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Expressions in Janis #10

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wants to merge 141 commits into from
Closed

Expressions in Janis #10

wants to merge 141 commits into from

Commits on Jan 21, 2020

  1. Add operator class as test

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Commits on Jan 22, 2020

  1. Refactor selectors + add more to allow used as operators

    @illusional
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  2. Add when + replace Workflow.step tuple with StepOperator + fix effects

    @illusional
    illusional committed Jan 22, 2020
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  3. Add basic conditional translation for wdl + remember to bump wglgen vers

    @illusional
    illusional committed Jan 22, 2020
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  4. Add basic tests for new operators / conditionals functionality

    @illusional
    illusional committed Jan 22, 2020
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Commits on Jan 23, 2020

  1. Add specific check for bool in wdl translation

    @illusional
    illusional committed Jan 23, 2020
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  2. Quality syntax improvement in data_type isinstance check

    @illusional
    illusional committed Jan 23, 2020
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  3. Add more true receivedType for stdout + stderr (allow optional cascade)

    @illusional
    illusional committed Jan 23, 2020
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  4. Add conditionality => optional chaining to type system: inp/out override

    @illusional
    illusional committed Jan 23, 2020
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  5. Add basic "switch" concept for conditionals

    @illusional
    illusional committed Jan 23, 2020
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  6. Remove extra translate(wdl) statement

    @illusional
    illusional committed Jan 23, 2020
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  7. Return InputOperator by default from workflow for input node

    @illusional
    illusional committed Jan 23, 2020
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  8. Add test + skip for conditionals specific test

    @illusional
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  9. Move janis_unix import inside class

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Commits on Jan 24, 2020

  1. Rename "conditional" from "switch"

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Commits on Mar 23, 2020

  1. Merge branch 'master' into expressions 

    # Conflicts:
#	janis_core/types/selectors.py
#	janis_core/utils/__init__.py
#	janis_core/workflow/workflow.py
    @illusional
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  2. Remove first_element legacy arg from WildcardSelector 

    # Conflicts:
#	janis_core/types/selectors.py
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Commits on Mar 26, 2020

  1. Specify a translation should generically unwrap an expression

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  2. Add returntype to Selector to prepare for operator typing

    @illusional
    illusional committed Mar 26, 2020
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  3. Move logical operators to logical file

    @illusional
    illusional committed Mar 26, 2020
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  4. Move stringformatter to operators folder

    @illusional
    illusional committed Mar 26, 2020
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  5. Implement CWL required translation operator unwrap (half implemented)

    @illusional
    illusional committed Mar 26, 2020
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  6. Implement WDL required translation operator unwrap (half implemented)

    @illusional
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  7. Add UnionType to STRICTLY be used in operators (for now)

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  8. Add type var to 'first_value' to fix type suggestions

    @illusional
    illusional committed Mar 26, 2020
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  9. Fix imports due to recent refactor

    @illusional
    illusional committed Mar 26, 2020
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  10. Add _very_ basic tests for unions, many more required

    @illusional
    illusional committed Mar 26, 2020
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  11. Add standard library + basename operator

    @illusional
    illusional committed Mar 26, 2020
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  12. Migrate operator overloads to selector

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  13. Fix type annotation on UnionType + add AllType, NumericType

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  14. Migrate SingleValue, TwoValue operators to implement functional reqs

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  15. Make logical operators implement returntype and args per WDL / CWL rules

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  16. Migrate basename to use Operator instead of FunctionalOperator

    @illusional
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  17. Simplify workflow rewrap expression to just generic operator

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  18. Simplify WDL operator conversion to generic "Operator"

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  19. Implement unwrap_expression, doesn't translate operators yet

    @illusional
    illusional committed Mar 26, 2020
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  20. Fix tests

    @illusional
    illusional committed Mar 26, 2020
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Commits on Mar 27, 2020

  1. Merge branch 'master' into expressions

    @illusional
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  2. Modify StepTagInput to use selector instead of step node + string 

    Move scatter logic into Selector
    @illusional
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  3. Add IndexOperator + int indexing by a selector

    @illusional
    illusional committed Mar 27, 2020
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  4. Refactor workflow step to use Selector

    @illusional
    illusional committed Mar 27, 2020
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  5. Fix wdl translation to use returntype instead of stepnode collection

    @illusional
    illusional committed Mar 27, 2020
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Commits on Mar 30, 2020

  1. Basic (broken) WDL translation

    @illusional
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  2. Some test fixes (not finished yet)

    @illusional
    illusional committed Mar 30, 2020
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  3. Merge branch 'master' into expressions

    @illusional
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  4. Start to add rules to WDL translation re secondaries + scatter

    @illusional
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Commits on Apr 4, 2020

  1. Add cwlformatter to deps

    @illusional
    illusional committed Apr 4, 2020
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  2. Add transform operator

    @illusional
    illusional committed Apr 4, 2020
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  3. Add transform operator

    @illusional
    illusional committed Apr 4, 2020
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Commits on Apr 15, 2020

  1. Merge branch 'master' into expressions

    @illusional
    illusional committed Apr 15, 2020
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  2. Add IfThisOrElse operator

    @illusional
    illusional committed Apr 15, 2020
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  3. Fix bad type on CwlTranslator

    @illusional
    illusional committed Apr 15, 2020
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Commits on Apr 16, 2020

  1. Add more _get_instantiated_type calls

    @illusional
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  2. Cleanup minor log entry

    @illusional
    illusional committed Apr 16, 2020
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  3. Add echoTestTool for testing (copy of janis_unix)

    @illusional
    illusional committed Apr 16, 2020
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  4. Cleanup add wrt. string formatters 

    Added some different overrides for to_string_formatter,
though I do intend to deprecate this method
    @illusional
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  5. Fix type system when it experiences python literals

    @illusional
    illusional committed Apr 16, 2020
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  6. Ensure IfOrElse operator is unwrapping args

    @illusional
    illusional committed Apr 16, 2020
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  7. Apply similar type system treatment to Add operator

    @illusional
    illusional committed Apr 16, 2020
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  8. Add "IsDefined" operator

    @illusional
    illusional committed Apr 16, 2020
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  9. Fix TwoValueOperator translation

    @illusional
    illusional committed Apr 16, 2020
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  10. Fix cwl output translation param + add operator test

    @illusional
    illusional committed Apr 16, 2020
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  11. Ensure workflow.input returns an InputNodeSelector for consistency

    @illusional
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  12. Begin transition to use expressions on ToolOutput generation

    @illusional
    illusional committed Apr 16, 2020
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  13. Merge branch 'master' into expressions 

    # Conflicts:
#	janis_core/workflow/workflow.py
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Commits on Apr 17, 2020

  1. Adn id() to InputNodeSelector for convenience

    @illusional
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  2. Attempt new WDL implementation for output expressions 

    This has increased the complexity again, but I think I've simplified the process
for collecting the secondary files. There are cases I don't know how to handle
yet, but still working on them.
    @illusional
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  3. Start to fix tests

    @illusional
    illusional committed Apr 17, 2020
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  4. Fix test_workflow tests

    @illusional
    illusional committed Apr 17, 2020
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  5. Remove old commented out code

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  6. Allow the previous commit to function and not except early

    @illusional
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  7. Remove default from steptaginput

    @illusional
    illusional committed Apr 17, 2020
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  8. Rewrite WDL's translation of step node (big change) 

    Golly gosh this was a hard one, but I got it. Condensed the scattering and secondary logic into a shorter,
much more succinct block that still passes all the tests (so far).

Really, it was ensuring that the values are unwrapped correctly (essentially replace dotted_source with
`unwrap_expression` (as the input / stepoutput selectors are handled there) and rely on earlier Janis
checks to prohibit expressions when secondary files are involved.
    @illusional
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  9. Fix test per previous commit

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Commits on Apr 20, 2020

  1. Ensure WDL secondary inputs are mapped when input type is an array

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  2. Ensure output_name / output_tag works with revised InputNodeSelectors

    @illusional
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  3. Add type annotation to InputNodeSelector (maybe temporarily)

    @illusional
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  4. Add more test tools with secondary files

    @illusional
    illusional committed Apr 20, 2020
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  5. Feature parity with WDL

    @illusional
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  6. Remove optional value in stringformatter test

    @illusional
    illusional committed Apr 20, 2020
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  7. Minor quality refactor of WDL translation

    @illusional
    illusional committed Apr 20, 2020
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  8. Add "get_leaves()" to operator to get options required to alias

    @illusional
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  9. Rewrite CWL step translation to support initial operator aliasing

    @illusional
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Commits on Apr 21, 2020

  1. Refactor location of StringFormatter

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  2. Add basic abstract methods for StringFormatter (even though currently… 

    … it's stsrictly not an operator)
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  3. Fix tests from stringformatter location refactor

    @illusional
    illusional committed Apr 21, 2020
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  4. Add StepInput expression test for CWL

    @illusional
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  5. Refactor CWL stepinput expressions

    @illusional
    illusional committed Apr 21, 2020
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  6. Fix CWL array step input expressions

    @illusional
    illusional committed Apr 21, 2020
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  7. Migrate stepinput tests to WDL

    @illusional
    illusional committed Apr 21, 2020
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  8. Refactor IfThisOrElse to just "If" + token null support

    @illusional
    illusional committed Apr 21, 2020
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  9. Partly introduce JoinOperator 

    Waiting on openwdl/wdl#362 for more
information about how to join(array, "sep") in WDL command block.
    @illusional
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  10. Add partial validation to Operator args (no typecheck yet)

    @illusional
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  11. Add WDL test for separator (when sep function is clairifed)

    @illusional
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Commits on Apr 22, 2020

  1. Fix tests from next commit

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  2. Generalise translate methods to accept a "Tool" (instead of just work… 

    …flow)
    @illusional
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Commits on Apr 23, 2020

  1. Merge branch 'master' into expressions 

    # Conflicts:
#	janis_core/tests/test_translation_cwl.py
#	janis_core/tests/test_translation_wdl.py
#	janis_core/translations/cwl.py
#	janis_core/translations/translationbase.py
#	janis_core/translations/wdl.py
#	janis_core/utils/__init__.py
    @illusional
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  2. Add workflow input default expression to WDL 

    Still a bit more complicated for CWL
    @illusional
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  3. Fix tests

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Commits on Apr 28, 2020

  1. Add implementation for WDL join operator

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  2. Merge branch 'master' into expressions 

    # Conflicts:
#	janis_core/tool/commandtool.py
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  3. Merge branch 'master' into expressions

    @illusional
    illusional committed Apr 28, 2020
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  4. Add default for sep function call

    @illusional
    illusional committed Apr 28, 2020
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Commits on Apr 30, 2020

  1. Fix quoting in WDL

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Commits on May 1, 2020

  1. Merge branch 'master' into expressions 

    # Conflicts:
#	janis_core/tests/test_translation_cwl.py
#	janis_core/tests/test_translation_wdl.py
#	janis_core/tests/testtools.py
#	janis_core/translations/cwl.py
#	janis_core/translations/wdl.py
#	janis_core/types/common_data_types.py
    @illusional
    illusional committed May 1, 2020
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  2. Fix extra bracket in WDL commandline formatting

    @illusional
    illusional committed May 1, 2020
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  3. How about actually generating real CWL kthanks

    @illusional
    illusional committed May 1, 2020
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  4. Try again lol

    @illusional
    illusional committed May 1, 2020
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  5. Fix selectfirst

    @illusional
    illusional committed May 1, 2020
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  6. Add more checks for WDL

    @illusional
    illusional committed May 1, 2020
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  7. Keep committing until it works

    @illusional
    illusional committed May 1, 2020
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Commits on May 6, 2020

  1. Merge branch 'master' into expressions

    @illusional
    illusional committed May 6, 2020
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  2. Merge branch 'master' into expressions 

    # Conflicts:
#	janis_core/translations/wdl.py
#	janis_core/types/common_data_types.py
    @illusional
    illusional committed May 6, 2020
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Commits on May 7, 2020

  1. Merge branch 'master' into expressions 

    # Conflicts:
#	janis_core/translations/wdl.py
#	janis_core/types/common_data_types.py
    @illusional
    illusional committed May 7, 2020
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  2. Allow selector as workflow inpt default for CWL

    @illusional
    illusional committed May 7, 2020
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  3. Remove duplicated code + fix shell quoting flag

    @illusional
    illusional committed May 7, 2020
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  4. Pin wdlgen to higher version

    @illusional
    illusional committed May 7, 2020
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  5. Fix codetool exception handling

    @illusional
    illusional committed May 7, 2020
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  6. Fix WDL command line binding

    @illusional
    illusional committed May 7, 2020
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  7. Fix pythontool test

    @illusional
    illusional committed May 7, 2020
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  8. Merge branch 'master' into expressions 

    # Conflicts:
#	janis_core/translations/cwl.py
    @illusional
    illusional committed May 7, 2020
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Commits on May 8, 2020

  1. Add test_string_formatter for stepinput cwl

    @illusional
    illusional committed May 8, 2020
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  2. Introduce more operators

    @illusional
    illusional committed May 8, 2020
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Commits on May 11, 2020

  1. Fix a whole bunch of test that started breaking 

    They should've been breaking before...
    @illusional
    illusional committed May 11, 2020
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Commits on May 18, 2020

  1. Merge branch 'master' into expressions 

    # Conflicts:
#	janis_core/tests/test_translation_wdl.py
#	janis_core/translations/cwl.py
#	janis_core/translations/wdl.py
#	setup.py
    @illusional
    illusional committed May 18, 2020
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Commits on May 19, 2020

  1. Remove traceback logging

    @illusional
    illusional committed May 19, 2020
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  2. Add friendly_signature to operators

    @illusional
    illusional committed May 19, 2020
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Commits on May 20, 2020

  1. Add friendly_signature for stringformatter

    @illusional
    illusional committed May 20, 2020
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  2. Fix CWL test because cwlgen changed

    @illusional
    illusional committed May 20, 2020
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Commits on May 21, 2020

  1. Merge branch 'master' into expressions 

    # Conflicts:
#	janis_core/tests/test_translation_cwl.py
    @illusional
    illusional committed May 21, 2020
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Commits on May 26, 2020

  1. Merge branch 'master' into expressions 

    # Conflicts:
#	janis_core/graph/steptaginput.py
#	janis_core/tests/test_translation_cwl.py
#	janis_core/tests/test_translation_wdl.py
#	janis_core/translations/cwl.py
#	janis_core/translations/wdl.py
#	janis_core/workflow/workflow.py
#	setup.py
    @illusional
    illusional committed May 26, 2020
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  2. Allow tools to specify operators for cpu/memory

    @illusional
    illusional committed May 26, 2020
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  3. Allow tools to specify operators for cpu/memory

    @illusional
    illusional committed May 26, 2020
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Commits on May 28, 2020

  1. Fix CWL output collection with stringformatter

    @illusional
    illusional committed May 28, 2020
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  2. Fix secondaryFiles pattern generation (to be an array)

    @illusional
    illusional committed May 28, 2020
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Commits on Jun 1, 2020

  1. Merge branch 'master' into expressions 

    # Conflicts:
#	janis_core/tool/commandtool.py
#	janis_core/translations/cwl.py
    @illusional
    illusional committed Jun 1, 2020
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Commits on Jun 2, 2020

  1. Merge branch 'master' into expressions

    @illusional
    illusional committed Jun 2, 2020
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Commits on Jun 5, 2020

  1. Fix array separation for non-quoted values

    @illusional
    illusional committed Jun 5, 2020
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Commits on Jun 9, 2020

  1. Merge branch 'master' into expressions

    @illusional
    illusional committed Jun 9, 2020
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Commits on Jun 10, 2020

  1. Add ReadContentsOperator for WDL 

    (implementation for CWL still in testing)
    @illusional
    illusional committed Jun 10, 2020
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  2. Add requires_contents for CWL

    @illusional
    illusional committed Jun 10, 2020
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