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Re-architect backend tornado http server. Adds supporting decoupled library packages. (Large PR) #80

Merged
merged 133 commits into from
Sep 27, 2021

Commits on Jul 8, 2021

  1. add pathlib helper utilities

    Austin Raney committed Jul 8, 2021
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  2. unit test for pathlib utils

    Austin Raney committed Jul 8, 2021
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  3. remove erroneous shebang

    Austin Raney committed Jul 8, 2021
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  4. use relative imports instead of re-importing

    Austin Raney committed Jul 8, 2021
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  5. make utlities dir a python subpackage

    Austin Raney committed Jul 8, 2021
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  6. refactor ResourceManager constructor

    Austin Raney committed Jul 8, 2021
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  7. refactor authenticate and is_authenticated methods

    Austin Raney committed Jul 8, 2021
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  8. return user info on auth

    Austin Raney committed Jul 8, 2021
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  9. refactor save_resource_locally

    Austin Raney committed Jul 8, 2021
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Commits on Jul 9, 2021

  1. remove unnecessary shebang and imports

    Austin Raney committed Jul 9, 2021
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  2. add httpstatus import and use relative local imports

    Austin Raney committed Jul 9, 2021
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  5. override base class prepare to return 401 unauthorized if not authent…

    …icated
    Austin Raney committed Jul 9, 2021
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  6. use httpstatus enum to set options status in base class

    Austin Raney committed Jul 9, 2021
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Commits on Jul 14, 2021

  1. add pydantic as setup requirement

    Austin Raney committed Jul 14, 2021
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  2. start transition from hs_restclient to hsclient. Add sessionstruct an…

    …d some pydantic api models
    Austin Raney committed Jul 14, 2021
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  3. pydantic api models

    Austin Raney committed Jul 14, 2021
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  5. add session struct unit tests

    Austin Raney committed Jul 14, 2021
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Commits on Jul 15, 2021

  1. remove remember field from auth api model

    Austin Raney committed Jul 15, 2021
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  3. add prepare to base handler. Requires user auth or redirects. Also ad…

    …ds login url path to base handler
    Austin Raney committed Jul 15, 2021
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  4. mixin for mutating global session object. Allows for speration from c…

    …hild classes that don't need this functionality
    Austin Raney committed Jul 15, 2021
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  5. LoginHandler updated. Credentials no longer stored. A salted secure c…

    …ookie created post login is used to retain login state.
    Austin Raney committed Jul 15, 2021
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  6. update LoginHandler docstring

    Austin Raney committed Jul 15, 2021
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  7. replace previous server unit tests. More to come

    Austin Raney committed Jul 15, 2021
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  8. add pytest-tornado to development requirements

    Austin Raney committed Jul 15, 2021
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  9. pytest config file. By default print logs. Disable using 'pytest -o l…

    …og_cli=false'
    Austin Raney committed Jul 15, 2021
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  10. move server.py if name == main functionality to module level __main__…

    ….py. Now run using 'python -m hydroshare_jupyter_sync'
    Austin Raney committed Jul 15, 2021
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  11. add id field to SessionStruct

    Austin Raney committed Jul 15, 2021
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  12. update login logic to store user id

    Austin Raney committed Jul 15, 2021
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  13. fix session struct type hints

    Austin Raney committed Jul 15, 2021
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  15. remove if name == main from server.py

    Austin Raney committed Jul 15, 2021
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Commits on Jul 16, 2021

  1. add CLI to __main__. Can pass port, hostname, --no-debug, and config …

    …file. TODO: impliment config logic
    Austin Raney committed Jul 16, 2021
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  2. add username field and implimentation to session struct

    Austin Raney committed Jul 16, 2021
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  3. add note regarding Hsmd5Handler. Not sure that Hsmd5Handler is implim…

    …ented
    Austin Raney committed Jul 16, 2021
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  4. add and implement pydantic schema CollectionOfResourceMetadata. a lis…

    …t of hsclient.json_models::ResourcePreview fields that have been subset
    Austin Raney committed Jul 16, 2021
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  5. add tests for CollectionOfResourceMetadata

    Austin Raney committed Jul 16, 2021
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  6. add a few comments and todos to server endpoints

    Austin Raney committed Jul 16, 2021
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  8. add pathlib utils tests

    Austin Raney committed Jul 16, 2021
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Commits on Jul 19, 2021

  1. add configuration file parser that uses pydantic.

    Current configuration parameters are `data` and `log`. Both are
    directories. By default, hydroshare_juypter_sync looks for them at
    ~/.config/hydroshare_jupyter_sync/config and
    ~/.hydroshare_jupyter_sync_config in order. Meaning, if
    ~/.config/hydroshare_jupyter_sync/config is found first,
    ~/.hydroshare_jupyter_sync_config will not be read.
    
    Data and log parameters can be specified in multiple ways.
    1. Config files mentioned above using shell environment variable like
       semantics (i.e. DATA=/some/path).
    2. As environment variables (i.e. export DATA=/some/path)
    3. Using the CLI by passing a non-default configuration file
       (i.e. --config env_file).
    Austin Raney committed Jul 19, 2021
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  2. unit tests for configuration parser

    Austin Raney committed Jul 19, 2021
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  3. first_existing_file func added to utilites. Give a list of paths and …

    …it greedily returns the firs that exists
    Austin Raney committed Jul 19, 2021
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  5. update help message in --config cli argument

    Austin Raney committed Jul 19, 2021
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  6. move argparser to cli module. move parser to arg for main for dep inj…

    …ection purposes
    Austin Raney committed Jul 19, 2021
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  7. Rename ResourcesRootHandler to ListUserHydroShareResources. Comment o…

    …ut post action.
    
    The previous post action allowed for creation of a HS resource, for the
    purpose of the minimum viable product this feature has been removed. In
    the future this feature will be re-added.
    Austin Raney committed Jul 19, 2021
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  8. update ResourcesRootHandler to ListUserHydroShareResources handler in…

    … routing
    Austin Raney committed Jul 19, 2021
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Commits on Jul 21, 2021

  1. impliment configuration parser in main

    Austin Raney committed Jul 21, 2021
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  2. expand and resolve data and log paths in config

    Austin Raney committed Jul 21, 2021
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  3. add ResourceFiles pydantic api model. This is mainly for marshalling …

    …output
    Austin Raney committed Jul 21, 2021
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  4. Extend hsclient::HydroShare with HydroShareWithResourceCache. As the …

    …name implies, it adds caching by overriding the resource method in the base class
    Austin Raney committed Jul 21, 2021
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  5. add/replace rest api handlers for listing and downloading hydroshare …

    …resources/files
    Austin Raney committed Jul 21, 2021
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  6. add hs resource strategy class tree and strategy factory

    Austin Raney committed Jul 21, 2021
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  7. update gitignore to omit lib dir outside of root context

    Austin Raney committed Jul 21, 2021
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  8. add boolean api model

    Austin Raney committed Jul 21, 2021
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  9. update and rename resource handler to impliment resource factory. Now…

    … can download either files or folders
    Austin Raney committed Jul 21, 2021
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  11. add 'data_path' property to base handler.

    Austin Raney committed Jul 21, 2021
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Commits on Jul 23, 2021

  1. ResourceCreationRequest now uses regex to verify that path names do n…

    …ot contain ~ or ..
    Austin Raney committed Jul 23, 2021
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  2. add data_path property to base handler

    Austin Raney committed Jul 23, 2021
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  3. add LocalResourceEntityHandler for uploading local HS resource data t…

    …o hydroshare
    
    This handler assumes that a local version of a HydroShare
    resource (does not have to be entire resource, could just be a file in a
    resource) exists locally and is stored as it is canonically in
    HydroShare (i.e. {resource_id}/data/contents/). Meaning that the local
    file system mirrors the resource's file system structure on HydroShare.
    
    The handler accepts one or more files via a json object ({"files":
    [str]} in the request body using the POST HTTP verb. File names passed
    in the json `files` array must be in the file system context of the
    passed resource. They are specified relative to `/data/contents` or
    `{data}/{resource_id}` (meaning, you can include `/data/contents` if
    desired.) File paths passed outside {data}/{resource_id}/ ARE NOT
    ALLOWED. Additionally, file path names cannot include `~` or `..`. A 403
    Forbidden is returned in the response if they are passed.
    
    Files are zipped relative to `/data/contents` (maintains directory
    structure), uploaded to HydroShare, and unzipped. Files uploaded
    overwrite existing files present on HydroShare. This operation cannot be
    undone.
    Austin Raney committed Jul 23, 2021
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  4. unit test regex implimentation in ResourceFiles

    Austin Raney committed Jul 23, 2021
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  6. remove erroneous test_hello_world unit test

    Austin Raney committed Jul 23, 2021
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Commits on Jul 29, 2021

  1. add root.html template

    Austin Raney committed Jul 29, 2021
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  2. add template path to development Application object

    Austin Raney committed Jul 29, 2021
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  3. render root.html in catch all / handler. WIP: prepare method will nee…

    …d to change in the future. For now, it bypasses the redirect to /syncApi/login
    Austin Raney committed Jul 29, 2021
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  4. login route requires json content-type header. access control allow o…

    …rigin set to localhost for cors support. Will likely need to change in the future
    Austin Raney committed Jul 29, 2021
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  5. login cookie is now a session cookie instead of a 30 day persistant c…

    …ookie. This should reduce frontend login management complexity
    Austin Raney committed Jul 29, 2021
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  6. remove erroneous import in __main__

    Austin Raney committed Jul 29, 2021
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  7. add date_created and date_last_updated fields to ResourceMetadata api…

    … model
    Austin Raney committed Jul 29, 2021
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  8. update tests to support changes. Namely, /syncApi/login content-type …

    …header requirement and additions to ResourceMetadata api model
    Austin Raney committed Jul 29, 2021
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Commits on Aug 5, 2021

  1. Configuration menu
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  2. load config data from string not file object

    Austin Raney committed Aug 5, 2021
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Commits on Aug 13, 2021

  1. include labextension dir in manifest

    Austin Raney committed Aug 13, 2021
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  2. render static html from template; plus type hints

    Austin Raney committed Aug 13, 2021
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  3. add file system resource types

    Austin Raney committed Aug 13, 2021
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  4. fs resource map irepresenting the relationship between a local file (…

    …not directory) path to the file's MD5 Hash. adds interfaces and concrete implimentations.
    Austin Raney committed Aug 13, 2021
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  5. add __init__.py to make filesystem lib a module

    Austin Raney committed Aug 13, 2021
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  6. FS map interfaces and concrete implementations. These objects represe…

    …nt and communicate the relationship between HydroShare resources', resource files, and resource MD5 Hashes.
    Austin Raney committed Aug 13, 2021
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  7. AggregateFSMap conrete implementation. Encapsulates a local and remot…

    …e FS map and allows for treating them as one FSMap
    Austin Raney committed Aug 13, 2021
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  8. AggregateFSResourceMapSyncState is a pydantic model that describes th…

    …e state of an AggregateFSResourceMap. Namely, are resources in/out of sync, only local/remote.
    Austin Raney committed Aug 13, 2021
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  9. filesystem lib specific expections

    Austin Raney committed Aug 13, 2021
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  10. simple event library. subscribe, unsubscribe, and dispatch events. Ev…

    …ents are to be described as passed as an Enum
    Austin Raney committed Aug 13, 2021
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  11. application specific event enum

    Austin Raney committed Aug 13, 2021
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  12. application specific object interface describing objects necessary to…

    … observer, manage, and communicate local and remote hydroshare resources
    Austin Raney committed Aug 13, 2021
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  13. application specific event listeners implimentations

    Austin Raney committed Aug 13, 2021
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  14. SessionSyncStruct. conglomerate object that implements the setup and …

    …teardown process for resources that handle tracking, managing, and communicating the sync status of local and remote hydroshare resources that bookend a session.
    Austin Raney committed Aug 13, 2021
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  15. application specific watchdog event handler factory. Creates file sys…

    …tem event handlers for observing a local hydroshare resource directory. Observations are used to update a LocalFSResourceMap instance and dispatching events used elsewhere in the application (i.e. file added).
    Austin Raney committed Aug 13, 2021
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  16. add FileSystemEventWebSocketHandler tornado websocket handler. the sy…

    …nc status between local and remote resources are pushed to the client across this websocket.
    Austin Raney committed Aug 13, 2021
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  17. add _SessionSyncSingleton. A thin wrapper for managing a SessionSyncS…

    …truct as a singleton.
    Austin Raney committed Aug 13, 2021
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  19. add logic to tornado handlers that download and upload hydroshare res…

    …ources. These events are now dispatched using an event system to update state elsewhere in application.
    Austin Raney committed Aug 13, 2021
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  20. update server unit tests

    Austin Raney committed Aug 13, 2021
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  21. add unit tests for AggregateFSMap and FSResourceMaps

    Austin Raney committed Aug 13, 2021
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Commits on Aug 17, 2021

  1. add handlers msubpackage This is a WIP. Handlers previously found in …

    …server.py will be moved to the handlers subpackage.
    Austin Raney committed Aug 17, 2021
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  2. comment out websocket handler in server.py. Causes circular import. W…

    …ill be completely removed in future. Currently functionality is retained in __init__.py of the handlers subpackage
    Austin Raney committed Aug 17, 2021
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  3. __main__.py and __init__.py now import get_route_handlers from the ha…

    …ndlers subpackage
    Austin Raney committed Aug 17, 2021
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Commits on Aug 18, 2021

  1. use data_path and log_path as config file deserialized names. These s…

    …till reference their respective alias values data and log in config files
    Austin Raney committed Aug 18, 2021
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  2. update config file unit tests

    Austin Raney committed Aug 18, 2021
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  3. no longer manually set application config settings in TestApp. instea…

    …d, unpack dictionary
    Austin Raney committed Aug 18, 2021
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  5. add deprecated comment to handlers no longer used. Aid in future refa…

    …ctor and make hydroshare#80's reviewer's lives easier.
    Austin Raney committed Aug 18, 2021
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Commits on Aug 23, 2021

  1. update fs_event_handler_factory docstring to note the one-to-one rela…

    …tionship between resources and FSEventHandlers
    Austin Raney committed Aug 23, 2021
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  2. change FSEventHanlder logging from INFO to DEBUG level

    Austin Raney committed Aug 23, 2021
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Commits on Aug 25, 2021

  1. add watchdog dep to setup.py

    Austin Raney committed Aug 25, 2021
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  4. update references from 'data_dir' to 'contents_dir' in application sp…

    …ecific code
    Austin Raney committed Aug 25, 2021
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  7. remove extraneous imports from lib filesystem

    Austin Raney committed Aug 25, 2021
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Commits on Sep 27, 2021

  1. update jupyter lab plugin entry point function name. _jupyter_server_…

    …extension_points is not _jupyter_server_extension_paths
    Austin Raney committed Sep 27, 2021
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  2. enum, fs_events.Events, uses auto for enumeration instead of duplicat…

    …e type hint declarations. Previous imp, causes duplicate value fields, to be 'removed'
    Austin Raney committed Sep 27, 2021
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  3. fix bug in resource_strategies. intermediary directories now create t…

    …he correct intermediate baggit like structure.
    Austin Raney committed Sep 27, 2021
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  4. add authors and creator field to ResourceMetadata pydantic model. Cov…

    …ers issue in hsclient. See hsclient hydroshare#23.
    Austin Raney committed Sep 27, 2021
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  5. add DataDir pydantic model. Main use if for conveying the configured …

    …path where hydroshare resources are stored.
    Austin Raney committed Sep 27, 2021
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  6. resolve bug in tornado entity handlers. Path to resources files impro…

    …perly malformed
    Austin Raney committed Sep 27, 2021
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  7. add DataDirectoryHandler which returns the configured hydroshare jupy…

    …ter sync data directory via a GET request. Does not require login
    Austin Raney committed Sep 27, 2021
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  8. add DataDirectoryHandler to handlers registery

    Austin Raney committed Sep 27, 2021
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  9. SessionSyncEventListeners.resource_entity_downloaded bug fix (include…

    …s TODO action). When resource entity is downloaded, both local and remote resource are updated, meaning, at the resource level, all the md5 checksums are recomputed and the remote is re-queired for changes in the manifest-md5.txt file
    Austin Raney committed Sep 27, 2021
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  10. add missing event type subscriptions to websocket handler. also, adds…

    … debug level logging for tx'd messages
    Austin Raney committed Sep 27, 2021
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  12. add LocalResourceEntityHandler unit tests

    Austin Raney committed Sep 27, 2021
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  13. update fs resource map unit tests to create the corrent intermediate …

    …directories
    Austin Raney committed Sep 27, 2021
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