# HG changeset patch
# User tduigou
# Date 1767699505 0
# Node ID ef59587326918eb734d74143b4b96224e7dcfdb7
# Parent 9ab8b3673816ae76c54ddbbe6bd3e9bfdab0df08
planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools/parameters_maystro commit e8c8f102cab10531ed588be4ecb8a0d01e797f09
diff -r 9ab8b3673816 -r ef5958732691 maystro.py
--- a/maystro.py Wed Jul 23 09:39:39 2025 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,98 +0,0 @@
-import argparse
-import tempfile
-import os
-import json
-import shutil
-
-
-def parse_command_line_args():
- parser = argparse.ArgumentParser(description="Maystro JSON Handler")
-
- parser.add_argument("--distribute_json", required=True, help="true or false")
- parser.add_argument("--json_from_workflow", required=False, nargs='+', help="JSON files from tools", default=[])
- parser.add_argument("--json_from_user", required=False, help="User-provided JSON")
- parser.add_argument("--json_name_mapping", required=True, help="map the real json name")
- parser.add_argument("--output_workflow", required=True, help="JSON output for next workflow steps")
- parser.add_argument("--output_user", required=True, help="Final JSON output to user")
-
- return parser.parse_args()
-
-
-def parse_file_name_mapping(mapping_str):
- mapping = {}
- if mapping_str:
- for pair in mapping_str.split(','):
- stored, original = pair.strip().split(':', 1)
- # Strip .json from original
- real_name = os.path.splitext(original)[0]
- mapping[os.path.basename(stored)] = real_name
- return mapping
-
-
-def handle_distribute_json_false(args):
- temp_dir = tempfile.mkdtemp(prefix="maystro_merge_")
- print(f"[INFO] Watching temp dir for new JSONs: {temp_dir}")
-
- try:
- # Collect JSONs from json_from_workflow
- initial_jsons = list(filter(os.path.isfile, args.json_from_workflow))
- print(f"[INFO] Initial JSONs from workflow: {initial_jsons}")
-
- # Parse filename mapping if provided
- filename_mapping = parse_file_name_mapping(getattr(args, 'json_name_mapping', ''))
-
- # Merge all together
- merged = {}
- for file_path in initial_jsons:
- try:
- with open(file_path, 'r') as f:
- data = json.load(f)
- basename = os.path.basename(file_path)
- real_name = filename_mapping.get(basename, basename) # fallback if not in mapping
- merged[real_name] = data
- print(f"[INFO] Added data under key: {real_name}")
- except json.JSONDecodeError as e:
- print(f"[WARN] Skipping invalid JSON file {file_path}: {e}")
-
- with open(args.output_user, "w") as f:
- json.dump(merged, f, indent=2)
- print(f"[INFO] Merged JSON written to: {args.output_user}")
-
- finally:
- print(f"[INFO] Cleaning up: {temp_dir}")
- shutil.rmtree(temp_dir)
-
-
-def merge_json_files(paths):
- merged = {}
- for path in paths:
- try:
- with open(path, "r") as f:
- data = json.load(f)
- merged.update(data)
- except Exception as e:
- print(f"[WARN] Skipping {path}: {e}")
- return merged
-
-
-def handle_distribute_json_true(args):
- if not args.json_from_user:
- raise ValueError("json_from_user is required when distribute_json is true")
-
- with open(args.json_from_user, 'r') as in_f:
- user_data = json.load(in_f)
-
- with open(args.output_workflow, 'w') as out_f:
- json.dump(user_data, out_f, indent=2)
-
-
-def main():
- args = parse_command_line_args()
-
- if args.distribute_json.lower() == 'false':
- handle_distribute_json_false(args)
- else:
- handle_distribute_json_true(args)
-
-if __name__ == "__main__":
- main()
diff -r 9ab8b3673816 -r ef5958732691 output.html
--- a/output.html Wed Jul 23 09:39:39 2025 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,291 +0,0 @@
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-
- Test Results (powered by Planemo)
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\ No newline at end of file
diff -r 9ab8b3673816 -r ef5958732691 output.json
--- a/output.json Wed Jul 23 09:39:39 2025 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,168 +0,0 @@
-{
- "summary": {
- "num_errors": 0,
- "num_failures": 0,
- "num_skips": 0,
- "num_tests": 2
- },
- "tests": [
- {
- "data": {
- "inputs": {
- "DB|annotation_column": "annotation",
- "DB|db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
- "DB|execution": true,
- "DB|fragment_column": "fragment",
- "DB|sequence_column": "sequence",
- "DB|table_name": "sample",
- "DnaOptimizationProblemClass": "DnaOptimizationProblem",
- "assembly_plan_name": "Type2sRestrictionAssembly",
- "avoid_patterns": "BsaI_site nNotI_site nXbaI_site nClaI_site n8x1mer",
- "enzyme": "auto",
- "gc_constraints": "mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100",
- "hairpin_constraints": "stem_size=20, hairpin_window=200",
- "kmer_size": "15",
- "methylation_protection": true,
- "topology": "circular"
- },
- "job": {
- "command_line": "python3 -c \"import json; params = { 'DnaOptimizationProblemClass': 'DnaOptimizationProblem', 'methylation_protection': 'true', 'allow_edits': 'true', 'avoid_patterns': 'BsaI_site nNotI_site nXbaI_site nClaI_site n8x1mer', 'hairpin_constraints': 'stem_size=20, hairpin_window=200', 'gc_constraints': 'mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100', 'kmer_size': '15', 'assembly_plan_name': 'Type2sRestrictionAssembly', 'topology': 'circular', 'enzyme': 'auto', 'execution': 'true', 'db_uri': 'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db', 'table': 'sample', 'fragment_column': 'fragment', 'sequence_column': 'sequence', 'annotation_column': 'annotation' }; f = open('/tmp/tmpnxavcgf5/job_working_directory/000/1/outputs/dataset_53ffa695-5fab-48b3-b5f5-ff93f77bfc10.dat', 'w'); json.dump(params, f, indent=4); f.close()\" && echo DEBG && cat '/tmp/tmpnxavcgf5/job_working_directory/000/1/outputs/dataset_53ffa695-5fab-48b3-b5f5-ff93f77bfc10.dat' && echo DEBG && cat '/tmp/tmpnxavcgf5/job_working_directory/000/1/outputs/dataset_53ffa695-5fab-48b3-b5f5-ff93f77bfc10.dat'",
- "command_version": "",
- "copied_from_job_id": null,
- "create_time": "2025-07-17T12:08:28.832103",
- "dependencies": [],
- "exit_code": 0,
- "external_id": "135810",
- "galaxy_version": "25.0",
- "handler": null,
- "history_id": "d952758136b0c83c",
- "id": "d952758136b0c83c",
- "inputs": {},
- "job_messages": [],
- "job_metrics": [],
- "job_runner_name": null,
- "job_stderr": "",
- "job_stdout": "",
- "model_class": "Job",
- "output_collections": {},
- "outputs": {
- "output_json": {
- "id": "d952758136b0c83c",
- "src": "hda",
- "uuid": "53ffa695-5fab-48b3-b5f5-ff93f77bfc10"
- }
- },
- "params": {
- "DB": "{\"annotation_column\": \"annotation\", \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\", \"execution\": true, \"fragment_column\": \"fragment\", \"sequence_column\": \"sequence\", \"table_name\": \"sample\", \"user_json\": null}",
- "DnaOptimizationProblemClass": "\"DnaOptimizationProblem\"",
- "__input_ext": "\"input\"",
- "allow_edits": "true",
- "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
- "avoid_patterns": "\"BsaI_site nNotI_site nXbaI_site nClaI_site n8x1mer\"",
- "chromInfo": "\"/tmp/tmpnxavcgf5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
- "dbkey": "\"?\"",
- "enzyme": "\"auto\"",
- "gc_constraints": "\"mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100\"",
- "hairpin_constraints": "\"stem_size=20, hairpin_window=200\"",
- "kmer_size": "\"15\"",
- "methylation_protection": "true",
- "topology": "\"circular\""
- },
- "state": "ok",
- "stderr": "",
- "stdout": "DEBG\n{\n \"DnaOptimizationProblemClass\": \"DnaOptimizationProblem\",\n \"methylation_protection\": \"true\",\n \"allow_edits\": \"true\",\n \"avoid_patterns\": \"BsaI_site nNotI_site nXbaI_site nClaI_site n8x1mer\",\n \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\",\n \"gc_constraints\": \"mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100\",\n \"kmer_size\": \"15\",\n \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n \"topology\": \"circular\",\n \"enzyme\": \"auto\",\n \"execution\": \"true\",\n \"db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n \"table\": \"sample\",\n \"fragment_column\": \"fragment\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\"\n}DEBG\n{\n \"DnaOptimizationProblemClass\": \"DnaOptimizationProblem\",\n \"methylation_protection\": \"true\",\n \"allow_edits\": \"true\",\n \"avoid_patterns\": \"BsaI_site nNotI_site nXbaI_site nClaI_site n8x1mer\",\n \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\",\n \"gc_constraints\": \"mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100\",\n \"kmer_size\": \"15\",\n \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n \"topology\": \"circular\",\n \"enzyme\": \"auto\",\n \"execution\": \"true\",\n \"db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n \"table\": \"sample\",\n \"fragment_column\": \"fragment\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\"\n}",
- "tool_id": "parameters_maystro_workflow_2",
- "tool_stderr": "",
- "tool_stdout": "DEBG\n{\n \"DnaOptimizationProblemClass\": \"DnaOptimizationProblem\",\n \"methylation_protection\": \"true\",\n \"allow_edits\": \"true\",\n \"avoid_patterns\": \"BsaI_site nNotI_site nXbaI_site nClaI_site n8x1mer\",\n \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\",\n \"gc_constraints\": \"mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100\",\n \"kmer_size\": \"15\",\n \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n \"topology\": \"circular\",\n \"enzyme\": \"auto\",\n \"execution\": \"true\",\n \"db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n \"table\": \"sample\",\n \"fragment_column\": \"fragment\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\"\n}DEBG\n{\n \"DnaOptimizationProblemClass\": \"DnaOptimizationProblem\",\n \"methylation_protection\": \"true\",\n \"allow_edits\": \"true\",\n \"avoid_patterns\": \"BsaI_site nNotI_site nXbaI_site nClaI_site n8x1mer\",\n \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\",\n \"gc_constraints\": \"mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100\",\n \"kmer_size\": \"15\",\n \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n \"topology\": \"circular\",\n \"enzyme\": \"auto\",\n \"execution\": \"true\",\n \"db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n \"table\": \"sample\",\n \"fragment_column\": \"fragment\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\"\n}",
- "update_time": "2025-07-17T12:08:33.771569",
- "user_email": "planemo@galaxyproject.org",
- "user_id": "d952758136b0c83c"
- },
- "status": "success",
- "test_index": 0,
- "time_seconds": 5.093859434127808,
- "tool_id": "parameters_maystro_workflow_2",
- "tool_version": "0.1.0"
- },
- "has_data": true,
- "id": "parameters_maystro_workflow_2-0"
- },
- {
- "data": {
- "inputs": {
- "DB|user_json": {
- "id": "b08444d846605ee4",
- "src": "hda"
- }
- },
- "job": {
- "command_line": "cp '/tmp/tmpnxavcgf5/files/b/b/d/dataset_bbd9a440-a787-439e-9b36-2c1c45dae0a3.dat' '/tmp/tmpnxavcgf5/job_working_directory/000/3/outputs/dataset_6eed7c7c-77ce-4d77-b2ef-0a367df7e250.dat' && echo DEBG && cat '/tmp/tmpnxavcgf5/job_working_directory/000/3/outputs/dataset_6eed7c7c-77ce-4d77-b2ef-0a367df7e250.dat'",
- "command_version": "",
- "copied_from_job_id": null,
- "create_time": "2025-07-17T12:08:43.857384",
- "dependencies": [],
- "exit_code": 0,
- "external_id": "135995",
- "galaxy_version": "25.0",
- "handler": null,
- "history_id": "b08444d846605ee4",
- "id": "e67c2cbedbcb0da1",
- "inputs": {
- "DB|user_json": {
- "id": "b08444d846605ee4",
- "src": "hda",
- "uuid": "bbd9a440-a787-439e-9b36-2c1c45dae0a3"
- }
- },
- "job_messages": [],
- "job_metrics": [],
- "job_runner_name": null,
- "job_stderr": "",
- "job_stdout": "",
- "model_class": "Job",
- "output_collections": {},
- "outputs": {
- "output_json": {
- "id": "e67c2cbedbcb0da1",
- "src": "hda",
- "uuid": "6eed7c7c-77ce-4d77-b2ef-0a367df7e250"
- }
- },
- "params": {
- "DB": "{\"annotation_column\": null, \"db_uri\": null, \"execution\": false, \"fragment_column\": null, \"sequence_column\": null, \"table_name\": null, \"user_json\": {\"values\": [{\"id\": 2, \"src\": \"hda\"}]}}",
- "DnaOptimizationProblemClass": "\"DnaOptimizationProblem\"",
- "__input_ext": "\"input\"",
- "allow_edits": "true",
- "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
- "avoid_patterns": null,
- "chromInfo": "\"/tmp/tmpnxavcgf5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
- "dbkey": "\"?\"",
- "enzyme": "\"auto\"",
- "gc_constraints": null,
- "hairpin_constraints": null,
- "kmer_size": "\"\"",
- "methylation_protection": "false",
- "topology": "\"circular\""
- },
- "state": "ok",
- "stderr": "",
- "stdout": "DEBG\n{\n \"DnaOptimizationProblemClass\":\"DnaOptimizationProblem\",\n \"avoid_patterns\": \"BsaI_site\\nNotI_site\\nXbaI_site\\nClaI_site\\n8x1mer\",\n \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\\nstem_size=10, hairpin_window=100\",\n \"gc_constraints\": \"mini=0.1, maxi=0.9\\nmini-0.3, maxi=0.7, window=50\",\n \"kmer_size\": \"15\",\n \"methylation_protection\":\"methylation_protection\",\n \"allow_edits\":\"True\",\n \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n \"topology\": \"circular\",\n \"enzyme\": \"auto\",\n \"execution\": \"true\",\n \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\",\n \"table\": \"sample\",\n \"fragment_column\": \"fragment\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\"\n}\n",
- "tool_id": "parameters_maystro_workflow_2",
- "tool_stderr": "",
- "tool_stdout": "DEBG\n{\n \"DnaOptimizationProblemClass\":\"DnaOptimizationProblem\",\n \"avoid_patterns\": \"BsaI_site\\nNotI_site\\nXbaI_site\\nClaI_site\\n8x1mer\",\n \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\\nstem_size=10, hairpin_window=100\",\n \"gc_constraints\": \"mini=0.1, maxi=0.9\\nmini-0.3, maxi=0.7, window=50\",\n \"kmer_size\": \"15\",\n \"methylation_protection\":\"methylation_protection\",\n \"allow_edits\":\"True\",\n \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n \"topology\": \"circular\",\n \"enzyme\": \"auto\",\n \"execution\": \"true\",\n \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\",\n \"table\": \"sample\",\n \"fragment_column\": \"fragment\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\"\n}\n",
- "update_time": "2025-07-17T12:08:49.096516",
- "user_email": "planemo@galaxyproject.org",
- "user_id": "d952758136b0c83c"
- },
- "status": "success",
- "test_index": 1,
- "time_seconds": 15.298557996749878,
- "tool_id": "parameters_maystro_workflow_2",
- "tool_version": "0.1.0"
- },
- "has_data": true,
- "id": "parameters_maystro_workflow_2-1"
- }
- ],
- "version": "0.1"
-}
\ No newline at end of file