Code

Add validate operation#691

Code

Merged

jamesaoverton merged 120 commits intomasterontodev/robot:masterfrom add_validate_operationontodev/robot:add_validate_operationCopy head branch name to clipboardAug 14, 2020

+4,210-112

Commits

Commits on Jun 16, 2019

• add stub for ValidateImmPort command

  

  Michael Cuffaro

  committed
  83d5517

• change stub of ValidateImmPort so that it accepts a JSON file as an argument. The eventual implementation will either get its input through the local filesystem or through ImmPort (either by direct…

  Show description for a71dfca
  

  Michael Cuffaro

  committed
  a71dfca

• add stub of a unit test for ValidateImmPortOperation

  

  Michael Cuffaro

  committed
  3840d63

• Merge branch 'master' into representing_immune_exposures

  

  Michael Cuffaro

  committed
  4d1ec38

• add comments etc.

  

  Michael Cuffaro

  committed
  c4f7c52

Commits on Jun 18, 2019

• rename ValidateImmPortOperation and ValidateImmPortCommand to ValidateOperation and ValidateCommand

  

  Michael Cuffaro

  committed
  4f6f60f

• change input parameter of validate operation to be a CSV instead of a JSON file

  

  Michael Cuffaro

  committed
  1c03979

Commits on Jun 19, 2019

• accept OWL file as input in addition to CSV file

  

  Michael Cuffaro

  committed
  59c605e

Commits on Jun 20, 2019

• pass reasonerFactory to validate() methof

  

  Michael Cuffaro

  committed
  adac33c

• pick out ancestor and validation column from CSV

  

  Michael Cuffaro

  committed
  4e27e13

Commits on Jul 3, 2019

• implement validation, but no writing of CSV data yet

  

  Michael Cuffaro

  committed
  9de6677

• implement csv output for validate operation

  

  Michael Cuffaro

  committed
  adf59df

• remove checks against column width, since this can be safely assumed to have been checked at the time this method is called

  

  Michael Cuffaro

  committed
  7f6bd33

Commits on Jul 4, 2019

• add unit test for validate operation

  

  Michael Cuffaro

  committed
  0e00fbf

• Merge branch 'master' into add_validate_operation

  

  Michael Cuffaro

  committed
  eb19004

Commits on Jul 30, 2019

• add immune exposures owl ontology validation

  

  Michael Cuffaro

  committed
  b803ba4

Commits on Jul 31, 2019

• small refactoring

  

  Michael Cuffaro

  committed
  659dc5b

• add immune exposures ncbi taxonomy validation

  

  Michael Cuffaro

  committed
  2d4e91c

Commits on Aug 3, 2019

• remove direct ncbi taxonomy references and add logic for retrieving and parsing a template row from the csv data

  

  Michael Cuffaro

  committed
  e788202

• add template row to csv

  

  Michael Cuffaro

  committed
  13dced3

Commits on Aug 4, 2019

• refactor code and merge different validation types

  

  Michael Cuffaro

  committed
  6f7c782

Commits on Aug 5, 2019

• Merge branch 'master' into add_validate_operation

  

  Michael Cuffaro

  committed
  b818aa9

Commits on Aug 7, 2019

• refactor code and remove some unneeded features (no "type" rule or "sc-label", "sc-iri" rules, etc. just "sc"). For a given cell, we now determine whether it is a label or iri on the fly.

  

  Michael Cuffaro

  committed
  f2e52ea

• update owl and csv files

  

  Michael Cuffaro

  committed
  9311d56

Commits on Aug 8, 2019

• refactor

  

  Michael Cuffaro

  committed
  f3c4258

• implement 'same-as' rule and add row and column number to error messages

  

  Michael Cuffaro

  committed
  7ebaab8

• add 'same-as' rules to csv

  

  Michael Cuffaro

  committed
  2b1701c

• make output better

  

  Michael Cuffaro

  committed
  8f1ac37

Commits on Aug 15, 2019

• add the beginnings of a validate_axioms() method to the ValidateOperation class

  

  Michael Cuffaro

  committed
  78e7355

Commits on Aug 16, 2019

• make row index and column index into static variables of the ValidateOperation class, and change naming convention: all static members of ValidateOperation (methods and variables) are named using u…

  Show description for ed12a54
  

  Michael Cuffaro

  committed
  ed12a54

• partially implement 'has-axiom' rule (with direct descendant query hard-coded)

  

  Michael Cuffaro

  committed
  d779b9b

• partially implement capability to handle different query types

  

  Michael Cuffaro

  committed
  15e64dc

• partially implement capability to handle different query types (commit csv and owl files)

  

  Michael Cuffaro

  committed
  39c3414

Commits on Aug 17, 2019

• Merge branch 'master' into add_validate_operation

  

  Michael Cuffaro

  committed
  b8372ec

• implement all other DL query types

  

  Michael Cuffaro

  committed
  3aaecfa

Commits on Aug 26, 2019

• make the following changes:

  Show description for 4f6ba0c
  

  Michael Cuffaro

  committed
  4f6ba0c

• add more representative rows to docs/examples/immune_exposures.csv

  

  Michael Cuffaro

  committed
  31d63ba

Commits on Aug 27, 2019

• Merge branch 'master' into add_validate_operation

  

  Michael Cuffaro

  committed
  bccb370

Commits on Aug 28, 2019

• Update immune exposure examples

  jamesaoverton

  committed
  c8d1b6f

Commits on Sep 3, 2019

• implement conditional command (still a work in progress) plus some small refactoring and optimisation

  

  Michael Cuffaro

  committed
  31cc6ba

• refactor code between validate_rule and execute_query, make when-clause regex capturing more greedy, and use HermiT reasoner instead of ELK

  

  Michael Cuffaro

  committed
  70ef206

• remove old required rule

  

  Michael Cuffaro

  committed
  47f8652

Commits on Sep 4, 2019

• add the new version of the 'required' rule, add an 'excluded' rule that is the opposite of required, allow the 'writeout' function to behave like the String.format() function

  

  Michael Cuffaro

  committed
  5839643

• in when clause, allow a colon after the rule type, and make form of all calls to 'writeout' consistent

  

  Michael Cuffaro

  committed
  e386df6

Commits on Sep 13, 2019

• implement rule types and rules required to capture 'representing immune exposures' document

  

  Michael Cuffaro

  committed
  373b342

Commits on Sep 14, 2019

• implement rule types and rules required to capture 'representing immune exposures' document, second part of commit

  

  Michael Cuffaro

  committed
  bb80401

• add wrapper around logger

  

  Michael Cuffaro

  committed
  6e06371

• reorganise code in ValidateOperation.java

  

  Michael Cuffaro

  committed
  fbfa990

Commits on Sep 15, 2019

• improve logging and output

  

  Michael Cuffaro

  committed
  3317269

Commits on Sep 16, 2019

• do quoting properly during interpolation

  

  Michael Cuffaro

  committed
  85dcb15

Commits on Sep 20, 2019

• replace ManchesterSyntaxTool with ManchesterOWLSyntaxClassExpressionParser, change rule syntax slightly (no more colons after rule type directives), make true the implicit rule for is-required and …

  Show description for de88a8d
  

  Michael Cuffaro

  committed
  de88a8d

• add more documentation, add back the logging enum

  

  Michael Cuffaro

  committed
  b116a18

Commits on Sep 21, 2019

• check all sub-ruletypes and not just the primary one when parsing a when-clause

  

  Michael Cuffaro

  committed
  9b15556

Commits on Sep 26, 2019

• add unit test for validate operation and format code according to google style

  

  Michael Cuffaro

  committed
  4e31428

• move validate documentation from the source file to its own markdown in the docs directory, and use the new interface to HermiT

  

  Michael Cuffaro

  committed
  9577377

• Merge branch 'master' into add_validate_operation

  

  Michael Cuffaro

  committed
  cdec19d

Commits on Sep 29, 2019

• allow individual data cells to have multiple data elements separated by pipes ('|')

  

  Michael Cuffaro

  committed
  f9a95dd

• change name of method wildcard_to_label() to get_wildcard_contents() and don't automatically convert wildcard contents to a label

  

  Michael Cuffaro

  committed
  17823fd

• refactoring: put when-clause evaluation into its own function

  

  Michael Cuffaro

  committed
  89d32d9

• determine class expression before calling execute_query() instead of after

  

  Michael Cuffaro

  committed
  e34152d

Commits on Oct 1, 2019

• refactor in preparation for generalised query handling

  

  Michael Cuffaro

  committed
  4303a29

• add logic for executing queries over generalised class expressions in data cells

  

  Michael Cuffaro

  committed
  f52b921

Commits on Oct 4, 2019

• add more documentation and touch-up code

  

  Michael Cuffaro

  committed
  0f3ea10

• add new immune_exposures.csv file to test/resources/

  

  Michael Cuffaro

  committed
  3031e54

• update markdown for validate command

  

  Michael Cuffaro

  committed
  f952380

Commits on Oct 10, 2019

• add excel output capability (code is in need of cleanup)

  

  Michael Cuffaro

  committed
  2c3e9a2

• fix unit test for ValidateOperation that got broken after the previous commit

  

  Michael Cuffaro

  committed
  733fa68

Commits on Oct 11, 2019

• optimization: don't auto-size a column everytime you add a cell

  

  Michael Cuffaro

  committed
  807a5fa

• add header columns to xlsx output

  

  Michael Cuffaro

  committed
  84c72d2

Commits on Oct 13, 2019

• code cleanup and documentation

  

  Michael Cuffaro

  committed
  0225d45

Commits on Oct 14, 2019

• rename command line options (--owl -> --input, --csv -> --table) and make reasoner configurable via the --reasoner option

  

  Michael Cuffaro

  committed
  4c4fc8f

• gracefully handle exceptions thrown by reasoners that are thrown by reasoners that do not support the isEntailed() operation needed for validating generalised class expressions

  

  Michael Cuffaro

  committed
  10f07a1

Commits on Oct 18, 2019

• add support for chaining to validate

  

  Michael Cuffaro

  committed
  f523807

Commits on Oct 20, 2019

• add section on error messages to validate documentation

  

  Michael Cuffaro

  committed
  05a6415

• add invalide presence rule error to validation documentation

  

  Michael Cuffaro

  committed
  1634765

• add column out of range error to validate doc

  

  Michael Cuffaro

  committed
  c68fff5

• add no main error to validate doc

  

  Michael Cuffaro

  committed
  512e6ad

• add malformed when clause error to validate doc

  

  Michael Cuffaro

  committed
  1fd5d1a

• add invalid when rule type error to validate doc

  

  Michael Cuffaro

  committed
  f0778aa

• add unrecognized rule type error and unrecognized query type error to validate doc

  

  Michael Cuffaro

  committed
  61875c5

• add more errors to documentation for validate command

  

  Michael Cuffaro

  committed
  c311947

• use robot's internal exception handling mechanism when reporting certain critical errors

  

  Michael Cuffaro

  committed
  6bab1c8

• Merge branch 'master' into add_validate_operation

  

  Michael Cuffaro

  committed
  f10c617

Commits on Nov 28, 2019

• Merge branch 'master' into add_validate_operation

  

  Michael Cuffaro

  committed
  b055d0c

Commits on Dec 12, 2019

• add ability to generate an HTML version of the validation report

  

  Michael Cuffaro

  committed
  2abc3da

Commits on Dec 20, 2019

• when writing to a HTML report, convert any named objects within cells to hyperlinks

  

  Michael Cuffaro

  committed
  b8a4116

Commits on Jan 14, 2020

• refactor interpolation logic, improve html output, allow multi-cells as the targets of rules

  

  Michael Cuffaro

  committed
  9b172e1

Commits on Jan 22, 2020

• change command line syntax for validate; allow multiple table files to be specified, and instead of an output file specify an output directory and a format option.

  

  Michael Cuffaro

  committed
  da4159b

• small change to usage message that should have been in with the last commit

  

  Michael Cuffaro

  committed
  eb99c9f

• Merge branch 'master' into add_validate_operation

  

  Michael Cuffaro

  committed
  6b9b193

Commits on Jan 25, 2020

• refactor ValidateOperation into a static part representing the operation and a dynamic part representing each validation instance corresponding to a particular table to be validated.

  

  Michael Cuffaro

  committed
  6ebd8d5

• add [--skip-row k] option to the validate command, for to skip the kth row of a table when validating it

  

  Michael Cuffaro

  committed
  f191b2d

Commits on Jan 27, 2020

• do not generate html links for columns that do not contain query-type rules, and ignore values of --skip-row that are less than 1

  

  Michael Cuffaro

  committed
  7ba9b35

Commits on Jan 28, 2020

• in output to STDOUT, when writing the table name, only write the basename and extension and not the full path

  

  Michael Cuffaro

  committed
  37ada05

Commits on Jan 29, 2020

• add integration tests for validate operation

  

  Michael Cuffaro

  committed
  023d9d7

• update documentation for validate: add doc relating to multi-cells

  

  Michael Cuffaro

  committed
  319967c

• fix markdown problem in validate.md

  

  Michael Cuffaro

  committed
  638744e

Commits on Feb 17, 2020

• fix bugs: 1) IndexOutOfBoundsError when parsing rows that have less columns than the header columns, even if the last header columns are empty, 2) NullPointerException for rules with '|' in method …

  Show description for 5d4a9cd
  

  Michael Cuffaro

  committed
  5d4a9cd

• Merge branch 'master' into add_validate_operation

  

  Michael Cuffaro

  committed
  53de60e

Commits on Apr 16, 2020

• Merge branch 'master' into add_validate_operation

  

  rctauber

  committed
  27f86da

Commits on May 12, 2020

• Update validate to use export code

  

  rctauber

  committed
  231206c

• Fix rendering of HTML links, column headers

  

  rctauber

  committed
  5c234a6

• Merge branch 'master' into add_validate_operation

  

  rctauber

  committed
  e9cc471

• Update CHANGELOG

  

  rctauber

  committed
  8a2bca5

• Add java docs

  

  rctauber

  committed
  3c2a15d

• Remove unneeded changes to robot-command pom

  

  rctauber

  committed
  2111cb2

• Remove unneeded pom additions

  

  rctauber

  committed
  3f720e6

Commits on Jun 26, 2020

• Add better logging, fail on any rule violations

  

  rctauber

  committed
  703f840

• Add new options to README

  

  rctauber

  committed
  d60b690

Commits on Jun 27, 2020

• Add not options

  

  rctauber

  committed
  0063335

Commits on Jun 28, 2020

• Rework docs, fix examples, fix HTML formatting/tooltips

  

  rctauber

  committed
  933f270

• Add other not statements

  

  rctauber

  committed
  121f340

Commits on Jun 29, 2020

• Add option to write all files, clarify docs

  

  rctauber

  committed
  4ee2864

Commits on Jul 28, 2020

• Add --errors option to validate

  

  rctauber

  committed
  66bd568

• Update docs & add unit test for A1 notation

  

  rctauber

  committed
  34b5658

Commits on Aug 3, 2020

• Change rule name to be more descriptive

  

  rctauber

  committed
  62b5c88

Commits on Aug 10, 2020

• Merge branch 'master' into add_validate_operation

  

  rctauber

  committed
  3aaefc1

Commits on Aug 11, 2020

• Small fixes based on feedback

  

  rctauber

  committed
  17c3d4e

• Fix standalone in docs

  

  rctauber

  committed
  647065b

Commits on Aug 12, 2020

• Fix reporting row numbers after skipping

  

  rctauber

  committed
  fa728ce