Add batch Foldseek structure search via /ticket/foldseek/batch#119
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igmorv-genesis wants to merge 12 commits intosoedinglab:masterfrom
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Add batch Foldseek structure search via /ticket/foldseek/batch#119igmorv-genesis wants to merge 12 commits intosoedinglab:masterfrom
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Enable searching multiple structures with different motifs in a single request. The API accepts queries[] and motifs[] arrays (multipart or URL-encoded), writes individual structure files and a tab-separated batch file, and invokes folddisco with -q <batch_file> instead of single -p/-q flags. Also removes the motif flag requirement from database validation so any registered database can be used for Folddisco queries. Made-with: Cursor
Reuse the same first-line check in both ismmCIFFile and WriteBatchFiles instead of duplicating the heuristic inline. Also adds TrimSpace to the batch path for consistency. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Only databases with the Motif flag (i.e. a valid folddisco index) should be accepted for Folddisco queries. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Allows clients to control how many neighbors are returned via a "top" form parameter, defaulting to 1000 for backwards compatibility. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Each motifs[] form value can now contain multiple motifs separated by ";", so a single structure file can be searched with several motif specifications without re-uploading. WriteBatchFiles emits one batch line per (file, motif) pair. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Add batch mode support for Folddisco queries
Folddisco batch mode (-q batchfile) writes results to stdout instead of the -o file. Wrap the batch command in sh -c with stdout redirection to create the expected output file for post-processing. Made-with: Cursor
folddisco writes batch results to stdout, and concurrent threads interleave their output mid-line, corrupting the TSV. Force -t 1 for batch queries to produce clean output. Made-with: Cursor
…ding Instead of using folddisco's built-in batch mode (which writes all results to stdout, causing interleaved output with multiple threads), run each (structure, motif) pair as a separate `folddisco query` invocation with its own `-o` output file. Each query gets full multi-threading via `-t`, and the per-query results are concatenated into the final output file. This replaces the previous `-t 1` workaround which sacrificed parallelism within each query. Made-with: Cursor
folddisco batch format supports an optional 3rd column for per-query output file paths. Use this to write each query's results to its own file, then concatenate. This runs a single folddisco process with full threading instead of N sequential invocations. Made-with: Cursor
Run batch folddisco queries individually for proper --top N and threading
New endpoint POST /ticket/foldseek/batch accepts queries[] (multiple
structure files), database[], mode, and taxfilter parameters. Query
structures are written to a queries/ directory and passed to foldseek
easy-search, which natively handles multi-query directory input.
Per-query results are returned via GET /result/foldseek/{ticket} as
a JSON object with per-query alignment arrays, reusing the existing
ReadAlignments infrastructure.
Worker detects batch mode by checking for the queries/ directory on
disk (unexported struct fields are not preserved across JSON
serialization).
Route uses /ticket/foldseek/batch to avoid gorilla/mux 405 conflict
with the /ticket/{ticket} variable route.
Made-with: Cursor
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Summary
POST /ticket/foldseek/batchacceptsqueries[](multiple uploaded structure files),database[],mode,email, andtaxfilterqueries/directory and passed tofoldseek easy-search, which natively handles multi-query directory input and produces per-query entries in the output alignment DBGET /result/foldseek/{ticket}endpoint returns all per-query results by reading all entries from the alignment DB, reusing the existingReadAlignmentsinfrastructurequeries/directory on disk (unexported struct fields aren't preserved across JSON serialization)/ticket/foldseek/batchto avoid gorilla/mux v1.8.0 405 conflict with the existing/ticket/{ticket}variable routeExample usage
Test plan
/ticketendpoint unaffected