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DTS Manifest parsing #210
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Merged
DTS Manifest parsing #210
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24d608c
do the parsing, update schema
briehl aa3e8df
remove commented code
briehl c099ca5
Merge branch 'dts-manifest-schema' into dts-manifest-parse
briehl 1c8ef68
update parser, tests
briehl 33ffb2c
simply and reformat
briehl 84e8b2f
Merge branch 'dts-manifest-schema' into dts-manifest-parse
briehl 6136140
minor tweaks
briehl 499dfe4
ruff formatting
briehl 224153a
fix typo
briehl d0e08b9
ruff formatting
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81 changes: 81 additions & 0 deletions
81
tests/import_specifications/test_data/manifest_errors.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,81 @@ | ||
| { | ||
| "name": "manifest", | ||
| "resources": [ | ||
| { | ||
| "id": "JDP:555518eb0d8785178e712d88", | ||
| "name": "61564.assembled", | ||
| "path": "img/submissions/61564/61564.assembled.gff", | ||
| "format": "gff", | ||
| "media_type": "text/plain", | ||
| "bytes": 455161, | ||
| "hash": "", | ||
| "credit": { | ||
| "comment": "", | ||
| "content_url": "", | ||
| "contributors": null, | ||
| "credit_metadata_source": "", | ||
| "dates": null, | ||
| "descriptions": null, | ||
| "funding": null, | ||
| "identifier": "JDP:555518eb0d8785178e712d88", | ||
| "license": { | ||
| "id": "", | ||
| "url": "" | ||
| }, | ||
| "publisher": { | ||
| "organization_id": "", | ||
| "organization_name": "" | ||
| }, | ||
| "related_identifiers": null, | ||
| "resource_type": "dataset", | ||
| "titles": null, | ||
| "url": "", | ||
| "version": "" | ||
| } | ||
| }, | ||
| { | ||
| "id": "JDP:555518eb0d8785178e712d84", | ||
| "name": "61564.assembled", | ||
| "path": "img/submissions/61564/61564.assembled.fna", | ||
| "format": "fasta", | ||
| "media_type": "text/plain", | ||
| "bytes": 6354414, | ||
| "hash": "", | ||
| "credit": { | ||
| "comment": "", | ||
| "content_url": "", | ||
| "contributors": null, | ||
| "credit_metadata_source": "", | ||
| "dates": null, | ||
| "descriptions": null, | ||
| "funding": null, | ||
| "identifier": "JDP:555518eb0d8785178e712d84", | ||
| "license": { | ||
| "id": "", | ||
| "url": "" | ||
| }, | ||
| "publisher": { | ||
| "organization_id": "", | ||
| "organization_name": "" | ||
| }, | ||
| "related_identifiers": null, | ||
| "resource_type": "dataset", | ||
| "titles": null, | ||
| "url": "", | ||
| "version": "" | ||
| } | ||
| } | ||
| ], | ||
| "instructions": { | ||
| "protocol": "KBase narrative import", | ||
| "objects": [ | ||
| { | ||
| "data_type": "gff_metagenome", | ||
| "parameters": { | ||
| "param1": "value1", | ||
| "param2": "value2" | ||
| } | ||
| } | ||
| ] | ||
| } | ||
| } |
62 changes: 62 additions & 0 deletions
62
tests/import_specifications/test_data/manifest_multiple.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,62 @@ | ||
| { | ||
| "name": "manifest", | ||
| "resources": [ | ||
| { | ||
| "id": "JDP:555518eb0d8785178e712d88", | ||
| "name": "61564.assembled", | ||
| "path": "img/submissions/61564/61564.assembled.gff", | ||
| "format": "gff" | ||
| }, | ||
| { | ||
| "id": "JDP:555518eb0d8785178e712d84", | ||
| "name": "61564.assembled", | ||
| "path": "img/submissions/61564/61564.assembled.fna", | ||
| "format": "fasta" | ||
| }, | ||
| { | ||
| "id": "JDP:555518ec0d8785178e712d9f", | ||
| "name": "61567.assembled", | ||
| "path": "img/submissions/61567/61567.assembled.gff", | ||
| "format": "gff" | ||
| }, | ||
| { | ||
| "id": "JDP:555518ec0d8785178e712d9b", | ||
| "name": "61567.assembled", | ||
| "path": "img/submissions/61567/61567.assembled.fna", | ||
| "format": "fasta" | ||
| } | ||
| ], | ||
| "instructions": { | ||
| "protocol": "KBase narrative import", | ||
| "objects": [ | ||
| { | ||
| "data_type": "gff_metagenome", | ||
| "parameters": { | ||
| "mg_param1": "value1", | ||
| "mg_param2": "value2" | ||
| } | ||
| }, | ||
| { | ||
| "data_type": "gff_metagenome", | ||
| "parameters": { | ||
| "mg_param1": "value3", | ||
| "mg_param2": "value4" | ||
| } | ||
| }, | ||
| { | ||
| "data_type": "gff_genome", | ||
| "parameters": { | ||
| "gen_param1": "value1", | ||
| "gen_param2": "value2" | ||
| } | ||
| }, | ||
| { | ||
| "data_type": "gff_genome", | ||
| "parameters": { | ||
| "gen_param1": "value3", | ||
| "gen_param2": "value4" | ||
| } | ||
| } | ||
| ] | ||
| } | ||
| } |
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So the DTS has to know the app parameter names for each datatype it processes? IOW the DTS is coupled to the apps?
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I also assume the file names / locations in the staging area are in the parameters? They can't be anywhere else...
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Yes to both. We talked about doing some references from the parameters to file paths, but if we do that'll be in a later version.
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Well, that seems less than ideal, but if you've agreed that that's how it'll work so be it