Params - Old

1. Params - Old Step4 : {exon:5} Step2: {text:kinase} Step5: {left:#4, right:#2} EnumParam FlatVocabParam AnswerParam StringParam DatasetParam TimestampParam Abs.EnumParam timestamp id list term list text raw step id timestamp user_dataset_id term list/hash text/hash dependent step id timestamp dataset_id term list/hash text/hash independent answer checksum quoted internal list quoted term list number/quoted text raw text an SQL to cache step_id an SQL to dataset values user_dataset_id timestamp internal wdk cache comp db dataset_indices clob_values clob_values wdkengine dataset_values steps user_datasets2 userlogins4

2. Params - New Step1 : {exon:6} Step2: {text:kinase} Step3: {left:#1:{exon:6}, right:#2:{text:kinase}} EnumParam FlatVocabParam AnswerParam StringParam DatasetParam TimestampParam Abs.EnumParam Dataset timestamp String[] text parsed Step timestamp dataset_id term list text stable step id timestamp content checksum sorted term list text signature answer checksum number/quoted text raw text quoted internal list quoted term list an SQL to cache step_id an SQL to dataset values dataset_id timestamp Internal wdk cache SELECT comp db datasets userlogins5 steps dataset_values

3. Proposed Changes • All params • Raw values will be a separate notion, and the raw values are processed into stable values before validation; • The validation happens on the stable values only; • Value transformations are done in ParamHandler; • Raw  Stable • Stable  Raw • Stable  Internal • Stable  Signature

4. Proposed Changes • AnswerParam • Include step version# in the value: 123:#1 • Needed for in-place step editing; • When a step is revised, it’ll notify next/parent steps to update the chekcksum in the values of the corresponding answerParam; • The update will be propagated back to root; • Boolean and other combined steps will be able to generate new cache with this. • StringParam • Store the original text in reference value, and into steps.display_params; • Skip compression/decompression, deprecate wdkengine.clob_values; • processQuestion.do creates step, and showSummary.do always expects a step_id

5. Proposed Changes • Enum/FlatVocabParam • Store the term list in reference value, into steps.display_params; • Avoid compression/decompression, deprecate wdkengine.clob_values; • processQuestion.do creates step, and showSummary.do always expects a step_id; • DatasetParam • Original raw value stored in wdkengine.dataset_indices; • Unchanged: user_datasets2 stores upload file name; • A type sub-param is passed in through context values • Sub-params • Method: post a list, upload file, basket, strategy • Type: types from parsers: • list of ids, WDK default • Gff • fasta • DatasetParser plugin framework • Properties: • parsers: a comma separated list of parser classes; • parser_name.prop_name: the parser name will be stripped from prop name, and the prop value will be set to each individual parser.