Code

WIP: 0.9#432

Code

Merged

tyarkoni merged 116 commits intomasterbids-standard/pybids:masterfrom sqlalchemybids-standard/pybids:sqlalchemyCopy head branch name to clipboardMay 14, 2019

+2,628-1,526

Commits

Commits on Mar 21, 2019

• Merge branch 'enh-sorted' of https://github.com/yarikoptic/pybids into yarikoptic-enh-sorted

  tyarkoni

  committed
  f9b651e

  Copy full SHA for f9b651e

Commits on Mar 27, 2019

• update authors/affils

  tyarkoni

  committed
  1bd8ecc

  Copy full SHA for 1bd8ecc

• WIP: add sqlalchemy models

  tyarkoni

  committed
  4f98a07

  Copy full SHA for 4f98a07

Commits on Mar 28, 2019

• first partially working solution

  tyarkoni

  committed
  a050b95

  Copy full SHA for a050b95

• fix dtype handling in Tag init

  tyarkoni

  committed
  e272021

  Copy full SHA for e272021

• load or create database on Layout init

  tyarkoni

  committed
  d05b1ba

  Copy full SHA for d05b1ba

• make SQLAlchemy session globally accessible

  tyarkoni

  committed
  835bd7c

  Copy full SHA for 835bd7c

• add Config SQLAlchemy model

  tyarkoni

  committed
  0187bfe

  Copy full SHA for 0187bfe

• test Config model

  tyarkoni

  committed
  b8f3a7f

  Copy full SHA for b8f3a7f

• add Scope model

  tyarkoni

  committed
  4d9d441

  Copy full SHA for 4d9d441

• fix relationships

  tyarkoni

  committed
  d55c1f2

  Copy full SHA for d55c1f2

• placeholder test for Scope

  tyarkoni

  committed
  2a18a40

  Copy full SHA for 2a18a40

• temporarily replace core classes with SQLAlchemy models

  tyarkoni

  committed
  c0ceb5e

  Copy full SHA for c0ceb5e

Commits on Mar 29, 2019

• kill old classes and restructure modules

  tyarkoni

  committed
  ee925ae

  Copy full SHA for ee925ae

• various fixes

  tyarkoni

  committed
  5947faa

  Copy full SHA for 5947faa

• make sure dtypes are represented as strings before serialization

  tyarkoni

  committed
  5b1273a

  Copy full SHA for 5b1273a

• index metadata

  tyarkoni

  committed
  c326f47

  Copy full SHA for c326f47

• update get_file to work with DB models

  tyarkoni

  committed
  3f7860c

  Copy full SHA for 3f7860c

Commits on Apr 8, 2019

• add JSON handling to Tag; fix dtype conversion

  tyarkoni

  committed
  c560bba

  Copy full SHA for c560bba

• ~working reimplementation of get() method

  tyarkoni

  committed
  3805e8f

  Copy full SHA for 3805e8f

• fix model tests

  tyarkoni

  committed
  d57452c

  Copy full SHA for d57452c

• fix failing test and temporarily comment out unimplemented test

  tyarkoni

  committed
  1e30148

  Copy full SHA for 1e30148

Commits on Apr 9, 2019

• comment out MetadataIndex and make sure session gets passed to Config.load()

  tyarkoni

  committed
  6e9997a

  Copy full SHA for 6e9997a

• add extension entity

  tyarkoni

  committed
  69953d6

  Copy full SHA for 69953d6

• fixes to indexing

  tyarkoni

  committed
  6e18c55

  Copy full SHA for 6e18c55

• update get_metadata to query the DB

  tyarkoni

  committed
  1135d5c

  Copy full SHA for 1135d5c

• track whether BIDSFiles are directories

  tyarkoni

  committed
  c91c0bf

  Copy full SHA for c91c0bf

• return existing Config from .load() if one exists

  tyarkoni

  committed
  259c27a

  Copy full SHA for 259c27a

• mostly working purely DB-based implementation

  tyarkoni

  committed
  38a4cbd

  Copy full SHA for 38a4cbd

• improved efficiency in to_df() and added metadata flag

  tyarkoni

  committed
  0df3f8d

  Copy full SHA for 0df3f8d

• remove Scope model in favor of multiple-DB solution

  tyarkoni

  committed
  4c22cc1

  Copy full SHA for 4c22cc1

• add in_scope method to determine if layout is in passed scope

  tyarkoni

  committed
  ce03f4b

  Copy full SHA for ce03f4b

• add test of _in_scope

  tyarkoni

  committed
  e79c5d5

  Copy full SHA for e79c5d5

Commits on Apr 10, 2019

• fix _get_layouts_in_scope()

  tyarkoni

  committed
  97fc7fe

  Copy full SHA for 97fc7fe

• reorder attributes and populate .entities from database

  tyarkoni

  committed
  b8c12a1

  Copy full SHA for b8c12a1

• add getters for files and entities

  tyarkoni

  committed
  263a08f

  Copy full SHA for 263a08f

• .entities and .files should have maximal scope by default

  tyarkoni

  committed
  d8f8629

  Copy full SHA for d8f8629

• collect results from all in-scope layouts

  tyarkoni

  committed
  b5d6183

  Copy full SHA for b5d6183

• extensions --> extension

  tyarkoni

  committed
  a99be43

  Copy full SHA for a99be43

• allow leading periods in extension filter for backwards compatibility

  tyarkoni

  committed
  836880d

  Copy full SHA for 836880d

• fix get_metadata--return values, not file paths

  tyarkoni

  committed
  a38169a

  Copy full SHA for a38169a

• fix metadata indexing

  tyarkoni

  committed
  d5a707f

  Copy full SHA for d5a707f

• disallow list values when regex search is enabled

  tyarkoni

  committed
  80af17b

  Copy full SHA for 80af17b

• add regexp function and handle list values

  tyarkoni

  committed
  eb0511d

  Copy full SHA for eb0511d

• fix tests

  tyarkoni

  committed
  11bcd71

  Copy full SHA for 11bcd71

• fix get_file query

  tyarkoni

  committed
  df0ef7b

  Copy full SHA for df0ef7b

• don't test copying until we figure out what to do about it

  tyarkoni

  committed
  bd59381

  Copy full SHA for bd59381

• BIDSFiles no longer have access to layout, so update __repr__

  tyarkoni

  committed
  a682ec5

  Copy full SHA for a682ec5

• replace .metadata property with get_metadata(), and fix DB call

  tyarkoni

  committed
  3268893

  Copy full SHA for 3268893

• fix get_nearest by making 'extension' default for ignore_strict_entities

  tyarkoni

  committed
  183add1

  Copy full SHA for 183add1

• eager load Tag and Entity associations in get() otherwise we have session management issues

  tyarkoni

  committed
  db35c2c

  Copy full SHA for db35c2c

• add warning in case derivatives were requested but none were found

  tyarkoni

  committed
  d9091b6

  Copy full SHA for d9091b6

• fix force indexing--make sure arg is passed to indexing

  tyarkoni

  committed
  80a48e6

  Copy full SHA for 80a48e6

• fixes to test_core, even though it's going to disappear soon

  tyarkoni

  committed
  c3e3af5

  Copy full SHA for c3e3af5

• drop metadata index tests now that there's no metadata index

  tyarkoni

  committed
  4510e93

  Copy full SHA for 4510e93

• fix path writing tests

  tyarkoni

  committed
  7b4f2cc

  Copy full SHA for 7b4f2cc

• fix get_metadata to accept scope arg

  tyarkoni

  committed
  8446a4d

  Copy full SHA for 8446a4d

• extensions --> extension

  tyarkoni

  committed
  1d0dbe5

  Copy full SHA for 1d0dbe5

• add get_data skeleton

  tyarkoni

  committed
  2225311

  Copy full SHA for 2225311

• kill off 'extensions' argument for good

  tyarkoni

  committed
  559d396

  Copy full SHA for 559d396

• move layout fixtures into conftest.py

  tyarkoni

  committed
  6f19781

  Copy full SHA for 6f19781

Commits on Apr 11, 2019

• add get_df() method to BIDSFile

  tyarkoni

  committed
  6b1faee

  Copy full SHA for 6b1faee

• defines association relation; see #431

  tyarkoni

  committed
  7ce8df1

  Copy full SHA for 7ce8df1

• enable filtering by association type

  tyarkoni

  committed
  44c5b7f

  Copy full SHA for 44c5b7f

• privatize associations

  tyarkoni

  committed
  2b5dfec

  Copy full SHA for 2b5dfec

• refactor indexing--separate metadata indexing for readability

  tyarkoni

  committed
  476485c

  Copy full SHA for 476485c

• bulk commit for speed

  tyarkoni

  committed
  1e306d7

  Copy full SHA for 1e306d7

• create FileAssociations for metadata

  tyarkoni

  committed
  096ba0d

  Copy full SHA for 096ba0d

• create FileAssociation records for inheritance

  tyarkoni

  committed
  e2ecbf2

  Copy full SHA for e2ecbf2

Commits on Apr 12, 2019

• fix layout test and various minor tweaks

  tyarkoni

  committed
  6dd1f8b

  Copy full SHA for 6dd1f8b

• fix relative path layouts: always index using absolute paths

  tyarkoni

  committed
  fc9c5ed

  Copy full SHA for fc9c5ed

• add option to include ancestor BIDSFiles in association list

  tyarkoni

  committed
  057a9a0

  Copy full SHA for 057a9a0

• allow either 'filename' or 'file' as get() return_type arg

  tyarkoni

  committed
  726364a

  Copy full SHA for 726364a

• add file associations between files, and associated test

  tyarkoni

  committed
  87483c4

  Copy full SHA for 87483c4

• add BIDSLayout arg to control metadata indexing

  tyarkoni

  committed
  e8a7e97

  Copy full SHA for e8a7e97

• fix i/o tests

  tyarkoni

  committed
  a1d410d

  Copy full SHA for a1d410d

• better handling of duplicate entity columns

  tyarkoni

  committed
  594655a

  Copy full SHA for 594655a

• fix failing tests to work with changes

  tyarkoni

  committed
  b7cede5

  Copy full SHA for b7cede5

• Merge branch 'master' into sqlalchemy

  tyarkoni

  committed
  7d567de

  Copy full SHA for 7d567de

• just when I thought it was gone, they pull it back in

  tyarkoni

  committed
  cf21aee

  Copy full SHA for cf21aee

• fix breaking test

  tyarkoni

  committed
  e03f213

  Copy full SHA for e03f213

Commits on Apr 18, 2019

• fix tests

  tyarkoni

  committed
  d3d27df

  Copy full SHA for d3d27df

Commits on Apr 19, 2019

• add arguments controlling location/reindexing of SQLite database

  tyarkoni

  committed
  dd95b08

  Copy full SHA for dd95b08

• conditionalize reindexing

  tyarkoni

  committed
  9141555

  Copy full SHA for 9141555

• add custom REGEXP function on begin event

  tyarkoni

  committed
  a0c321f

  Copy full SHA for a0c321f

• make sure all test fixtures re-index datasets

  tyarkoni

  committed
  5cca84e

  Copy full SHA for 5cca84e

• revert to using in-memory DB by default

  tyarkoni

  committed
  85f9767

  Copy full SHA for 85f9767

• add ability to save in-memory DB to file via .save()

  tyarkoni

  committed
  5f96e3b

  Copy full SHA for 5f96e3b

• Python 2 doesn't like em-dashes

  tyarkoni

  committed
  e9f3647

  Copy full SHA for e9f3647

• avoid Python 3 argument unpacking

  tyarkoni

  committed
  6cf7e54

  Copy full SHA for 6cf7e54

Commits on Apr 20, 2019

• fixes BIDSVariable deepcopy error by ensuring we have no connection to the DB

  tyarkoni

  committed
  e7b2816

  Copy full SHA for e7b2816

• add deprecation warning for 'extensions' arg to get and improve docstrings

  tyarkoni

  committed
  604d560

  Copy full SHA for 604d560

• update models.py docstrings

  tyarkoni

  committed
  30767c8

  Copy full SHA for 30767c8

Commits on Apr 21, 2019

• reorganize indexing/validation code for better readability/modularity

  tyarkoni

  committed
  1931bb2

  Copy full SHA for 1931bb2

• fix inclusion/exclusion handling and add tests

  tyarkoni

  committed
  f0925b3

  Copy full SHA for f0925b3

• add missing test file

  tyarkoni

  committed
  7d87fa2

  Copy full SHA for 7d87fa2

Commits on Apr 22, 2019

• refactor BIDSFile into hierarchy of classes

  tyarkoni

  committed
  85cb8d3

  Copy full SHA for 85cb8d3

• ignore external and setup-related files

  tyarkoni

  committed
  1624a91

  Copy full SHA for 1624a91

• fix BIDSDataFile test and clean up

  tyarkoni

  committed
  60af65b

  Copy full SHA for 60af65b

Commits on Apr 30, 2019

• CHANGELOG updates

  tyarkoni

  committed
  2bcdd85

  Copy full SHA for 2bcdd85

• Merge branch 'master' into sqlalchemy

  tyarkoni

  committed
  e197d62

  Copy full SHA for e197d62

• update CHANGELOG

  tyarkoni

  committed
  7072482

  Copy full SHA for 7072482

• ugly-ass fix for Python 3.5 test failure, and cleanup

  tyarkoni

  committed
  eeb80a7

  Copy full SHA for eeb80a7

Commits on May 1, 2019

• include FileAssociation kind in uniqueness constraint

  tyarkoni

  committed
  2af4650

  Copy full SHA for 2af4650

• don't commit redundant FileAssociations

  tyarkoni

  committed
  cc462c0

  Copy full SHA for cc462c0

• fix wrong order of args

  tyarkoni

  committed
  0ac80d0

  Copy full SHA for 0ac80d0

Commits on May 7, 2019

• add get_entities method to BIDSFile and reorder attributes

  tyarkoni

  committed
  5e8308e

  Copy full SHA for 5e8308e

• rename is_metadata argument to just metadata

  tyarkoni

  committed
  2b68130

  Copy full SHA for 2b68130

• reorganize BIDSFile tests

  tyarkoni

  committed
  a3b07d1

  Copy full SHA for a3b07d1

• add BIDSFile.get_entities() method and tests

  tyarkoni

  committed
  7f689fe

  Copy full SHA for 7f689fe

• updated and expanded tutorial

  tyarkoni

  committed
  52c6a7f

  Copy full SHA for 52c6a7f

Commits on May 10, 2019

• no need for JSON column when a String will do; closes #437

  tyarkoni

  committed
  29b1014

  Copy full SHA for 29b1014

• lose the JSON import

  tyarkoni

  committed
  85eee6e

  Copy full SHA for 85eee6e

• update CHANGELOG in prep for release

  tyarkoni

  committed
  b518712

  Copy full SHA for b518712

• Merge branch 'master' into sqlalchemy

  tyarkoni

  committed
  528f253

  Copy full SHA for 528f253

• Merge branch 'master' into sqlalchemy

  tyarkoni

  committed
  b93b272

  Copy full SHA for b93b272