exon-gff 0.3.8-beta.2

A library for reading and writing GFF files with Exon.
Documentation 
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// Copyright 2023 WHERE TRUE Technologies.
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
//     http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.

use std::sync::Arc;

use arrow::datatypes::{DataType, Field, Schema, SchemaRef};
use object_store::ObjectStore;

pub struct GFFSchemaBuilder {
    fields: Vec<Field>,
}

impl GFFSchemaBuilder {
    pub fn new(fields: Vec<Field>) -> Self {
        Self { fields }
    }

    pub fn append(mut self, field: Field) -> Self {
        self.fields.push(field);
        self
    }

    pub fn extend(mut self, fields: Vec<Field>) -> Self {
        self.fields.extend(fields);
        self
    }

    pub fn build(self) -> SchemaRef {
        Arc::new(Schema::new(self.fields))
    }
}

impl Default for GFFSchemaBuilder {
    fn default() -> Self {
        let attribute_key_field = Field::new("keys", DataType::Utf8, false);

        // attribute_value_field is a list of strings
        let value_field = Field::new("item", DataType::Utf8, true);
        let attribute_value_field =
            Field::new("values", DataType::List(Arc::new(value_field)), true);

        let fields = vec![
            Field::new("seqname", DataType::Utf8, false),
            Field::new("source", DataType::Utf8, true),
            Field::new("type", DataType::Utf8, false),
            Field::new("start", DataType::Int64, false),
            Field::new("end", DataType::Int64, false),
            Field::new("score", DataType::Float32, true),
            Field::new("strand", DataType::Utf8, false),
            Field::new("phase", DataType::Utf8, true),
            Field::new_map(
                "attributes",
                "entries",
                attribute_key_field,
                attribute_value_field,
                false,
                true,
            ),
        ];

        Self::new(fields)
    }
}

/// Configuration for a GFF data source.
pub struct GFFConfig {
    /// The number of rows to read at a time.
    pub batch_size: usize,

    /// The schema of the GFF file. This is static.
    pub file_schema: SchemaRef,

    /// The object store to use for reading GFF files.
    pub object_store: Arc<dyn ObjectStore>,

    /// Any projections to apply to the resulting batches.
    pub projection: Option<Vec<usize>>,
}

impl GFFConfig {
    /// Create a new GFF configuration.
    pub fn new(object_store: Arc<dyn ObjectStore>) -> Self {
        let file_schema = GFFSchemaBuilder::default().build();

        Self {
            file_schema,
            object_store,
            batch_size: 8096,
            projection: None,
        }
    }

    /// Set the file schema.
    pub fn with_schema(mut self, file_schema: SchemaRef) -> Self {
        self.file_schema = file_schema;
        self
    }

    /// Set the batch size.
    pub fn with_batch_size(mut self, batch_size: usize) -> Self {
        self.batch_size = batch_size;
        self
    }

    /// Set the projection.
    pub fn with_projection(mut self, projection: Vec<usize>) -> Self {
        let file_projection = projection
            .iter()
            .filter(|f| **f < self.file_schema.fields().len())
            .cloned()
            .collect::<Vec<_>>();

        self.projection = Some(file_projection);
        self
    }
}