 96741 relevant lines covered (87.79%)

79640.1 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

95.68

/operators/src/source/csv.rs

use std::path::PathBuf;
use std::pin::Pin;
use std::sync::{Arc, Mutex};
use std::{fs::File, sync::atomic::AtomicBool};

use csv::{Position, Reader, StringRecord};
use futures::stream::BoxStream;
use futures::task::{Context, Poll};
use futures::{Stream, StreamExt};
use geoengine_datatypes::dataset::DataId;
use geoengine_datatypes::primitives::VectorQueryRectangle;
use serde::{Deserialize, Serialize};
use snafu::{ensure, OptionExt, ResultExt};
use tracing::{span, Level};

use geoengine_datatypes::collections::{
    BuilderProvider, GeoFeatureCollectionRowBuilder, MultiPointCollection, VectorDataType,
};
use geoengine_datatypes::{
    primitives::{BoundingBox2D, Coordinate2D, TimeInterval},
    spatial_reference::SpatialReference,
};

use crate::engine::{CreateSpan, QueryProcessor};
use crate::engine::{
    InitializedVectorOperator, OperatorData, OperatorName, QueryContext, SourceOperator,
    TypedVectorQueryProcessor, VectorOperator, VectorQueryProcessor, VectorResultDescriptor,
};
use crate::error;
use crate::util::Result;
use async_trait::async_trait;
use std::sync::atomic::Ordering;

/// Parameters for the CSV Source Operator
///
/// # Examples
///
/// ```rust
/// use serde_json::{Result, Value};
/// use geoengine_operators::source::{CsvSourceParameters, CsvSource};
/// use geoengine_operators::source::{CsvGeometrySpecification, CsvTimeSpecification};
///
/// let json_string = r#"
///     {
///         "type": "CsvSource",
///         "params": {
///             "filePath": "/foo/bar.csv",
///             "fieldSeparator": ",",
///             "geometry": {
///                 "type": "xy",
///                 "x": "x",
///                 "y": "y"
///             }
///         }
///     }"#;
///
/// let operator: CsvSource = serde_json::from_str(json_string).unwrap();
///
/// assert_eq!(operator, CsvSource {
///     params: CsvSourceParameters {
///         file_path: "/foo/bar.csv".into(),
///         field_separator: ',',
///         geometry: CsvGeometrySpecification::XY { x: "x".into(), y: "y".into() },
///         time: CsvTimeSpecification::None,
///     },
/// });
/// ```
#[derive(Debug, PartialEq, Eq, Serialize, Deserialize, Clone)]
#[serde(rename_all = "camelCase")]
pub struct CsvSourceParameters {
    pub file_path: PathBuf,
    pub field_separator: char,
    pub geometry: CsvGeometrySpecification,
    #[serde(default)]
    pub time: CsvTimeSpecification,
}

#[derive(Debug, PartialEq, Eq, Serialize, Deserialize, Clone)]
#[serde(tag = "type", rename_all = "lowercase")]
pub enum CsvGeometrySpecification {
    #[allow(clippy::upper_case_acronyms)]
    XY { x: String, y: String },
}

#[derive(Debug, PartialEq, Eq, Serialize, Deserialize, Clone)]
pub enum CsvTimeSpecification {
    None,
}

impl Default for CsvTimeSpecification {
    fn default() -> Self {
        Self::None
    }
}

enum ReaderState {
    Untouched(Reader<File>),
    OnGoing {
        header: ParsedHeader,
        records: csv::StringRecordsIntoIter<File>,
    },
    Error,
}

impl ReaderState {
    pub fn setup_once(&mut self, geometry_specification: CsvGeometrySpecification) -> Result<()> {
        if let ReaderState::Untouched(..) = self {
            // pass
        } else {
            return Ok(());
        }

        let old_state = std::mem::replace(self, ReaderState::Error);

        if let ReaderState::Untouched(mut csv_reader) = old_state {
            let header = match CsvSourceStream::setup_read(geometry_specification, &mut csv_reader)
            {
                Ok(header) => header,
                Err(error) => return Err(error),
            };

            let mut records = csv_reader.into_records();

            // consume the first row, which is the header
            if header.has_header {
                // TODO: throw error
                records.next();
            }

            *self = ReaderState::OnGoing { header, records }
        }

        Ok(())
    }
}

pub struct CsvSourceStream {
    parameters: CsvSourceParameters,
    bbox: BoundingBox2D,
    chunk_size: usize,
    reader_state: Arc<Mutex<ReaderState>>,
    thread_is_computing: Arc<AtomicBool>,
    #[allow(clippy::option_option)]
    poll_result: Arc<Mutex<Option<Option<Result<MultiPointCollection>>>>>,
}

pub type CsvSource = SourceOperator<CsvSourceParameters>;

impl OperatorName for CsvSource {
    const TYPE_NAME: &'static str = "CsvSource";
}

impl OperatorData for CsvSourceParameters {
    fn data_ids_collect(&self, _data_ids: &mut Vec<DataId>) {}
}

#[typetag::serde]
#[async_trait]
impl VectorOperator for CsvSource {
    async fn _initialize(
        self: Box<Self>,
        _context: &dyn crate::engine::ExecutionContext,
    ) -> Result<Box<dyn InitializedVectorOperator>> {
        let initialized_source = InitializedCsvSource {
            result_descriptor: VectorResultDescriptor {
                data_type: VectorDataType::MultiPoint, // TODO: get as user input
                spatial_reference: SpatialReference::epsg_4326().into(), // TODO: get as user input
                columns: Default::default(), // TODO: get when source allows loading other columns
                time: None,
                bbox: None,
            },
            state: self.params,
        };

        Ok(initialized_source.boxed())
    }

    span_fn!(CsvSource);
}

pub struct InitializedCsvSource {
    result_descriptor: VectorResultDescriptor,
    state: CsvSourceParameters,
}

impl InitializedVectorOperator for InitializedCsvSource {
    fn query_processor(&self) -> Result<crate::engine::TypedVectorQueryProcessor> {
        Ok(TypedVectorQueryProcessor::MultiPoint(
            CsvSourceProcessor {
                params: self.state.clone(),
            }
            .boxed(),
        ))
    }

    fn result_descriptor(&self) -> &VectorResultDescriptor {
        &self.result_descriptor
    }
}

impl CsvSourceStream {
    /// Creates a new `CsvSource`
    ///
    /// # Errors
    ///
    /// This constructor fails if the delimiter is not an ASCII character.
    /// Furthermore, there are IO errors from the reader.
    ///
    // TODO: include time interval, e.g. QueryRectangle parameter
    pub fn new(
        parameters: CsvSourceParameters,
        bbox: BoundingBox2D,
        chunk_size: usize,
    ) -> Result<Self> {
        ensure!(
            parameters.field_separator.is_ascii(),
            error::CsvSource {
                details: "Delimiter must be ASCII character"
            }
        );

        Ok(Self {
            reader_state: Arc::new(Mutex::new(ReaderState::Untouched(
                csv::ReaderBuilder::new()
                    .delimiter(parameters.field_separator as u8)
                    .has_headers(true)
                    .from_path(parameters.file_path.as_path())
                    .context(error::CsvSourceReader {})?,
            ))),
            thread_is_computing: Arc::new(AtomicBool::new(false)),
            poll_result: Arc::new(Mutex::new(None)),
            parameters,
            bbox,
            chunk_size,
        })
    }

    fn setup_read(
        geometry_specification: CsvGeometrySpecification,
        csv_reader: &mut Reader<File>,
    ) -> Result<ParsedHeader> {
        csv_reader
            .seek(Position::new())
            .context(error::CsvSourceReader {})?; // start at beginning

        ensure!(
            csv_reader.has_headers(),
            error::CsvSource {
                details: "CSV file must contain header",
            }
        );

        let header = csv_reader.headers().context(error::CsvSourceReader)?;

        let CsvGeometrySpecification::XY { x, y } = geometry_specification;
        let x_index = header
            .iter()
            .position(|v| v == x)
            .context(error::CsvSource {
                details: "Cannot find x index in csv header",
            })?;
        let y_index = header
            .iter()
            .position(|v| v == y)
            .context(error::CsvSource {
                details: "Cannot find y index in csv header",
            })?;

        Ok(ParsedHeader {
            has_header: true,
            x_index,
            y_index,
        })
    }

    /// Parse a single CSV row
    fn parse_row(header: &ParsedHeader, row: &StringRecord) -> Result<ParsedRow> {
        let x: f64 = row
            .get(header.x_index)
            .context(error::CsvSource {
                details: "Cannot find x index key",
            })?
            .parse()
            .map_err(|_error| error::Error::CsvSource {
                details: "Cannot parse x coordinate".to_string(),
            })?;
        let y: f64 = row
            .get(header.y_index)
            .context(error::CsvSource {
                details: "Cannot find y index key",
            })?
            .parse()
            .map_err(|_error| error::Error::CsvSource {
                details: "Cannot parse y coordinate".to_string(),
            })?;

        Ok(ParsedRow {
            coordinate: (x, y).into(),
            time_interval: TimeInterval::default(),
        })
    }
}

impl Stream for CsvSourceStream {
    type Item = Result<MultiPointCollection>;

    fn poll_next(self: Pin<&mut Self>, cx: &mut Context<'_>) -> Poll<Option<Self::Item>> {
        // TODO: handle lock poisoning on multiple occasions

        if self.thread_is_computing.load(Ordering::Relaxed) {
            return Poll::Pending;
        }

        let mut poll_result = self.poll_result.lock().unwrap();
        if poll_result.is_some() {
            let x = poll_result.take().unwrap();
            return Poll::Ready(x);
        }

        self.thread_is_computing.store(true, Ordering::Relaxed);

        let is_working = self.thread_is_computing.clone();
        let reader_state = self.reader_state.clone();
        let poll_result = self.poll_result.clone();

        let bbox = self.bbox;
        let chunk_size = self.chunk_size;
        let parameters = self.parameters.clone();
        let waker = cx.waker().clone();

        crate::util::spawn_blocking(move || {
            let mut csv_reader = reader_state.lock().unwrap();
            let computation_result = || -> Result<Option<MultiPointCollection>> {
                // TODO: is clone necessary?
                let geometry_specification = parameters.geometry.clone();
                csv_reader.setup_once(geometry_specification)?;

                let (header, records) = match &mut *csv_reader {
                    ReaderState::OnGoing { header, records } => (header, records),
                    ReaderState::Error => return Ok(None),
                    ReaderState::Untouched(_) => unreachable!(),
                };

                let mut builder = MultiPointCollection::builder().finish_header();
                let mut number_of_entries = 0; // TODO: add size/len to builder

                while number_of_entries < chunk_size {
                    let Some(record) = records.next() else { break; };

                    let row = record.context(error::CsvSourceReader)?;
                    let parsed_row = CsvSourceStream::parse_row(header, &row)?;

                    // TODO: filter time
                    if bbox.contains_coordinate(&parsed_row.coordinate) {
                        builder.push_geometry(parsed_row.coordinate.into());
                        builder.push_time_interval(parsed_row.time_interval);
                        builder.finish_row();

                        number_of_entries += 1;
                    }
                }

                // TODO: is this the correct cancellation criterion?
                if number_of_entries > 0 {
                    let collection = builder.build()?;
                    Ok(Some(collection))
                } else {
                    Ok(None)
                }
            }();

            *poll_result.lock().unwrap() = Some(match computation_result {
                Ok(Some(collection)) => Some(Ok(collection)),
                Ok(None) => None,
                Err(e) => Some(Err(e)),
            });
            is_working.store(false, Ordering::Relaxed);

            waker.wake();
        });

        Poll::Pending
    }
}

#[derive(Debug)]
struct CsvSourceProcessor {
    params: CsvSourceParameters,
}

#[async_trait]
impl QueryProcessor for CsvSourceProcessor {
    type Output = MultiPointCollection;
    type SpatialBounds = BoundingBox2D;

    async fn _query<'a>(
        &'a self,
        query: VectorQueryRectangle,
        _ctx: &'a dyn QueryContext,
    ) -> Result<BoxStream<'a, Result<Self::Output>>> {
        // TODO: properly handle chunk_size
        Ok(CsvSourceStream::new(self.params.clone(), query.spatial_bounds, 10)?.boxed())
    }
}

#[derive(Clone, Copy, Debug)]
struct ParsedHeader {
    pub has_header: bool,
    pub x_index: usize,
    pub y_index: usize,
}

struct ParsedRow {
    pub coordinate: Coordinate2D,
    pub time_interval: TimeInterval,
    // TODO: fields
}

#[cfg(test)]
mod tests {
    use std::io::{Seek, SeekFrom, Write};

    use geoengine_datatypes::primitives::SpatialResolution;

    use super::*;
    use crate::engine::MockQueryContext;
    use geoengine_datatypes::collections::{FeatureCollectionInfos, ToGeoJson};

    #[tokio::test]
    async fn read_points() {
        let mut fake_file = tempfile::NamedTempFile::new().unwrap();
        write!(
            fake_file,
            "\
x,y
0,1
2,3
4,5
"
        )
        .unwrap();
        fake_file.seek(SeekFrom::Start(0)).unwrap();

        let mut csv_source = CsvSourceStream::new(
            CsvSourceParameters {
                file_path: fake_file.path().into(),
                field_separator: ',',
                geometry: CsvGeometrySpecification::XY {
                    x: "x".into(),
                    y: "y".into(),
                },
                time: CsvTimeSpecification::None,
            },
            BoundingBox2D::new_unchecked((0., 0.).into(), (5., 5.).into()),
            2,
        )
        .unwrap();

        assert_eq!(csv_source.next().await.unwrap().unwrap().len(), 2);
        assert_eq!(csv_source.next().await.unwrap().unwrap().len(), 1);
        assert!(csv_source.next().await.is_none());
    }

    #[tokio::test]
    async fn erroneous_point_rows() {
        let mut fake_file = tempfile::NamedTempFile::new().unwrap();
        write!(
            fake_file,
            "\
x,y
0,1
CORRUPT
4,5
"
        )
        .unwrap();
        fake_file.seek(SeekFrom::Start(0)).unwrap();

        let mut csv_source = CsvSourceStream::new(
            CsvSourceParameters {
                file_path: fake_file.path().into(),
                field_separator: ',',
                geometry: CsvGeometrySpecification::XY {
                    x: "x".into(),
                    y: "y".into(),
                },
                time: CsvTimeSpecification::None,
            },
            BoundingBox2D::new_unchecked((0., 0.).into(), (5., 5.).into()),
            1,
        )
        .unwrap();

        assert_eq!(csv_source.next().await.unwrap().unwrap().len(), 1);
        assert!(csv_source.next().await.unwrap().is_err());
        assert_eq!(csv_source.next().await.unwrap().unwrap().len(), 1);
        assert!(csv_source.next().await.is_none());
    }

    #[tokio::test]
    async fn corrupt_point_header() {
        let mut fake_file = tempfile::NamedTempFile::new().unwrap();
        write!(
            fake_file,
            "\
x,z
0,1
2,3
4,5
"
        )
        .unwrap();
        fake_file.seek(SeekFrom::Start(0)).unwrap();

        let mut csv_source = CsvSourceStream::new(
            CsvSourceParameters {
                file_path: fake_file.path().into(),
                field_separator: ',',
                geometry: CsvGeometrySpecification::XY {
                    x: "x".into(),
                    y: "y".into(),
                },
                time: CsvTimeSpecification::None,
            },
            BoundingBox2D::new_unchecked((0., 0.).into(), (5., 5.).into()),
            1,
        )
        .unwrap();

        assert!(csv_source.next().await.unwrap().is_err());
        assert!(csv_source.next().await.is_none());
    }

    #[tokio::test]
    async fn processor() {
        let mut fake_file = tempfile::NamedTempFile::new().unwrap();
        write!(
            fake_file,
            "\
x,y
0,1
2,3
4,5
"
        )
        .unwrap();
        fake_file.seek(SeekFrom::Start(0)).unwrap();

        let params = CsvSourceParameters {
            file_path: fake_file.path().into(),
            field_separator: ',',
            geometry: CsvGeometrySpecification::XY {
                x: "x".into(),
                y: "y".into(),
            },
            time: CsvTimeSpecification::None,
        };

        let p = CsvSourceProcessor { params };

        let query = VectorQueryRectangle {
            spatial_bounds: BoundingBox2D::new_unchecked(
                Coordinate2D::new(0., 0.),
                Coordinate2D::new(3., 3.),
            ),
            time_interval: TimeInterval::new_unchecked(0, 1),
            spatial_resolution: SpatialResolution::zero_point_one(),
        };
        let ctx = MockQueryContext::new((10 * 8 * 2).into());

        let r: Vec<Result<MultiPointCollection>> =
            p.query(query, &ctx).await.unwrap().collect().await;

        assert_eq!(r.len(), 1);

        assert_eq!(
            r[0].as_ref().unwrap().to_geo_json(),
            serde_json::json!({
                "type": "FeatureCollection",
                "features": [{
                    "type": "Feature",
                    "geometry": {
                        "type": "Point",
                        "coordinates": [0.0, 1.0]
                    },
                    "properties": {},
                    "when": {
                        "start": "-262144-01-01T00:00:00+00:00",
                        "end": "+262143-12-31T23:59:59.999+00:00",
                        "type": "Interval"
                    }
                }, {
                    "type": "Feature",
                    "geometry": {
                        "type": "Point",
                        "coordinates": [2.0, 3.0]
                    },
                    "properties": {},
                    "when": {
                        "start": "-262144-01-01T00:00:00+00:00",
                        "end": "+262143-12-31T23:59:59.999+00:00",
                        "type": "Interval"
                    }
                }]
            })
            .to_string()
        );
    }

    #[test]
    fn operator() {
        let mut temp_file = tempfile::NamedTempFile::new().unwrap();
        write!(
            temp_file,
            "\
x;y
0;1
2;3
4;5
"
        )
        .unwrap();
        temp_file.seek(SeekFrom::Start(0)).unwrap();

        let params = CsvSourceParameters {
            file_path: temp_file.path().into(),
            field_separator: ';',
            geometry: CsvGeometrySpecification::XY {
                x: "x".into(),
                y: "y".into(),
            },
            time: CsvTimeSpecification::None,
        };

        let operator = CsvSource { params }.boxed();

        let operator_json = serde_json::to_value(&operator).unwrap();

        assert_eq!(
            operator_json,
            serde_json::json!({
                "type": "CsvSource",
                "params": {
                    "filePath": temp_file.path(),
                    "fieldSeparator": ";",
                    "geometry": {
                        "type": "xy",
                        "x": "x",
                        "y": "y"
                    },
                    "time": "None"
                }
            })
        );

        let _operator: Box<dyn VectorOperator> = serde_json::from_value(operator_json).unwrap();
    }
}

1	use std::path::PathBuf;
2	use std::pin::Pin;
3	use std::sync::{Arc, Mutex};
4	use std::{fs::File, sync::atomic::AtomicBool};
5
6	use csv::{Position, Reader, StringRecord};
7	use futures::stream::BoxStream;
8	use futures::task::{Context, Poll};
9	use futures::{Stream, StreamExt};
10	use geoengine_datatypes::dataset::DataId;
11	use geoengine_datatypes::primitives::VectorQueryRectangle;
12	use serde::{Deserialize, Serialize};
13	use snafu::{ensure, OptionExt, ResultExt};
14	use tracing::{span, Level};
15
16	use geoengine_datatypes::collections::{
17	BuilderProvider, GeoFeatureCollectionRowBuilder, MultiPointCollection, VectorDataType,
18	};
19	use geoengine_datatypes::{
20	primitives::{BoundingBox2D, Coordinate2D, TimeInterval},
21	spatial_reference::SpatialReference,
22	};
23
24	use crate::engine::{CreateSpan, QueryProcessor};
25	use crate::engine::{
26	InitializedVectorOperator, OperatorData, OperatorName, QueryContext, SourceOperator,
27	TypedVectorQueryProcessor, VectorOperator, VectorQueryProcessor, VectorResultDescriptor,
28	};
29	use crate::error;
30	use crate::util::Result;
31	use async_trait::async_trait;
32	use std::sync::atomic::Ordering;
33
34	/// Parameters for the CSV Source Operator
35	///
36	/// # Examples
37	///
38	/// ```rust
39	/// use serde_json::{Result, Value};
40	/// use geoengine_operators::source::{CsvSourceParameters, CsvSource};
41	/// use geoengine_operators::source::{CsvGeometrySpecification, CsvTimeSpecification};
42	///
43	/// let json_string = r#"
44	/// {
45	/// "type": "CsvSource",
46	/// "params": {
47	/// "filePath": "/foo/bar.csv",
48	/// "fieldSeparator": ",",
49	/// "geometry": {
50	/// "type": "xy",
51	/// "x": "x",
52	/// "y": "y"
53	/// }
54	/// }
55	/// }"#;
56	///
57	/// let operator: CsvSource = serde_json::from_str(json_string).unwrap();
58	///
59	/// assert_eq!(operator, CsvSource {
60	/// params: CsvSourceParameters {
61	/// file_path: "/foo/bar.csv".into(),
62	/// field_separator: ',',
63	/// geometry: CsvGeometrySpecification::XY { x: "x".into(), y: "y".into() },
64	/// time: CsvTimeSpecification::None,
65	/// },
66	/// });
67	/// ```
68	#[derive(Debug, PartialEq, Eq, Serialize, Deserialize, Clone)]	34✔
69	#[serde(rename_all = "camelCase")]
70	pub struct CsvSourceParameters {
71	pub file_path: PathBuf,
72	pub field_separator: char,
73	pub geometry: CsvGeometrySpecification,
74	#[serde(default)]
75	pub time: CsvTimeSpecification,
76	}
77
78	#[derive(Debug, PartialEq, Eq, Serialize, Deserialize, Clone)]	49✔
79	#[serde(tag = "type", rename_all = "lowercase")]
80	pub enum CsvGeometrySpecification {
81	#[allow(clippy::upper_case_acronyms)]
82	XY { x: String, y: String },
83	}
84
85	#[derive(Debug, PartialEq, Eq, Serialize, Deserialize, Clone)]	34✔
86	pub enum CsvTimeSpecification {
87	None,
88	}
89
90	impl Default for CsvTimeSpecification {
91	fn default() -> Self {	×
92	Self::None	×
93	}	×
94	}
95
96	enum ReaderState {
97	Untouched(Reader<File>),
98	OnGoing {
99	header: ParsedHeader,
100	records: csv::StringRecordsIntoIter<File>,
101	},
102	Error,
103	}
104
105	impl ReaderState {
106	pub fn setup_once(&mut self, geometry_specification: CsvGeometrySpecification) -> Result<()> {	15✔
107	if let ReaderState::Untouched(..) = self {	15✔
108	// pass	6✔
109	} else {	6✔
110	return Ok(());	9✔
111	}
112
113	let old_state = std::mem::replace(self, ReaderState::Error);	6✔
114
115	if let ReaderState::Untouched(mut csv_reader) = old_state {	6✔
116	let header = match CsvSourceStream::setup_read(geometry_specification, &mut csv_reader)	6✔
117	{
118	Ok(header) => header,	5✔
119	Err(error) => return Err(error),	1✔
120	};
121
122	let mut records = csv_reader.into_records();	5✔
123		5✔
124	// consume the first row, which is the header	5✔
125	if header.has_header {	5✔
126	// TODO: throw error	5✔
127	records.next();	5✔
128	}	5✔
129
130	*self = ReaderState::OnGoing { header, records }	5✔
131	}	×
132
133	Ok(())	5✔
134	}	15✔
135	}
136
137	pub struct CsvSourceStream {
138	parameters: CsvSourceParameters,
139	bbox: BoundingBox2D,
140	chunk_size: usize,
141	reader_state: Arc<Mutex<ReaderState>>,
142	thread_is_computing: Arc<AtomicBool>,
143	#[allow(clippy::option_option)]
144	poll_result: Arc<Mutex<Option<Option<Result<MultiPointCollection>>>>>,
145	}
146
147	pub type CsvSource = SourceOperator<CsvSourceParameters>;
148
149	impl OperatorName for CsvSource {
150	const TYPE_NAME: &'static str = "CsvSource";
151	}
152
153	impl OperatorData for CsvSourceParameters {
154	fn data_ids_collect(&self, _data_ids: &mut Vec<DataId>) {}	×
155	}
156
157	#[typetag::serde]	1✔
158	#[async_trait]
159	impl VectorOperator for CsvSource {
160	async fn _initialize(	3✔
161	self: Box<Self>,	3✔
162	_context: &dyn crate::engine::ExecutionContext,	3✔
163	) -> Result<Box<dyn InitializedVectorOperator>> {	3✔
164	let initialized_source = InitializedCsvSource {	3✔
165	result_descriptor: VectorResultDescriptor {	3✔
166	data_type: VectorDataType::MultiPoint, // TODO: get as user input	3✔
167	spatial_reference: SpatialReference::epsg_4326().into(), // TODO: get as user input	3✔
168	columns: Default::default(), // TODO: get when source allows loading other columns	3✔
169	time: None,	3✔
170	bbox: None,	3✔
171	},	3✔
172	state: self.params,	3✔
173	};	3✔
174		3✔
175	Ok(initialized_source.boxed())	3✔
176	}	3✔
177
178	span_fn!(CsvSource);	×
179	}
180
181	pub struct InitializedCsvSource {
182	result_descriptor: VectorResultDescriptor,
183	state: CsvSourceParameters,
184	}
185
186	impl InitializedVectorOperator for InitializedCsvSource {
187	fn query_processor(&self) -> Result<crate::engine::TypedVectorQueryProcessor> {	2✔
188	Ok(TypedVectorQueryProcessor::MultiPoint(	2✔
189	CsvSourceProcessor {	2✔
190	params: self.state.clone(),	2✔
191	}	2✔
192	.boxed(),	2✔
193	))	2✔
194	}	2✔
195
196	fn result_descriptor(&self) -> &VectorResultDescriptor {	3✔
197	&self.result_descriptor	3✔
198	}	3✔
199	}
200
201	impl CsvSourceStream {
202	/// Creates a new `CsvSource`
203	///
204	/// # Errors
205	///
206	/// This constructor fails if the delimiter is not an ASCII character.
207	/// Furthermore, there are IO errors from the reader.
208	///
209	// TODO: include time interval, e.g. QueryRectangle parameter
210	pub fn new(	6✔
211	parameters: CsvSourceParameters,	6✔
212	bbox: BoundingBox2D,	6✔
213	chunk_size: usize,	6✔
214	) -> Result<Self> {	6✔
215	ensure!(	6✔
216	parameters.field_separator.is_ascii(),	6✔
217	error::CsvSource {	×
218	details: "Delimiter must be ASCII character"	×
219	}	×
220	);
221
222	Ok(Self {
223	reader_state: Arc::new(Mutex::new(ReaderState::Untouched(
224	csv::ReaderBuilder::new()	6✔
225	.delimiter(parameters.field_separator as u8)	6✔
226	.has_headers(true)	6✔
227	.from_path(parameters.file_path.as_path())	6✔
228	.context(error::CsvSourceReader {})?,	6✔
229	))),
230	thread_is_computing: Arc::new(AtomicBool::new(false)),	6✔
231	poll_result: Arc::new(Mutex::new(None)),	6✔
232	parameters,	6✔
233	bbox,	6✔
234	chunk_size,	6✔
235	})
236	}	6✔
237
238	fn setup_read(
239	geometry_specification: CsvGeometrySpecification,
240	csv_reader: &mut Reader<File>,
241	) -> Result<ParsedHeader> {
242	csv_reader	6✔
243	.seek(Position::new())	6✔
244	.context(error::CsvSourceReader {})?; // start at beginning	6✔
245
246	ensure!(	6✔
247	csv_reader.has_headers(),	6✔
248	error::CsvSource {	×
249	details: "CSV file must contain header",	×
250	}	×
251	);
252
253	let header = csv_reader.headers().context(error::CsvSourceReader)?;	6✔
254
255	let CsvGeometrySpecification::XY { x, y } = geometry_specification;	6✔
256	let x_index = header	6✔
257	.iter()	6✔
258	.position(\|v\| v == x)	6✔
259	.context(error::CsvSource {	6✔
260	details: "Cannot find x index in csv header",	6✔
261	})?;	6✔
262	let y_index = header	6✔
263	.iter()	6✔
264	.position(\|v\| v == y)	12✔
265	.context(error::CsvSource {	6✔
266	details: "Cannot find y index in csv header",	6✔
267	})?;	6✔
268
269	Ok(ParsedHeader {	5✔
270	has_header: true,	5✔
271	x_index,	5✔
272	y_index,	5✔
273	})	5✔
274	}	6✔
275
276	/// Parse a single CSV row
277	fn parse_row(header: &ParsedHeader, row: &StringRecord) -> Result<ParsedRow> {	14✔
278	let x: f64 = row	14✔
279	.get(header.x_index)	14✔
280	.context(error::CsvSource {	14✔
281	details: "Cannot find x index key",	14✔
282	})?	14✔
283	.parse()	14✔
284	.map_err(\|_error\| error::Error::CsvSource {	14✔
285	details: "Cannot parse x coordinate".to_string(),	×
286	})?;	14✔
287	let y: f64 = row	14✔
288	.get(header.y_index)	14✔
289	.context(error::CsvSource {	14✔
290	details: "Cannot find y index key",	14✔
291	})?	14✔
292	.parse()	14✔
293	.map_err(\|_error\| error::Error::CsvSource {	14✔
294	details: "Cannot parse y coordinate".to_string(),	×
295	})?;	14✔
296
297	Ok(ParsedRow {	14✔
298	coordinate: (x, y).into(),	14✔
299	time_interval: TimeInterval::default(),	14✔
300	})	14✔
301	}	14✔
302	}
303
304	impl Stream for CsvSourceStream {
305	type Item = Result<MultiPointCollection>;
306
307	fn poll_next(self: Pin<&mut Self>, cx: &mut Context<'_>) -> Poll<Option<Self::Item>> {	30✔
308	// TODO: handle lock poisoning on multiple occasions	30✔
309		30✔
310	if self.thread_is_computing.load(Ordering::Relaxed) {	30✔
311	return Poll::Pending;	×
312	}	30✔
313		30✔
314	let mut poll_result = self.poll_result.lock().unwrap();	30✔
315	if poll_result.is_some() {	30✔
316	let x = poll_result.take().unwrap();	15✔
317	return Poll::Ready(x);	15✔
318	}	15✔
319		15✔
320	self.thread_is_computing.store(true, Ordering::Relaxed);	15✔
321		15✔
322	let is_working = self.thread_is_computing.clone();	15✔
323	let reader_state = self.reader_state.clone();	15✔
324	let poll_result = self.poll_result.clone();	15✔
325		15✔
326	let bbox = self.bbox;	15✔
327	let chunk_size = self.chunk_size;	15✔
328	let parameters = self.parameters.clone();	15✔
329	let waker = cx.waker().clone();	15✔
330		15✔
331	crate::util::spawn_blocking(move \|\| {	15✔
332	let mut csv_reader = reader_state.lock().unwrap();	15✔
333	let computation_result = \|\| -> Result<Option<MultiPointCollection>> {	15✔
334	// TODO: is clone necessary?	15✔
335	let geometry_specification = parameters.geometry.clone();	15✔
336	csv_reader.setup_once(geometry_specification)?;	15✔
337
338	let (header, records) = match &mut *csv_reader {	14✔
339	ReaderState::OnGoing { header, records } => (header, records),	13✔
340	ReaderState::Error => return Ok(None),	1✔
341	ReaderState::Untouched(_) => unreachable!(),	×
342	};
343
344	let mut builder = MultiPointCollection::builder().finish_header();	13✔
345	let mut number_of_entries = 0; // TODO: add size/len to builder	13✔
346
347	while number_of_entries < chunk_size {	27✔
348	let Some(record) = records.next() else { break; };	24✔
349
350	let row = record.context(error::CsvSourceReader)?;	15✔
351	let parsed_row = CsvSourceStream::parse_row(header, &row)?;	14✔
352
353	// TODO: filter time
354	if bbox.contains_coordinate(&parsed_row.coordinate) {	14✔
355	builder.push_geometry(parsed_row.coordinate.into());	13✔
356	builder.push_time_interval(parsed_row.time_interval);	13✔
357	builder.finish_row();	13✔
358		13✔
359	number_of_entries += 1;	13✔
360	}	13✔
361	}
362
363	// TODO: is this the correct cancellation criterion?
364	if number_of_entries > 0 {	12✔
365	let collection = builder.build()?;	7✔
366	Ok(Some(collection))	7✔
367	} else {
368	Ok(None)	5✔
369	}
370	}();	15✔
371
372	*poll_result.lock().unwrap() = Some(match computation_result {	15✔
373	Ok(Some(collection)) => Some(Ok(collection)),	7✔
374	Ok(None) => None,	6✔
375	Err(e) => Some(Err(e)),	2✔
376	});
377	is_working.store(false, Ordering::Relaxed);	15✔
378		15✔
379	waker.wake();	15✔
380	});	15✔
381		15✔
382	Poll::Pending	15✔
383	}	30✔
384	}
385
386	#[derive(Debug)]	×
387	struct CsvSourceProcessor {
388	params: CsvSourceParameters,
389	}
390
391	#[async_trait]
392	impl QueryProcessor for CsvSourceProcessor {
393	type Output = MultiPointCollection;
394	type SpatialBounds = BoundingBox2D;
395
396	async fn _query<'a>(	3✔
397	&'a self,	3✔
398	query: VectorQueryRectangle,	3✔
399	_ctx: &'a dyn QueryContext,	3✔
400	) -> Result<BoxStream<'a, Result<Self::Output>>> {	3✔
401	// TODO: properly handle chunk_size
402	Ok(CsvSourceStream::new(self.params.clone(), query.spatial_bounds, 10)?.boxed())	3✔
403	}	6✔
404	}
405
406	#[derive(Clone, Copy, Debug)]	×
407	struct ParsedHeader {
408	pub has_header: bool,
409	pub x_index: usize,
410	pub y_index: usize,
411	}
412
413	struct ParsedRow {
414	pub coordinate: Coordinate2D,
415	pub time_interval: TimeInterval,
416	// TODO: fields
417	}
418
419	#[cfg(test)]
420	mod tests {
421	use std::io::{Seek, SeekFrom, Write};
422
423	use geoengine_datatypes::primitives::SpatialResolution;
424
425	use super::*;
426	use crate::engine::MockQueryContext;
427	use geoengine_datatypes::collections::{FeatureCollectionInfos, ToGeoJson};
428
429	#[tokio::test]	1✔
430	async fn read_points() {	1✔
431	let mut fake_file = tempfile::NamedTempFile::new().unwrap();	1✔
432	write!(	1✔
433	fake_file,	1✔
434	"\	1✔
435	x,y	1✔
436	0,1	1✔
437	2,3	1✔
438	4,5	1✔
439	"	1✔
440	)	1✔
441	.unwrap();	1✔
442	fake_file.seek(SeekFrom::Start(0)).unwrap();	1✔
443		1✔
444	let mut csv_source = CsvSourceStream::new(	1✔
445	CsvSourceParameters {	1✔
446	file_path: fake_file.path().into(),	1✔
447	field_separator: ',',	1✔
448	geometry: CsvGeometrySpecification::XY {	1✔
449	x: "x".into(),	1✔
450	y: "y".into(),	1✔
451	},	1✔
452	time: CsvTimeSpecification::None,	1✔
453	},	1✔
454	BoundingBox2D::new_unchecked((0., 0.).into(), (5., 5.).into()),	1✔
455	2,	1✔
456	)	1✔
457	.unwrap();	1✔
458
459	assert_eq!(csv_source.next().await.unwrap().unwrap().len(), 2);	1✔
460	assert_eq!(csv_source.next().await.unwrap().unwrap().len(), 1);	1✔
461	assert!(csv_source.next().await.is_none());	1✔
462	}
463
464	#[tokio::test]	1✔
465	async fn erroneous_point_rows() {	1✔
466	let mut fake_file = tempfile::NamedTempFile::new().unwrap();	1✔
467	write!(	1✔
468	fake_file,	1✔
469	"\	1✔
470	x,y	1✔
471	0,1	1✔
472	CORRUPT	1✔
473	4,5	1✔
474	"	1✔
475	)	1✔
476	.unwrap();	1✔
477	fake_file.seek(SeekFrom::Start(0)).unwrap();	1✔
478		1✔
479	let mut csv_source = CsvSourceStream::new(	1✔
480	CsvSourceParameters {	1✔
481	file_path: fake_file.path().into(),	1✔
482	field_separator: ',',	1✔
483	geometry: CsvGeometrySpecification::XY {	1✔
484	x: "x".into(),	1✔
485	y: "y".into(),	1✔
486	},	1✔
487	time: CsvTimeSpecification::None,	1✔
488	},	1✔
489	BoundingBox2D::new_unchecked((0., 0.).into(), (5., 5.).into()),	1✔
490	1,	1✔
491	)	1✔
492	.unwrap();	1✔
493
494	assert_eq!(csv_source.next().await.unwrap().unwrap().len(), 1);	1✔
495	assert!(csv_source.next().await.unwrap().is_err());	1✔
496	assert_eq!(csv_source.next().await.unwrap().unwrap().len(), 1);	1✔
497	assert!(csv_source.next().await.is_none());	1✔
498	}
499
500	#[tokio::test]	1✔
501	async fn corrupt_point_header() {	1✔
502	let mut fake_file = tempfile::NamedTempFile::new().unwrap();	1✔
503	write!(	1✔
504	fake_file,	1✔
505	"\	1✔
506	x,z	1✔
507	0,1	1✔
508	2,3	1✔
509	4,5	1✔
510	"	1✔
511	)	1✔
512	.unwrap();	1✔
513	fake_file.seek(SeekFrom::Start(0)).unwrap();	1✔
514		1✔
515	let mut csv_source = CsvSourceStream::new(	1✔
516	CsvSourceParameters {	1✔
517	file_path: fake_file.path().into(),	1✔
518	field_separator: ',',	1✔
519	geometry: CsvGeometrySpecification::XY {	1✔
520	x: "x".into(),	1✔
521	y: "y".into(),	1✔
522	},	1✔
523	time: CsvTimeSpecification::None,	1✔
524	},	1✔
525	BoundingBox2D::new_unchecked((0., 0.).into(), (5., 5.).into()),	1✔
526	1,	1✔
527	)	1✔
528	.unwrap();	1✔
529
530	assert!(csv_source.next().await.unwrap().is_err());	1✔
531	assert!(csv_source.next().await.is_none());	1✔
532	}
533
534	#[tokio::test]	1✔
535	async fn processor() {	1✔
536	let mut fake_file = tempfile::NamedTempFile::new().unwrap();	1✔
537	write!(	1✔
538	fake_file,	1✔
539	"\	1✔
540	x,y	1✔
541	0,1	1✔
542	2,3	1✔
543	4,5	1✔
544	"	1✔
545	)	1✔
546	.unwrap();	1✔
547	fake_file.seek(SeekFrom::Start(0)).unwrap();	1✔
548		1✔
549	let params = CsvSourceParameters {	1✔
550	file_path: fake_file.path().into(),	1✔
551	field_separator: ',',	1✔
552	geometry: CsvGeometrySpecification::XY {	1✔
553	x: "x".into(),	1✔
554	y: "y".into(),	1✔
555	},	1✔
556	time: CsvTimeSpecification::None,	1✔
557	};	1✔
558		1✔
559	let p = CsvSourceProcessor { params };	1✔
560		1✔
561	let query = VectorQueryRectangle {	1✔
562	spatial_bounds: BoundingBox2D::new_unchecked(	1✔
563	Coordinate2D::new(0., 0.),	1✔
564	Coordinate2D::new(3., 3.),	1✔
565	),	1✔
566	time_interval: TimeInterval::new_unchecked(0, 1),	1✔
567	spatial_resolution: SpatialResolution::zero_point_one(),	1✔
568	};	1✔
569	let ctx = MockQueryContext::new((10 * 8 * 2).into());	1✔
570
571	let r: Vec<Result<MultiPointCollection>> =	1✔
572	p.query(query, &ctx).await.unwrap().collect().await;	2✔
573
574	assert_eq!(r.len(), 1);	1✔
575
576	assert_eq!(	1✔
577	r[0].as_ref().unwrap().to_geo_json(),	1✔
578	serde_json::json!({	1✔
579	"type": "FeatureCollection",	1✔
580	"features": [{	1✔
581	"type": "Feature",	1✔
582	"geometry": {	1✔
583	"type": "Point",	1✔
584	"coordinates": [0.0, 1.0]	1✔
585	},	1✔
586	"properties": {},	1✔
587	"when": {	1✔
588	"start": "-262144-01-01T00:00:00+00:00",	1✔
589	"end": "+262143-12-31T23:59:59.999+00:00",	1✔
590	"type": "Interval"	1✔
591	}	1✔
592	}, {	1✔
593	"type": "Feature",	1✔
594	"geometry": {	1✔
595	"type": "Point",	1✔
596	"coordinates": [2.0, 3.0]	1✔
597	},	1✔
598	"properties": {},	1✔
599	"when": {	1✔
600	"start": "-262144-01-01T00:00:00+00:00",	1✔
601	"end": "+262143-12-31T23:59:59.999+00:00",	1✔
602	"type": "Interval"	1✔
603	}	1✔
604	}]	1✔
605	})	1✔
606	.to_string()	1✔
607	);	1✔
608	}
609
610	#[test]	1✔
611	fn operator() {	1✔
612	let mut temp_file = tempfile::NamedTempFile::new().unwrap();	1✔
613	write!(	1✔
614	temp_file,	1✔
615	"\	1✔
616	x;y	1✔
617	0;1	1✔
618	2;3	1✔
619	4;5	1✔
620	"	1✔
621	)	1✔
622	.unwrap();	1✔
623	temp_file.seek(SeekFrom::Start(0)).unwrap();	1✔
624		1✔
625	let params = CsvSourceParameters {	1✔
626	file_path: temp_file.path().into(),	1✔
627	field_separator: ';',	1✔
628	geometry: CsvGeometrySpecification::XY {	1✔
629	x: "x".into(),	1✔
630	y: "y".into(),	1✔
631	},	1✔
632	time: CsvTimeSpecification::None,	1✔
633	};	1✔
634		1✔
635	let operator = CsvSource { params }.boxed();	1✔
636		1✔
637	let operator_json = serde_json::to_value(&operator).unwrap();	1✔
638		1✔
639	assert_eq!(	1✔
640	operator_json,	1✔
641	serde_json::json!({	1✔
642	"type": "CsvSource",	1✔
643	"params": {	1✔
644	"filePath": temp_file.path(),	1✔
645	"fieldSeparator": ";",	1✔
646	"geometry": {	1✔
647	"type": "xy",	1✔
648	"x": "x",	1✔
649	"y": "y"	1✔
650	},	1✔
651	"time": "None"	1✔
652	}	1✔
653	})	1✔
654	);	1✔
655
656	let _operator: Box<dyn VectorOperator> = serde_json::from_value(operator_json).unwrap();	1✔
657	}	1✔
658	}

geo-engine / geoengine / 3929938005

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous