From b8405e27705e061d03a2fbb3a86d92269668ff74 Mon Sep 17 00:00:00 2001 From: Marijan Mihaljev Date: Mon, 6 Oct 2025 10:57:10 +0200 Subject: [PATCH 1/3] ODM-12805 Added supported extensions to /api/v1/jobs/import/expression/multipart endpoint --- openapi/v1/job.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/openapi/v1/job.yaml b/openapi/v1/job.yaml index f92f5296..5a04e524 100644 --- a/openapi/v1/job.yaml +++ b/openapi/v1/job.yaml @@ -381,8 +381,8 @@ paths: ## Metadata It is also possible to optionally supply the URL of a metadata file. This metadata will be used as the original metadata for the created objects. The file is expected to contain single record with metadata describing the uploaded signal file. ## Metadata file format - * Extension: any, `.zip` and `.gz` extensions are treated as archives and get decompressed - * Format: plain text, Tab-separated format (TSV), attribute names and record values are separated with tabs (`U+0009`), lines are separated with `CRLF` sequence (`U+000D U+000A`) + * Extension: `.zip`, `.gz`, `.br`, `.lz4` are supported, treated as archives and get decompressed + * Format: plain text, Gene Cluster Text (GCT), Tab-separated format (TSV), attribute names and record values are separated with tabs (`U+0009`), lines are separated with `CRLF` sequence (`U+000D U+000A`) * Header: the first line is treated as table header that contains attribute names * Records: the second line contains the values for each of the attributes described in the header line. Values represent single string or list of strings. List values are separated using the "pipe" `|` (`U+007C`) separator. Values are trimmed of whitespace before parsing, and a literal `|` (`U+007C`) character may be escaped by repeating it twice. * Skip zeros in original data file: If this option is selected, zeros in the file will be ignored, thus conserving time and space. This option is particularly useful for handling very sparse data such as Single Cell data. @@ -425,8 +425,8 @@ paths: ## Metadata It is also possible to optionally supply the URL of a metadata file. This metadata will be used as the original metadata for the created objects. The file is expected to contain single record with metadata describing the uploaded signal file. ## Metadata file format - * Extension: any, `.zip` and `.gz` extensions are treated as archives and get decompressed - * Format: plain text, Tab-separated format (TSV), attribute names and record values are separated with tabs (`U+0009`), lines are separated with `CRLF` sequence (`U+000D U+000A`) + * Extension: `.zip`, `.gz`, `.br`, `.lz4` are supported, treated as archives and get decompressed + * Format: plain text, Gene Cluster Text (GCT), Tab-separated format (TSV), attribute names and record values are separated with tabs (`U+0009`), lines are separated with `CRLF` sequence (`U+000D U+000A`) * Header: the first line is treated as table header that contains attribute names * Records: the second line contains the values for each of the attributes described in the header line. Values represent single string or list of strings. List values are separated using the "pipe" `|` (`U+007C`) separator. Values are trimmed of whitespace before parsing, and a literal `|` (`U+007C`) character may be escaped by repeating it twice. * Skip zeros in original data file: If this option is selected, zeros in the file will be ignored, thus conserving time and space. This option is particularly useful for handling very sparse data such as Single Cell data. From 089f13927c37c470dcdade0ee9b449f3b1ed4610 Mon Sep 17 00:00:00 2001 From: Marijan Mihaljev Date: Mon, 6 Oct 2025 11:34:13 +0200 Subject: [PATCH 2/3] ODM-12805 Changed order for Format and Extension in /api/v1/jobs/import/expression/multipart endpoint description --- openapi/v1/job.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/openapi/v1/job.yaml b/openapi/v1/job.yaml index 5a04e524..5d9234f9 100644 --- a/openapi/v1/job.yaml +++ b/openapi/v1/job.yaml @@ -381,8 +381,8 @@ paths: ## Metadata It is also possible to optionally supply the URL of a metadata file. This metadata will be used as the original metadata for the created objects. The file is expected to contain single record with metadata describing the uploaded signal file. ## Metadata file format - * Extension: `.zip`, `.gz`, `.br`, `.lz4` are supported, treated as archives and get decompressed * Format: plain text, Gene Cluster Text (GCT), Tab-separated format (TSV), attribute names and record values are separated with tabs (`U+0009`), lines are separated with `CRLF` sequence (`U+000D U+000A`) + * Extension: `.zip`, `.gz`, `.br`, `.lz4` are supported, treated as archives and get decompressed * Header: the first line is treated as table header that contains attribute names * Records: the second line contains the values for each of the attributes described in the header line. Values represent single string or list of strings. List values are separated using the "pipe" `|` (`U+007C`) separator. Values are trimmed of whitespace before parsing, and a literal `|` (`U+007C`) character may be escaped by repeating it twice. * Skip zeros in original data file: If this option is selected, zeros in the file will be ignored, thus conserving time and space. This option is particularly useful for handling very sparse data such as Single Cell data. @@ -425,8 +425,8 @@ paths: ## Metadata It is also possible to optionally supply the URL of a metadata file. This metadata will be used as the original metadata for the created objects. The file is expected to contain single record with metadata describing the uploaded signal file. ## Metadata file format - * Extension: `.zip`, `.gz`, `.br`, `.lz4` are supported, treated as archives and get decompressed * Format: plain text, Gene Cluster Text (GCT), Tab-separated format (TSV), attribute names and record values are separated with tabs (`U+0009`), lines are separated with `CRLF` sequence (`U+000D U+000A`) + * Extension: `.zip`, `.gz`, `.br`, `.lz4` are supported, treated as archives and get decompressed * Header: the first line is treated as table header that contains attribute names * Records: the second line contains the values for each of the attributes described in the header line. Values represent single string or list of strings. List values are separated using the "pipe" `|` (`U+007C`) separator. Values are trimmed of whitespace before parsing, and a literal `|` (`U+007C`) character may be escaped by repeating it twice. * Skip zeros in original data file: If this option is selected, zeros in the file will be ignored, thus conserving time and space. This option is particularly useful for handling very sparse data such as Single Cell data. From 4147778792e825d7af1b21e143cc83ecf0b23252 Mon Sep 17 00:00:00 2001 From: Marijan Mihaljev Date: Mon, 6 Oct 2025 14:56:32 +0200 Subject: [PATCH 3/3] ODM-12805 Removed 'plain text' from Format in /api/v1/jobs/import/expression/(multipart) endpoint description --- openapi/v1/job.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/openapi/v1/job.yaml b/openapi/v1/job.yaml index 5d9234f9..53c9e682 100644 --- a/openapi/v1/job.yaml +++ b/openapi/v1/job.yaml @@ -381,7 +381,7 @@ paths: ## Metadata It is also possible to optionally supply the URL of a metadata file. This metadata will be used as the original metadata for the created objects. The file is expected to contain single record with metadata describing the uploaded signal file. ## Metadata file format - * Format: plain text, Gene Cluster Text (GCT), Tab-separated format (TSV), attribute names and record values are separated with tabs (`U+0009`), lines are separated with `CRLF` sequence (`U+000D U+000A`) + * Format: Gene Cluster Text (GCT) and Tab-separated format (TSV), attribute names and record values are separated with tabs (`U+0009`), lines are separated with `CRLF` sequence (`U+000D U+000A`) * Extension: `.zip`, `.gz`, `.br`, `.lz4` are supported, treated as archives and get decompressed * Header: the first line is treated as table header that contains attribute names * Records: the second line contains the values for each of the attributes described in the header line. Values represent single string or list of strings. List values are separated using the "pipe" `|` (`U+007C`) separator. Values are trimmed of whitespace before parsing, and a literal `|` (`U+007C`) character may be escaped by repeating it twice. @@ -425,7 +425,7 @@ paths: ## Metadata It is also possible to optionally supply the URL of a metadata file. This metadata will be used as the original metadata for the created objects. The file is expected to contain single record with metadata describing the uploaded signal file. ## Metadata file format - * Format: plain text, Gene Cluster Text (GCT), Tab-separated format (TSV), attribute names and record values are separated with tabs (`U+0009`), lines are separated with `CRLF` sequence (`U+000D U+000A`) + * Format: Gene Cluster Text (GCT) and Tab-separated format (TSV), attribute names and record values are separated with tabs (`U+0009`), lines are separated with `CRLF` sequence (`U+000D U+000A`) * Extension: `.zip`, `.gz`, `.br`, `.lz4` are supported, treated as archives and get decompressed * Header: the first line is treated as table header that contains attribute names * Records: the second line contains the values for each of the attributes described in the header line. Values represent single string or list of strings. List values are separated using the "pipe" `|` (`U+007C`) separator. Values are trimmed of whitespace before parsing, and a literal `|` (`U+007C`) character may be escaped by repeating it twice.