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Associated with worksheet/table

• Incorrect links to column oriented worksheets.
  • For example, in worksheet 19 of h1_hesc KB /xl/worksheets/sheet19.xml 'Cell'!$B$0:$XFD$0 should be 'Cell'!$B$1:$XFD$1

    <dataValidation type="list" errorStyle="warning" allowBlank="1" showInputMessage="1" showErrorMessage="1" errorTitle="Cell" error="Value must be a value from &quot;Cell:0&quot; or blank." promptTitle="Cell" prompt="Select a value from &quot;Cell:0&quot; or blank." sqref="B1:B2">
      <formula1>'Cell'!$B$0:$XFD$0</formula1>
    </dataValidation>
    

• Incorrect links to parent models which are represented by multiple worksheets. For example,
  • Reference to "Polymer species types" from "Polymer" column of "Genes" worksheet. This should not reference a worksheet because PolymerSpeciesType is a parent class which is represented by multiple worksheets.

Table header: \n!!SBtab ... \n

Example:

!!SBtab   TableID='def_table' SBtabVersion='1.0' TableType='Definition'   TableName='Allowed_types'

... if they make sense

If you want this feature, please provide a use case to motivate this

while very handy, pprint() produces too much output. filter it.

• Allow unused columns not to be printed
• Check that unprinted columns all have None values

See example problem Andrew encountered and I debugged.

Add a test of ParsedExpression.__prep_expr_for_tokenization() to obj_model/tests/test_expression.py. It's covered because it's always called, but the substitutions it makes need to be tested.

ILLEGAL_TOKENS_NAMES --> LEGAL_TOKENS_NAMES

• Add attribute to obj_model.Model.Meta to define column groupings and the heading for the group
• Export additional row with merged cells that are headings for multiple individual columns
• Update Excel import

consider this code:

is_attr = False
for base in bases:
    if attr_name in dir(base):
        is_attr = True

this code is risky, because dir(base) may contain a string that matches attr_name
but is not an attribute inherited from base. E.g., the name of a method could match.
a better approach would be to directly check whether attr_name is an attribute of a base that is an obj_model.core.Models. namespace doesn't have the same problem.

add migrate commands to H1 & Mp
remove branch from Git metadata
expose the optional locations for migrated files
obtain schema commit metadata from pip installed package
detect erroneous schema changes file annotations
ensure that the Git version of a data file is a sentinel commit
enforce this invariant: each sentinel commit must be identified by one schema changes file

In the return values of obj_model.io.get_fields(), what's the difference between attrs
& sub_attrs? Docs say:

    :obj:`list` of :obj:`Attribute`: attributes in the order they should be printed
    :obj:`list` of tuple of :obj:`Attribute`: attributes in the order they should be printed

A modeler writing a wc_lang spreadsheet might have trouble fixing this error:

   ValueError: The model cannot be loaded because '2_species_1_reaction.xlsx' contains error(s):
  Taxon
    The attributes must be defined in this order:
      Id
      Name
      Rank
      Comments
      References
  Submodel
    The attributes must be defined in this order:
      Id
      Name
      Algorithm
      Compartment
      Biomass reaction
      Objective function
      Comments
      References
  Compartment
    The attributes must be defined in this order:
      Id
      Name
      Initial volume
      Comments
      References
  SpeciesType
    The attributes must be defined in this order:
      Id
      Name
      Structure
      Empirical formula
      Molecular weight
      Charge
      Type
      Comments
      References
  Observable
    The attributes must be defined in this order:
      Id
      Name
      Species
      Observables
      Comments
  Function
    The attributes must be defined in this order:
      Id
      Name
      Expression
      Comments
  StopCondition
    The attributes must be defined in this order:
      Id
      Name
      Expression
      Comments
  Reference
    The attributes must be defined in this order:
      Id
      Name
      Title
      Author
      Editor
      Year
      Type
      Publication
      Publisher
      Series
      Volume
      Number
      Issue
      Edition
      Chapter
      Pages
      Comments

my file "Cash transactions 2017" is a counter-example

Generates

            decoded = {}
            for json_obj in json_objs:
>               model = models_by_name[json_obj['__type']]
E               KeyError: 'DataRepoMetadata'

Hi Jonathan

In def set_value(self, obj, new_value), at ../obj_model/obj_model/core.py:3884: ValueError
an example error looks like:
ValueError: Attribute '<wc_lang.core.RateLaw object at 0x7fbb31678a58>' of '<wc_lang.core.RateLawEquation object at 0x7fbb31678b00>' must be None

I think it would be better if the first value was the string value of the attribute and the 2nd was something like the classname, id and name of the Model.
Thanks

Features

• traverse object graph in only one direction
• filter related objects by attributes

Example:

• Get DOIs of all nested references of a gene in a knowledge base
  • Get all nested objects
  • Filter for objects of type Identifier
  • Filter for namespace = DOI

ensure that subclasses of MigrationWrapper satisfy its method signatures type-checking statically with typing and using mypy.api to verify subclasses

Potentially use RestrictedPython when there is more documentation to understand how to use it.

Class methods

• cls.get_related_attributes() - returns names of all RelatedAttributes of the class
• cls.get_scalar_attributes() - returns all LiteralAttributes of the class
• cls.get_attributes() - returns names of all Attributes
• cls.get_related_name(attribute) - for a given RelatedAttribute of this class, get the related name

Instance methods

• self.get_empty_scalar_attributes() - returns LiteralAttributes that are set to None
• self.get_nonempty_scalar_attributes() - opposite of above
• self.get_empty_related_attributes() - returns RelatedAttributes that are set to None or []
• self.get_nonempty_related_attributes() - opposite of above

Check that all sheets and columns are provided

the line return self.default_cleaned_value() in

        if isinstance(self.default_cleaned_value, (
                six.types.FunctionType, six.types.MethodType, six.types.LambdaType)):
            return self.default_cleaned_value()

looks wrong. default_cleaned_value isn't defined as a function anywhere.

don't have time to investigate now.

• SlugAttribute --> custom
• IntAttribute --> Whole number (min, max)
• FloatAttribute --> Decmial (min, max)
• OneToOneAttribute --> List
• ManyToOneAttribute --> List
• DateAttribute --> Date
• TimeAttribute --> Time
• EnumAttribute --> List

Stored Models, such as spreadsheets and delimited files on disk, can become incompatible with updates to model definitions in obj_model. Create a utility that migrates stored models to be compatible with a modified model. E.g., Django has a migration utility, which was originally called fabric.

Verify that attribute_order is a tuple (or at least not a string) so that a model definition like this

class A(obj_model.Model):
    id = SlugAttribute()

    class Meta(obj_model.Model.Meta):
        attribute_order = ('id')

does not return an incomprehensible error like this:

                    raise ValueError("`attribute_order` must contain attribute names; '{}' not found in "
>                                    "attributes of {}".format(attr_name, name))
E                   ValueError: `attribute_order` must contain attribute names; 'i' not found in attributes of A

Listed in decreasing order of my subjective assessment of importance

0. avoid need for obj_model.core.ModelMeta.CHECK_SAME_RELATED_ATTRIBUTE_NAME by comparing related models by value, not name
1. use Model.revision to label git commit of wc_lang and automatically migrate models to current schema and report inconsistency between a schema and model file
2. move generate_wc_lang_migrator() to wc_lang
3. provide a well-documented example
4. YAML config examples with multiple existing_files and multiple migrated_files
5. use deepcopy on obj_model.ontology.OntologyAttribute attributes when deepcopy of pronto terms works
6. associate schema pairs with renaming maps
7. separately specified default value for attribute
8. improve performance of test_migration
9. obtain sort order of sheets in existing model file and replicate in migrated model file
10. confirm migration works for json, etc.
11. test sym links in Migrator.parse_module_path
12. use PARSED_EXPR everywhere applicable

http://www.igordejanovic.net/textX/

Unless a user knows that this problem is possible, they're unlikely to be able to debug it.

Sphinx generates 21 WARNINGs.