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Fds 1797 input graph api #1481

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Fds 1797 input graph api #1481

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Commits on Mar 25, 2024

  1. WIP: add export_as_graph flag to convert CLI command.

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  2. Add convert CLI test for exporting graph as a pickle.

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  3. Add export_as_graph to help.py and update the CLI click docs.

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  4. Change export_as_graph to output_format and specify graph, jsonld, or… 

    … all.
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  5. Add tests for CLI convert output_type options.

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  6. Change text of CLI convert output_type help.

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  7. Test that jsonld is created correctly by convert CLI

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Commits on Mar 26, 2024

  1. Add type hints to convert, clean up formatting issues from sonarcloud… 

    … scan.
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  2. Add convert CLI test for not specifying --output_type

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Commits on Apr 2, 2024

  1. Merge branch 'Sage-Bionetworks:develop' into FDS-1796-schema-convert-… 

    …export-pickle
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Commits on Apr 3, 2024

  1. parameterize the convert CLI test.

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  2. remove unused test code for the convert CLI.

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  3. run black on the updated files.

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  4. Use logger.info and logger.error instead of click.echo.

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Commits on Apr 9, 2024

  1. Trim pickle from end of filename, in addition to csv and jsonld.

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  2. add output_path alias for output_jsonld

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Commits on Apr 10, 2024

  1. Add combination of arguments to convert CLI tests

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  2. add export_graph to schema_utils.py to dump a pickle file

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  3. use export_graph util to save pickle file instead of handling that lo… 

    …gic in the CLI function
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  4. add docstrings to graph_export

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  5. Update tests to run different combinations of output_jsonld and outpu… 

    …t_type
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Commits on Apr 11, 2024

  1. Add data_model_graph_pickle to generator

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  2. Add ata_model_graph_pickle to metadata.py

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  3. Add data_model_graph to attributes_explorer

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  4. Add data_model_graph_pickle to tangled_tree

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Commits on Apr 18, 2024

  1. Add convert CLI test case where output_jsonld is pickle and output_pa… 

    …th is pickle. Also test both parameters are empty.
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  2. move tests into one function

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Commits on Apr 19, 2024

  1. Merge branch 'develop' into FDS-1796-schema-convert-export-pickle

    @afwillia
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  2. Run black on commands.py and schema_utils.py

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  3. fix single-letter variable names for pylint error

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    afwillia committed Apr 19, 2024
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Commits on May 7, 2024

  1. Merge branch 'develop' into FDS-1843-use-graph

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Commits on May 8, 2024

  1. Add data_model_graph argument to ManifestGenerator.create_manifests

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  2. use pickle.load to read pickle file

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  3. Add data model graph pickle to attributes_explorer

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  4. Add data model graph pickle to tangled_tree

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Commits on Jun 5, 2024

  1. return 0 to resolve a pylint error.

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  2. Merge branch 'develop' into FDS-1796-schema-convert-export-pickle

    @afwillia
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  3. remove extra function def from merge

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  4. run black on utils/schema_utils.py

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  5. Return 0 for all convert, but echo the filepath created

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  6. Merge branch 'develop' into FDS-1843-use-graph

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Commits on Jun 6, 2024

  1. Fix mix-up between parsed data model and graph data model

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  2. Add data model pickle parsing to tanlged_tree

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  3. Add data_model_pickle file to tests

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  4. Add data model pickle file

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  5. run black

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  6. fix a couple sonarcloud issues with the graph_data_model variable

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  7. Add data_model_graph_pickle to metadata.py and tests

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  8. run black on generator.py

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  9. remove type check from networkx

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  10. fix pylint issues

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Commits on Jun 7, 2024

  1. remove pickle from metadata test because it wasn't created with data_… 

    …model_labels=display_label
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  2. create two metadata_model objects with different data_model_label gra… 

    …ph files
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  3. add display_label graph pickle

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Commits on Jun 26, 2024

  1. Merge branch 'develop' into FDS-1843-use-graph

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Commits on Jun 28, 2024

  1. Add multiple combinations of jsonld and pickle to test_viz attribute_… 

    …explorer
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  2. Fix missing variables in tangled_tree when jsonld and pickle are supp… 

    …lied
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  3. Add combinations of jsonld and pickle to tangled_tree tests

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  4. add graph_data_model argument description

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  5. add data_model_graph_pickle description to MetadataModel

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Commits on Aug 26, 2024

  1. run black on test_viz.py

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  2. Update schematic/manifest/generator.py 

    Co-authored-by: BryanFauble <[email protected]>
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  3. Add read_pickle function to read a binary pickle file

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  4. Use read_pickle instead of importing pickle and opening file

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  5. Add note for pickle files that don't fit in memory. Not sure if this … 

    …will ever be an issue
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  6. Use read_pickle to load the pickle file in metadata.py

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  7. read_pickle instead of import pickle in attributes_explorer

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  8. set self.graph_data_model and update it if data_model_grapher is not … 

    …provided
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  9. use if ... is not None instead of if not ...

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  10. use if ... is not None instead of if not ...

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  11. add an input to read_pickle

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Commits on Aug 27, 2024

  1. run black on io_utils.py

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  2. use read_pickle to read pickle file. Set default data_model_labels

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  3. set default data_model_labels

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  4. alter logic for setting graph_data_model from pickle or DataModelGrap… 

    …h object
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  5. fix pickle reading logic in tangled tree

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  6. fix logic checking for None parameters in attributes_explorer.py

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  7. import "import pickle" should be placed before "from schematic import… 

    … LOADER"
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  8. Use literal for output_type parameter and remove unnecessary try/exce… 

    …pt statement
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  9. use logger.exception instead of logger.error

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  10. move return statement inside the output_type check block

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  11. run black

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  12. import Literal from typing

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  13. add tests for export_graph

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  14. run black

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  15. add graph_url spec to manifest/generate endpoint

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  16. add function to download temp pickle file from url. Add data_model_pi… 

    …ckle parameter to manifest/generate
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  17. use data_model_graph_pickle argument in manifest/generate endpoint

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  18. download temp pickle in manifest/generate endpoint

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  19. check that files are created in schema convert

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  20. update docstring and use if ... is not None instead of if not ...

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  21. use if ... is None instead of if ... is not None

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Commits on Aug 28, 2024

  1. Merge branch 'FDS-1796-schema-convert-export-pickle' into FDS-1797-in… 

    …put-graph-api
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  2. Merge branch 'FDS-1843-use-graph' into FDS-1797-input-graph-api

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  3. add graph_url to validate and submission endpoints

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  4. add graph_url to validate and submission endpoints

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  5. add pickled htan data model for testing

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  6. remove data model graph parameter from validation and submission. It'… 

    …s only available for manifest generation. Also rework some logic with reading the graph pickle
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  7. remove graph_url from validation and submission endpoints

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  8. Merge branch 'develop' into FDS-1797-input-graph-api

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  9. run black on routes.py

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  10. set graph_data_model to None before looking for graph_url

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  11. add DataModelParser back to tangled_tree.py

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Commits on Sep 10, 2024

  1. change logger.info to click.echo

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  2. Check if pickle file contains a networkx MultiDiGraph object

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  3. explain options to schema convert output_type

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    afwillia committed Sep 10, 2024
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  4. update data_model_graph_pickle docstring for ManifestGenerator

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    afwillia committed Sep 10, 2024
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  5. don't return 0 at the end of schema convert

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    afwillia committed Sep 10, 2024
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  6. raise a valueError instead of logger.error for passing a bad filepath… 

    … to schema convert
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    afwillia committed Sep 10, 2024
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  7. return 0 at the end of schema convert to avoid error 'error: Return v… 

    …alue expected [return-value]'
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    afwillia committed Sep 10, 2024
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  8. Raise an actual exception and valueError for bad filepath to schema c… 

    …onvert
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    afwillia committed Sep 10, 2024
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  9. add more information to schema convert when saving the graph as a pic… 

    …kle.
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    afwillia committed Sep 10, 2024
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  10. add argument and return types to get_temp_pickle

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    afwillia committed Sep 10, 2024
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  11. run the black code formatter

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    afwillia committed Sep 10, 2024
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  12. turn a single line that pylint states is too long into two shorter li… 

    …nes of satisfactory length
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    afwillia committed Sep 10, 2024
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  13. swap the f in logger.echo to avoid 'Using an f-string that does not h… 

    …ave any interpolated variables'
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    afwillia committed Sep 10, 2024
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  14. Merge branch 'develop' into FDS-1797-input-graph-api

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    afwillia authored Sep 10, 2024
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  15. message where graph is saved in schema convert cli

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    afwillia committed Sep 10, 2024
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  16. check for FileNotFound error instead of generic exception

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    afwillia committed Sep 10, 2024
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  17. change test variables to camel case

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    afwillia committed Sep 10, 2024
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  18. Merge branch 'FDS-1797-input-graph-api' of https://github.com/Sage-Bi… 

    …onetworks/schematic into FDS-1797-input-graph-api
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    afwillia committed Sep 10, 2024
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  19. document schema convert tests

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    afwillia committed Sep 10, 2024
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  20. turn get_temp_ functions into one single function

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    afwillia committed Sep 10, 2024
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  21. remove unhelpful comments and whitespace

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    afwillia committed Sep 10, 2024
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  22. clarify test cases for attributes explorer

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    afwillia committed Sep 10, 2024
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