Scottx611x/derived node attributes bugfix #2076
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…tputs' into scottx611x/analysis_groups
…ived from, and in turn gain information about which analysis group said output belongs to.
…owTool._get_refinery_input_file_id()`
…n solr. Add test coverage.
… scottx611x/derived_node_attributes_bugfix
…llections were never considered
…tputs' into scottx611x/derived_node_attributes_bugfix # Resolved Conflicts: # refinery/tool_manager/models.py # refinery/tool_manager/tests.py
7 tasks
Codecov Report
@@ Coverage Diff @@
## scottx611x/associate_workflow_outputs #2076 +/- ##
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- Coverage 45.5% 45.3% -0.21%
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Files 411 411
Lines 28362 27732 -630
Branches 1319 1305 -14
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- Hits 12906 12563 -343
+ Misses 15456 15169 -287
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scottx611x
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Sep 5, 2017
* Utilize Galaxy Tool parameters from frontend with test coverage * Exclude generic fields from file_browser2 columns and attributes * Properly format some code * Update analysis_manager.tasks to be able to run WorkflowTools in their entirety * Update Tool __str__() to be more resonable * Rename method to be more clear * Add `INPUT_STEP` constant * Remove comment * Add `galaxy_invocation_steps` as a property of WorkflowTool * Add subanalysis_number as a property of Workflowtool * Add method to create an Analysis and its related objects * Add method to create AnalysisNodeConnections for a WorkflowTool * Improve naming for Galaxy CollectionElements * Update methods to be private * Update docstrings * Add method to create WorkflowFilesDL objects * Add static method to construct the proper filename for a Galaxy Dataset * Add method to retrieve the list of Galaxy Datasets from our Galaxy WF invocation's History * Fix bug with the formatting of `subtask` arguments * Add method to get Node objects from the list of UUIDs the front-end gives us * Add method to get the dict representation of our Galaxy Workflow * Add method to get the `parameters` from our tool launch configuration * Add method to get the workflow step that a Galaxy Dataset was created from * Update docstring * Update `launch()` after analysis creation abstraction introduced * Update tests * Update Analysis naming * Add more context to invalid ToolAnnotation error messages * Add mock for a galaxy workflow dict * Fix method naming * Utilize an asynchronous approach for Galaxy File Imports * Add logging statements * We actually want the FileStoreitem's datafile name here * Fix failing tests due to new changes * Rework `update_file_relationships_with_galaxy_history_data()` to act upon a list instead of individual dicts * Add constant for `hdca` * Clearer naming for `_get_galaxy_datasets_list()` * Use newly renamed method * `_get_galaxy_workflow_invocation_steps()` didn't need to be a `@property` * Add test coverage * Fix test * Alleviate the need for this hack * Only replace first occurance in the case of duplicate nodes being launched * Provide some information about which parameters are editible for a given Galaxy Tool * Fix bug with boolean parameters with a default_value of False having a checked checkbox * Add `handle_bioblend_exceptions` decorator * Add getter for a workflow's interal_id field * Fix logging level, and reraise exception * Rename method to `get_galaxy_file_relationships` * Fix Test * Update Tool `__str__()` * Add mock data for a galaxy tool * `show_invocation()` here to yield more relevant information * Store information about Refinery files that are mapped to Datasets in the Galaxy history * Update test coverage * Set GALAXY_TO_REFINERY_MAPPING_LIST upon tool creation * Rename `subanalysis_number` to `analysis_group_number` * Use an existing constant * Clearer naming for `parameter` variable * Use existing property `galaxy_workflow_history_id` * Add getters to `WorkflowTool` * Fix tests * Tests pass locally. Add assertion to determine whats wrong on Travis * Try to patch the reference instead of the object as to not make use of a network call * Try to get some more information about the Travis error * Slim down mock galaxy data * Remove extra exception info for debugging travis * Code formatting * Mock the proper method as to not send messages to rabbitmq broker * Move duplicated mocks into their own `setUp()` * Fix these `return_values` * Assign to var then return to be more clear * Add docstring and handle base case * Rename method and members to illustrate its true functionality * Update docstrings * Add comments and clearer naming * Thin out galaxy mock data some more * Add test coverage * Remove use of `eval()` * Constant was confusing * Fix styling * Bump code out of loop and add comment * Assert that there is a corresponding galaxy workflow step for the galaxy dataset in question * Cast to `set` * Cast to list to support indexing * Add TODO in case a race condition is ever hit * Remove `bit.ly` links * Remove blank lines * Remove redundant decorator * Remove redundant "stringification" * Split `create_analysis_node_connections` into two separate methods * Fix styling * Add an assertion as a sanity check * Get the correct information in ui-grid table and facets after re-indexing. Only a hack at this point. * Add test coverage for `Node.get_analysis()` * Analysis name w/ time string was causing issues with faceting, and we already have records of their launch time * Remove weird `set()/list()` casting due to having bad test data * I hit these db constraints a couple of times recently. Incresing the ceiling. * Scottx611x/remove fastqc viz (#2042) * Remove integrated FastQC viewer * Remove a few more occurances from strings * Remove `refineryChart` dependency * Cleanup tests * Update Analyses names to be more user friendly * Add test coverage for how Analysis names should look * Scottx611x/analysis names in fb2 workaround (#2046) * Get the correct information in ui-grid table and facets after re-indexing. Only a hack at this point. * Add test coverage for `Node.get_analysis()` * Analysis name w/ time string was causing issues with faceting, and we already have records of their launch time * Cleanup tests * Update Analyses names to be more user friendly * Remove OutputFile model and its occurances. Ended up being an unnecessary feature. * Define a new entry in schema for `input_output_relationship` * Don't need this information in the Tool Launch Configuration * Remove lingering `chart.js` * Remove other instances of `OutputFiles` * Revert "Remove other instances of `OutputFiles`" This reverts commit 2d16c22. * Revert "Remove OutputFile model and its occurances. Ended up being an unnecessary feature." This reverts commit cb81f8d. * Revert changes to ToolDefinition schema * Fix race condition where galaxy_file_import state could be out of sync in th UI * Add test case to check if successful galaxy file import state is set * Remove all code related to OutputFile; This feature was never utilized. I can see its potential in the VisualizationTool relam, but I can also envision solutuions that are easier for the end user where they don't have to annotate tools with specific outputs that they'd like to retrieve. * Update regex * Fix bug to allow for legacy Analyses to be launched * Scottx611x/analysis groups (#2066) * Update Galaxy mock data * Fix `help` * Add constants * Dynamically create analysis group numbers based on the structure of our workflow * Fix docstring * Use temp var for easier readability * Add mechanism to derive which Refinery file a workflow output was derived from, and in turn gain information about which analysis group said output belongs to. * Fix tests * Fix typo * Add docstrings * Don't overuse `@property`. Make method private * Remove statements from debugging * Change to default value * Fix styling * Remove comment stating the obvious * Flip if/else logic to be more clear * Add constant * Add test coverage for `Workflowtool._has_dataset_collection_input()` * Fix typo * Add logic to determine analysis group numbering, and test coverage * Fix spelling * Add tests coverage for an edge case in the recursive calls to `WorkflowTool._get_refinery_input_file_id()` * Fix bug where incorrect AnnotatedNode information was being indexed in solr. Add test coverage. * Add test coverage for `_get_analysis_group_number` * Simplify logic * Tidy mock glaxy data * DRY: condense repeated calls in tests * Fix tests * Remove `analyis_group` from method sig. * Add comment about recursive call * Update test method to be more clear about its intentions * Update `WorkflowTool._get_analysis_group_number()` to be more clear about what we're achieving * Scottx611x/derived node attributes bugfix (#2076) * Update Galaxy mock data * Fix `help` * Add constants * Dynamically create analysis group numbers based on the structure of our workflow * Fix docstring * Use temp var for easier readability * Add mechanism to derive which Refinery file a workflow output was derived from, and in turn gain information about which analysis group said output belongs to. * Fix tests * Fix typo * Add docstrings * Don't overuse `@property`. Make method private * Remove statements from debugging * Change to default value * Fix styling * Remove comment stating the obvious * Flip if/else logic to be more clear * Add constant * Add test coverage for `Workflowtool._has_dataset_collection_input()` * Fix typo * Add logic to determine analysis group numbering, and test coverage * Fix spelling * Add tests coverage for an edge case in the recursive calls to `WorkflowTool._get_refinery_input_file_id()` * Fix bug where incorrect AnnotatedNode information was being indexed in solr. Add test coverage. * Add test coverage for `_get_analysis_group_number` * Simplify logic * Tidy mock glaxy data * DRY: condense repeated calls in tests * Fix tests * Address issue while creating expanded workflow graph where Dataset Collections were never considered * Update AnalysisNodeConnection input creation and update tests * Assert that we assign the correct name to input AnalysisNodeConnections
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galaxy_connector.galaxy_workflow.create_expanded_workflow_graph) where Dataset Collections were never considered, and parent nodes for derived data nodes were never created leaving the derived nodes with no inheritableAttributesReviewed w/ @mccalluc