Fix/export xlsx merge cells and write errors #487

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Merged

MartinKl merged 8 commits into main from fix/export-xlsx-merge-cells-and-write-errors

Dec 10, 2025

CHANGELOG.md

-Original file line number
+Diff line change
@@ Expand Up @@
     ## [Unreleased]
+    ### Changed
+    - export `xlsx`: No more parallel document processing in one export step, as this caused the exporter to crash when more than one file was present
+    - export `xlsx`: Better warning messages
+    ### Fixed
+    - import `xlsx`: Trim column names
     ## [0.44.1] - 2025-12-09
     ## [0.44.0] - 2025-12-08
@@ Expand Down @@

Cargo.toml

-Original file line number
+Diff line change
@@ Expand Up / @@ -15,6 +15,7 @@ version = "0.44.1" @@
     ansi_term = "0.12"
     anyhow = "1.0"
     bimap = "0.6.3"
+    chrono = "0.4.42"
     clap = { version = "4.0", features = ["derive", "env"] }
     console = "0.15"
     csv = "1.3"
@@ Expand Down @@

src/exporter/xlsx.rs

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -13,7 +13,6 @@ use graphannis_core::{
  
        util::join_qname,

    };

    use linked_hash_map::LinkedHashMap;

    use rayon::iter::{IntoParallelRefIterator, ParallelIterator};

    use serde::{Deserialize, Serialize};

    use tempfile::NamedTempFile;

    @@ -141,13 +140,20 @@ impl ExportXlsx {
  
            };

            let worksheet = if let Some(addr) = &self.update_datasheet {

                match addr {

                    SheetAddress::Numeric(i) => workbook

                        .get_sheet_mut(&(*i - 1))

                        .ok_or(anyhow!("Sheet with index {i} does not exist."))?,

                    SheetAddress::Name(s) => workbook

                        .get_sheet_by_name_mut(s)

                        .ok_or(anyhow!("Sheet with name {s} does not exist."))?,

                    SheetAddress::Numeric(i) => {

                        workbook.remove_sheet(*i - 1).map_err(|e| anyhow!(e))?;

                    }

                    SheetAddress::Name(s) => {

                        workbook.remove_sheet_by_name(s).map_err(|e| anyhow!(e))?;

                    }

                }

                let sheet_name = format!(

                    "{doc_name}-{}",

                    chrono::Local::now().format("%Y-%m-%d-%H-%M-%S-%9f")

                );

                workbook

                    .new_sheet(&sheet_name)

                    .map_err(|e| anyhow!("Could not create new sheet with name `{sheet_name}`: {e}"))?

            } else {

                workbook

                    .get_sheet_mut(&0)

    @@ -378,7 +384,7 @@ impl ExportXlsx {
  
                            for t in gs.get_outgoing_edges(span.node) {

                                let t = t?;

                                if let Some(row) = token_to_row.get(&t) {

                                    spanned_rows.insert(row);

                                    spanned_rows.insert(*row);

                                }

                            }

                        }

    @@ -388,13 +394,14 @@ impl ExportXlsx {
  
                        if let Some(first) = first_row

                            && let Some(last) = last_row

                        {

                            if spanned_rows.intersection(&written_rows).count() > 0 {

                                progress.warn(format!("Could not write span value {span_val} from row {first} to row {last} in column `{}`. A span already exists in at least of the affected rows.", span_anno_key.name))?;

                            let intersection_size = spanned_rows.intersection(&written_rows).count();

                            if intersection_size > 0 {

                                progress.warn(format!("Could not write span value {span_val} from row {first} to row {last} in column `{}` in document {}. A span already exists in at least of the affected rows. {intersection_size} node(s) overlap(s).", span_anno_key.name, worksheet.get_name()))?;

                                continue;

                            }

                            if *last - *first > 0 {

                                worksheet

                                    .get_cell_mut((*column_index, **first))

                                    .get_cell_mut((*column_index, *first))

                                    .set_value(span_val);

                                let column_letter =

                                    umya_spreadsheet::helper::coordinate::string_from_column_index(

    @@ -404,7 +411,7 @@ impl ExportXlsx {
  
                                worksheet.add_merge_cells(range);

                            } else {

                                worksheet

                                    .get_cell_mut((*column_index, **first))

                                    .get_cell_mut((*column_index, *first))

                                    .set_value(span_val);

                            }

                            written_rows.extend(spanned_rows);

    @@ -447,7 +454,7 @@ impl Exporter for ExportXlsx {
  
            std::fs::create_dir_all(output_path)?;

            let results: anyhow::Result<Vec<_>> = document_names

                .par_iter()

                .iter()

                .map(|(doc_name, doc_node_id)| {

                    self.export_document(doc_name, *doc_node_id, graph, output_path, &reporter)?;

                    reporter.worked(1)?;

    @@ -470,6 +477,7 @@ mod tests {
  
            path::{Path, PathBuf},

        };

        use graphannis::update::GraphUpdate;

        use insta::assert_snapshot;

        use sha2::{Digest, Sha256};

        use tempfile::{TempDir, tempdir};

    @@ -478,6 +486,7 @@ mod tests {
  
            ExporterStep, ImporterStep, ReadFrom, WriteAs,

            importer::{Importer, xlsx::ImportSpreadsheet},

            test_util::compare_graphs,

            util::example_generator,

        };

        use super::*;

    @@ -996,7 +1005,7 @@ mod tests {
  
            let wb = umya_spreadsheet::reader::xlsx::read(test_target);

            assert!(wb.is_ok());

            let book = wb.unwrap();

            let sheet = book.get_sheet(&1).unwrap();

            let sheet = book.get_sheet(&0).unwrap();

            let merge_cells = sheet.get_merge_cells();

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

            let merge_cell = merge_cells.get(0);

    @@ -1016,4 +1025,41 @@ mod tests {
  
                fnt.get_bold()

            ));

        }

        #[test]

        fn spans() {

            let g = AnnotationGraph::with_default_graphstorages(true);

            assert!(g.is_ok());

            let mut graph = g.unwrap();

            let mut u = GraphUpdate::default();

            example_generator::create_corpus_structure_simple(&mut u);

            example_generator::create_multiple_segmentations(&mut u, "root/doc1");

            assert!(graph.apply_update(&mut u, |_| {}).is_ok());

            let exporter = ExportXlsx {

                ..Default::default()

            };

            let target_dir = tempdir().unwrap();

            assert!(

                exporter

                    .export_corpus(

                        &graph,

                        target_dir.path(),

                        crate::StepID {

                            module_name: "test_export".to_string(),

                            path: None

                        },

                        None

                    )

                    .is_ok()

            );

            assert!(

                sheets_diff::core::diff::Diff::new(

                    "./tests/data/export/xlsx/span-target/doc1.xlsx",

                    &target_dir.path().join("doc1.xlsx").to_string_lossy()

                )

                .diff()

                .cell_diffs

                .is_empty()

            );

        }

    }

src/importer/xlsx.rs

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -245,7 +245,7 @@ impl<'a> DatasheetMapper<'a> {
  
                .reverse_col_map

                .keys()

                .chain(self.reverse_col_map.values())

                .map(|e| e.as_str())

                .map(|e| e.trim())

                .collect_vec();

            let mut merged_cells = self.collect_merged_cells(expected_names, progress)?;

            let base_tokens = self.build_tokens(update, doc_node_name)?;

    @@ -284,8 +284,8 @@ impl<'a> DatasheetMapper<'a> {
  
                || self.column_map.contains_key(&col_name);

            let anno_key = if is_segmentation {

                AnnoKey {

                    ns: ns.unwrap_or(name).into(), // prefer the namespace in the column header

                    name: name.into(),

                    ns: ns.unwrap_or(name.trim()).into(), // prefer the namespace in the column header

                    name: name.trim().into(),

                }

            } else if let Some(seg_name) = self

                .reverse_col_map

    @@ -294,8 +294,8 @@ impl<'a> DatasheetMapper<'a> {
  
                .or(self.fallback.as_ref())

            {

                AnnoKey {

                    ns: ns.unwrap_or(seg_name).into(), // prefer the namespace in the column header

                    name: name.into(),

                    ns: ns.unwrap_or(seg_name.trim()).into(), // prefer the namespace in the column header

                    name: name.trim().into(),

                }

            } else {

                let msg = format!(

    @@ -479,7 +479,7 @@ impl<'a> DatasheetMapper<'a> {
  
                    if start_col != end_col {

                        if (*start_col.get_num()..=*end_col.get_num()).any(|c| {

                            if let Some(cell) = self.sheet.get_cell((c, 1)) {

                                col_names.contains(&cell.get_raw_value().to_string().as_str())

                                col_names.contains(&cell.get_raw_value().to_string().trim())

                            } else {

                                false

                            }

tests/data/export/xlsx/span-target/doc1.xlsx

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Fix/export xlsx merge cells and write errors #487

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