[HLS-353] Add glue function docs #4

karenfeng · 2019-10-10T15:37:53Z

What changes are proposed in this pull request?

Glue function docs:

subset_struct
add_struct_fields
expand_struct
array_to_dense_vector
array_to_sparse_vector
vector_to_array
explode_matrix
genotype_states
hard_calls

How is this patch tested?

Unit tests
Integration tests
Manual tests

cd docs
make html
open build/html/index.html

henrydavidge · 2019-10-11T18:17:54Z

docs/source/api/glue-functions.rst

+Glue Functions
+==============
+
+To allow for interoperability between different bioinformatics tools, Glow includes a variety of glue functions.


"Glue includes a variety of glue functions for performing basic data manipulation"

henrydavidge

Thanks Karen! I had a comment on the first sentence (don't love the first clause). Otherwise looks good. Feel free to merge after addressing.

fnothaft · 2019-10-11T18:21:28Z

OOC, why do we call them "glue functions"? That terminology is unfamiliar to me.

henrydavidge · 2019-10-11T18:27:07Z

I've heard "glue _" be used to refer to the parts of a pipeline that don't perform business logic but are necessary for stitching together the parts that do. However, certainly open to other names. Do you think something like "utility functions" would be more clear?

kianfar77

Thanks. Made some comments.

kianfar77 · 2019-10-11T18:01:17Z

docs/source/api/glue-functions.rst

+Glue Functions
+==============
+
+To allow for interoperability between different bioinformatics tools, Glow includes a variety of glue functions.


I am not sure if a Glue function category is the best way to doc these. They are very different creatures. I think it is better we put each of these subcategories into the most relevant category in terms of type of analysis. We can leave it as is and decide after the rest of the doc is ready.

kianfar77 · 2019-10-11T18:02:47Z

docs/source/api/glue-functions.rst

+Struct transformations
+======================
+
+Subset or append fields based on an initial struct with the ``subset_struct`` and ``add_struct_fields`` functions


I think a list starting with the name of a function followed by a sentence as to what it does and its own example is a better format.

kianfar77 · 2019-10-11T18:04:38Z

docs/source/api/glue-functions.rst

+
+Struct transformations
+======================
+


I think some motivation or example as to why the user might need these functions is needed. interoperability between bioinformatics tools said above is too generic.

kianfar77 · 2019-10-11T18:06:52Z

docs/source/api/glue-functions.rst

+
+Spark ML transformations
+========================
+


Same two comments regarding motivation/example of need and list format.

kianfar77 · 2019-10-11T18:07:03Z

docs/source/api/glue-functions.rst

+
+Variant data transformations
+============================
+


Same two comments regarding motivation/example of need and list format.

# This is the 1st commit message: WIP # This is the commit message projectglow#2: Get jar working Don't use Kryo serializer Don't parallelize un-serializable Hadoop FileStatus Change descrip WIP Whoops bintray Not local Quiet logs Remove tmp file Actually rename bintray Setting version to 0.1.0 WIP WIP License fixup Resolver WIP Change version Setting version to 0.1.1 WIP Setting version to 0.1.2 Setting version to 0.1.3-SNAPSHOT WIP Setting version to 0.1.2 Setting version to 0.1.3-SNAPSHOT Exclude many GATK deps Setting version to 0.1.3 Setting version to 0.1.4-SNAPSHOT Setting version to 0.1.4 Setting version to 0.1.5-SNAPSHOT Whoops Setting version to 0.1.3 Setting version to 0.1.4-SNAPSHOT Setting version to 0.1.4 Setting version to 0.1.5-SNAPSHOT Setting version to 0.1.6 Setting version to 0.1.7-SNAPSHOT Yay deps Setting version to 0.1.7 Setting version to 0.1.8-SNAPSHOT Setting version to 0.1.8 Setting version to 0.1.9-SNAPSHOT Setting version to 0.1.1 Setting version to 0.1.2-SNAPSHOT Setting version to 0.1.10 Setting version to 0.1.11-SNAPSHOT Setting version to 0.1.15 Setting version to 0.1.16-SNAPSHOT Setting version to 0.1.9 Setting version to 0.1.10-SNAPSHOT WIP Setting version to 0.1.7 Setting version to 0.1.8-SNAPSHOT Setting version to 0.1.8 Setting version to 0.1.9-SNAPSHOT Setting version to 0.1.7 Setting version to 0.1.8-SNAPSHOT Add tests back Setting version to 0.1.8 Setting version to 0.1.9-SNAPSHOT Setting version to 0.1.7 Setting version to 0.1.8-SNAPSHOT Setting version to 0.1.13 Setting version to 0.1.14-SNAPSHOT WIP Setting version to 0.1.7 Setting version to 0.1.8-SNAPSHOT WIP Setting version to 0.1.7 Setting version to 0.1.8-SNAPSHOT WIP Setting version to 0.1.8 Setting version to 0.1.9-SNAPSHOT Setting version to 0.1.11 Setting version to 0.1.12-SNAPSHOT Setting version to 0.1.7 Setting version to 0.1.8-SNAPSHOT Exclude findbugs Setting version to 0.1.8 Setting version to 0.1.9-SNAPSHOT WIP Cleanup # This is the commit message projectglow#3: Rename org # This is the commit message projectglow#4: Rename env # This is the commit message projectglow#5: Setting version to 0.1.0 # This is the commit message projectglow#6: Setting version to 0.1.1-SNAPSHOT # This is the commit message projectglow#7: Rename # This is the commit message projectglow#8: Work on test.pypi # This is the commit message projectglow#9: Fix VCFFileWriterSuite (projectglow#63) # This is the commit message projectglow#10: Remove SpecificInternalRow buffer in RowConverter (projectglow#65) * Remove SpecificInternalRow buffer in RowConverter * comment

# This is the 1st commit message: WIP # This is the commit message projectglow#2: Get jar working Don't use Kryo serializer Don't parallelize un-serializable Hadoop FileStatus Change descrip WIP Whoops bintray Not local Quiet logs Remove tmp file Actually rename bintray Setting version to 0.1.0 WIP WIP License fixup Resolver WIP Change version Setting version to 0.1.1 WIP Setting version to 0.1.2 Setting version to 0.1.3-SNAPSHOT WIP Setting version to 0.1.2 Setting version to 0.1.3-SNAPSHOT Exclude many GATK deps Setting version to 0.1.3 Setting version to 0.1.4-SNAPSHOT Setting version to 0.1.4 Setting version to 0.1.5-SNAPSHOT Whoops Setting version to 0.1.3 Setting version to 0.1.4-SNAPSHOT Setting version to 0.1.4 Setting version to 0.1.5-SNAPSHOT Setting version to 0.1.6 Setting version to 0.1.7-SNAPSHOT Yay deps Setting version to 0.1.7 Setting version to 0.1.8-SNAPSHOT Setting version to 0.1.8 Setting version to 0.1.9-SNAPSHOT Setting version to 0.1.1 Setting version to 0.1.2-SNAPSHOT Setting version to 0.1.10 Setting version to 0.1.11-SNAPSHOT Setting version to 0.1.15 Setting version to 0.1.16-SNAPSHOT Setting version to 0.1.9 Setting version to 0.1.10-SNAPSHOT WIP Setting version to 0.1.7 Setting version to 0.1.8-SNAPSHOT Setting version to 0.1.8 Setting version to 0.1.9-SNAPSHOT Setting version to 0.1.7 Setting version to 0.1.8-SNAPSHOT Add tests back Setting version to 0.1.8 Setting version to 0.1.9-SNAPSHOT Setting version to 0.1.7 Setting version to 0.1.8-SNAPSHOT Setting version to 0.1.13 Setting version to 0.1.14-SNAPSHOT WIP Setting version to 0.1.7 Setting version to 0.1.8-SNAPSHOT WIP Setting version to 0.1.7 Setting version to 0.1.8-SNAPSHOT WIP Setting version to 0.1.8 Setting version to 0.1.9-SNAPSHOT Setting version to 0.1.11 Setting version to 0.1.12-SNAPSHOT Setting version to 0.1.7 Setting version to 0.1.8-SNAPSHOT Exclude findbugs Setting version to 0.1.8 Setting version to 0.1.9-SNAPSHOT WIP Cleanup # This is the commit message projectglow#3: Rename org # This is the commit message projectglow#4: Rename env # This is the commit message projectglow#5: Setting version to 0.1.0 # This is the commit message projectglow#6: Setting version to 0.1.1-SNAPSHOT # This is the commit message projectglow#7: Rename # This is the commit message projectglow#8: Work on test.pypi # This is the commit message projectglow#9: Fix VCFFileWriterSuite (projectglow#63) # This is the commit message projectglow#10: Remove SpecificInternalRow buffer in RowConverter (projectglow#65) * Remove SpecificInternalRow buffer in RowConverter * comment # This is the commit message projectglow#11: Update CircleCI badge # This is the commit message projectglow#12: Move build/test from README to wiki # This is the commit message projectglow#13: More cleanup # This is the commit message projectglow#14: Newline # This is the commit message projectglow#15: address comments # This is the commit message projectglow#16: Circleci fixups # This is the commit message projectglow#17: Un-exclude netlib from gatk # This is the commit message projectglow#18: CircleCI indents # This is the commit message projectglow#19: Change bintray org # This is the commit message projectglow#20: Setting version to 0.1.0 # This is the commit message projectglow#21: Bintray repo # This is the commit message projectglow#22: Move bintrayrepo # This is the commit message projectglow#23: Setting version to 0.1.1-SNAPSHOT

* Add license and notice * .txt Signed-off-by: Henry Davidge <[email protected]>

Add glue fns

96ad54d

karenfeng requested a review from henrydavidge October 10, 2019 15:40

karenfeng changed the title ~~Add glue function docs~~ [HLS-353] Add glue function docs Oct 10, 2019

karenfeng requested a review from kianfar77 October 10, 2019 21:54

henrydavidge reviewed Oct 11, 2019

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kianfar77 requested changes Oct 11, 2019

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karenfeng closed this Oct 15, 2019

henrydavidge added a commit to henrydavidge/glow that referenced this pull request Jun 22, 2020

License (projectglow#4)

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* Add license and notice * .txt Signed-off-by: Henry Davidge <[email protected]>

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[HLS-353] Add glue function docs #4

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		Struct transformations
		======================


		Spark ML transformations
		========================


		Variant data transformations
		============================

[HLS-353] Add glue function docs #4

[HLS-353] Add glue function docs #4

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karenfeng commented Oct 10, 2019

What changes are proposed in this pull request?

How is this patch tested?

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