code string | signature string | docstring string | loss_without_docstring float64 | loss_with_docstring float64 | factor float64 |
|---|---|---|---|---|---|
return DXHTTPRequest('/%s/close' % object_id, input_params, always_retry=always_retry, **kwargs) | def record_close(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /record-xxxx/close API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Data-Object-Lifecycle#API-method%3A-%2Fclass-xxxx%2Fclose | 3.249319 | 4.012622 | 0.809774 |
return DXHTTPRequest('/%s/describe' % object_id, input_params, always_retry=always_retry, **kwargs) | def record_describe(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /record-xxxx/describe API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Records#API-method%3A-%2Frecord-xxxx%2Fdescribe | 2.996892 | 3.395362 | 0.882643 |
return DXHTTPRequest('/%s/getDetails' % object_id, input_params, always_retry=always_retry, **kwargs) | def record_get_details(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /record-xxxx/getDetails API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Details-and-Links#API-method%3A-%2Fclass-xxxx%2FgetDetails | 3.285627 | 3.441417 | 0.954731 |
return DXHTTPRequest('/%s/listProjects' % object_id, input_params, always_retry=always_retry, **kwargs) | def record_list_projects(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /record-xxxx/listProjects API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Cloning#API-method%3A-%2Fclass-xxxx%2FlistProjects | 3.103227 | 3.870749 | 0.801712 |
return DXHTTPRequest('/%s/removeTags' % object_id, input_params, always_retry=always_retry, **kwargs) | def record_remove_tags(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /record-xxxx/removeTags API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Tags#API-method%3A-%2Fclass-xxxx%2FremoveTags | 2.987292 | 3.734895 | 0.799833 |
return DXHTTPRequest('/%s/removeTypes' % object_id, input_params, always_retry=always_retry, **kwargs) | def record_remove_types(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /record-xxxx/removeTypes API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Types#API-method%3A-%2Fclass-xxxx%2FremoveTypes | 2.999398 | 3.721841 | 0.805891 |
return DXHTTPRequest('/%s/rename' % object_id, input_params, always_retry=always_retry, **kwargs) | def record_rename(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /record-xxxx/rename API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Name#API-method%3A-%2Fclass-xxxx%2Frename | 2.82496 | 3.711251 | 0.761188 |
return DXHTTPRequest('/%s/setDetails' % object_id, input_params, always_retry=always_retry, **kwargs) | def record_set_details(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /record-xxxx/setDetails API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Details-and-Links#API-method%3A-%2Fclass-xxxx%2FsetDetails | 3.475237 | 3.34326 | 1.039476 |
return DXHTTPRequest('/%s/setProperties' % object_id, input_params, always_retry=always_retry, **kwargs) | def record_set_properties(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /record-xxxx/setProperties API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Properties#API-method%3A-%2Fclass-xxxx%2FsetProperties | 3.0497 | 3.541262 | 0.86119 |
return DXHTTPRequest('/%s/setVisibility' % object_id, input_params, always_retry=always_retry, **kwargs) | def record_set_visibility(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /record-xxxx/setVisibility API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Visibility#API-method%3A-%2Fclass-xxxx%2FsetVisibility | 3.618025 | 3.964073 | 0.912704 |
return DXHTTPRequest('/system/describeDataObjects', input_params, always_retry=always_retry, **kwargs) | def system_describe_data_objects(input_params={}, always_retry=True, **kwargs) | Invokes the /system/describeDataObjects API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/System-Methods#API-method:-/system/describeDataObjects | 3.448373 | 4.913497 | 0.701816 |
return DXHTTPRequest('/system/describeExecutions', input_params, always_retry=always_retry, **kwargs) | def system_describe_executions(input_params={}, always_retry=True, **kwargs) | Invokes the /system/describeExecutions API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/System-Methods#API-method:-/system/describeExecutions | 3.508651 | 4.316011 | 0.812938 |
return DXHTTPRequest('/system/describeProjects', input_params, always_retry=always_retry, **kwargs) | def system_describe_projects(input_params={}, always_retry=True, **kwargs) | Invokes the /system/describeProjects API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/System-Methods#API-method:-/system/describeProjects | 3.857428 | 4.527996 | 0.851906 |
return DXHTTPRequest('/system/findAffiliates', input_params, always_retry=always_retry, **kwargs) | def system_find_affiliates(input_params={}, always_retry=True, **kwargs) | Invokes the /system/findAffiliates API method. | 3.783201 | 3.340026 | 1.132686 |
return DXHTTPRequest('/system/findApps', input_params, always_retry=always_retry, **kwargs) | def system_find_apps(input_params={}, always_retry=True, **kwargs) | Invokes the /system/findApps API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Search#API-method%3A-%2Fsystem%2FfindApps | 3.823913 | 5.232074 | 0.73086 |
return DXHTTPRequest('/system/findDataObjects', input_params, always_retry=always_retry, **kwargs) | def system_find_data_objects(input_params={}, always_retry=True, **kwargs) | Invokes the /system/findDataObjects API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Search#API-method%3A-%2Fsystem%2FfindDataObjects | 3.656392 | 5.248327 | 0.696678 |
return DXHTTPRequest('/system/findGlobalWorkflows', input_params, always_retry=always_retry, **kwargs) | def system_find_global_workflows(input_params={}, always_retry=True, **kwargs) | Invokes the /system/findGlobalWorkflows API method. | 3.405236 | 3.041508 | 1.119588 |
return DXHTTPRequest('/system/resolveDataObjects', input_params, always_retry=always_retry, **kwargs) | def system_resolve_data_objects(input_params={}, always_retry=True, **kwargs) | Invokes the /system/resolveDataObjects API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/System-Methods#API-method:-/system/resolveDataObjects | 3.631024 | 5.007755 | 0.72508 |
return DXHTTPRequest('/system/findExecutions', input_params, always_retry=always_retry, **kwargs) | def system_find_executions(input_params={}, always_retry=True, **kwargs) | Invokes the /system/findExecutions API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Search#API-method%3A-%2Fsystem%2FfindExecutions | 3.485262 | 4.610849 | 0.755883 |
return DXHTTPRequest('/system/findAnalyses', input_params, always_retry=always_retry, **kwargs) | def system_find_analyses(input_params={}, always_retry=True, **kwargs) | Invokes the /system/findAnalyses API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Search#API-method%3A-%2Fsystem%2FfindAnalyses | 3.954512 | 5.015233 | 0.7885 |
return DXHTTPRequest('/system/findDatabases', input_params, always_retry=always_retry, **kwargs) | def system_find_databases(input_params={}, always_retry=True, **kwargs) | Invokes the /system/findDatabases API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Search#API-method%3A-%2Fsystem%2FfindDatabases | 3.816944 | 5.700819 | 0.669543 |
return DXHTTPRequest('/system/findJobs', input_params, always_retry=always_retry, **kwargs) | def system_find_jobs(input_params={}, always_retry=True, **kwargs) | Invokes the /system/findJobs API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Search#API-method%3A-%2Fsystem%2FfindJobs | 3.961932 | 5.104447 | 0.776173 |
return DXHTTPRequest('/system/findProjects', input_params, always_retry=always_retry, **kwargs) | def system_find_projects(input_params={}, always_retry=True, **kwargs) | Invokes the /system/findProjects API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Search#API-method%3A-%2Fsystem%2FfindProjects | 3.695713 | 5.335766 | 0.69263 |
return DXHTTPRequest('/system/findUsers', input_params, always_retry=always_retry, **kwargs) | def system_find_users(input_params={}, always_retry=True, **kwargs) | Invokes the /system/findUsers API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Search#API-method%3A-%2Fsystem%2FfindUsers | 3.731944 | 5.435518 | 0.686585 |
return DXHTTPRequest('/system/findProjectMembers', input_params, always_retry=always_retry, **kwargs) | def system_find_project_members(input_params={}, always_retry=True, **kwargs) | Invokes the /system/findProjectMembers API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Search#API-method:-/system/findProjectMembers | 3.42285 | 4.837612 | 0.70755 |
return DXHTTPRequest('/system/findOrgs', input_params, always_retry=always_retry, **kwargs) | def system_find_orgs(input_params={}, always_retry=True, **kwargs) | Invokes the /system/findOrgs API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Search#API-method:-/system/findOrgs | 3.558672 | 4.556001 | 0.781096 |
return DXHTTPRequest('/system/generateBatchInputs', input_params, always_retry=always_retry, **kwargs) | def system_generate_batch_inputs(input_params={}, always_retry=True, **kwargs) | Invokes the /system/generateBatchInputs API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Search#API-method:-/system/generateBatchInputs | 4.122595 | 4.622102 | 0.891931 |
return DXHTTPRequest('/system/globalSearch', input_params, always_retry=always_retry, **kwargs) | def system_global_search(input_params={}, always_retry=True, **kwargs) | Invokes the /system/globalSearch API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Search#API-method:-/system/globalSearch | 3.872365 | 5.521649 | 0.701306 |
return DXHTTPRequest('/system/greet', input_params, always_retry=always_retry, **kwargs) | def system_greet(input_params={}, always_retry=True, **kwargs) | Invokes the /system/greet API method. | 4.411052 | 3.749522 | 1.17643 |
return DXHTTPRequest('/system/headers', input_params, always_retry=always_retry, **kwargs) | def system_headers(input_params={}, always_retry=True, **kwargs) | Invokes the /system/headers API method. | 3.643879 | 3.843071 | 0.948169 |
return DXHTTPRequest('/system/shortenURL', input_params, always_retry=always_retry, **kwargs) | def system_shorten_url(input_params={}, always_retry=True, **kwargs) | Invokes the /system/shortenURL API method. | 3.678652 | 3.535676 | 1.040438 |
return DXHTTPRequest('/system/whoami', input_params, always_retry=always_retry, **kwargs) | def system_whoami(input_params={}, always_retry=True, **kwargs) | Invokes the /system/whoami API method. | 3.435854 | 3.799717 | 0.904239 |
return DXHTTPRequest('/%s/describe' % object_id, input_params, always_retry=always_retry, **kwargs) | def user_describe(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /user-xxxx/describe API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Users#API-method%3A-%2Fuser-xxxx%2Fdescribe | 3.063274 | 3.892719 | 0.786924 |
return DXHTTPRequest('/%s/update' % object_id, input_params, always_retry=always_retry, **kwargs) | def user_update(object_id, input_params={}, always_retry=False, **kwargs) | Invokes the /user-xxxx/update API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Users#API-method%3A-%2Fuser-xxxx%2Fupdate | 3.581838 | 4.298423 | 0.833291 |
return DXHTTPRequest('/%s/addStage' % object_id, input_params, always_retry=always_retry, **kwargs) | def workflow_add_stage(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /workflow-xxxx/addStage API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Workflows-and-Analyses#API-method%3A-%2Fworkflow-xxxx%2FaddStage | 3.609261 | 4.232947 | 0.852659 |
return DXHTTPRequest('/%s/addTags' % object_id, input_params, always_retry=always_retry, **kwargs) | def workflow_add_tags(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /workflow-xxxx/addTags API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Tags#API-method%3A-%2Fclass-xxxx%2FaddTags | 3.273696 | 3.843825 | 0.851677 |
return DXHTTPRequest('/%s/addTypes' % object_id, input_params, always_retry=always_retry, **kwargs) | def workflow_add_types(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /workflow-xxxx/addTypes API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Types#API-method%3A-%2Fclass-xxxx%2FaddTypes | 3.339802 | 3.881081 | 0.860534 |
return DXHTTPRequest('/%s/close' % object_id, input_params, always_retry=always_retry, **kwargs) | def workflow_close(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /workflow-xxxx/close API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Data-Object-Lifecycle#API-method%3A-%2Fclass-xxxx%2Fclose | 3.329723 | 4.315219 | 0.771623 |
return DXHTTPRequest('/%s/describe' % object_id, input_params, always_retry=always_retry, **kwargs) | def workflow_describe(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /workflow-xxxx/describe API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Workflows-and-Analyses#API-method%3A-%2Fworkflow-xxxx%2Fdescribe | 3.438823 | 3.860735 | 0.890717 |
return DXHTTPRequest('/%s/dryRun' % object_id, input_params, always_retry=always_retry, **kwargs) | def workflow_dry_run(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /workflow-xxxx/dryRun API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Workflows-and-Analyses#API-method%3A-%2Fworkflow-xxxx%2FdryRun | 3.835841 | 3.796051 | 1.010482 |
return DXHTTPRequest('/%s/getDetails' % object_id, input_params, always_retry=always_retry, **kwargs) | def workflow_get_details(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /workflow-xxxx/getDetails API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Details-and-Links#API-method%3A-%2Fclass-xxxx%2FgetDetails | 3.635269 | 3.720739 | 0.977029 |
return DXHTTPRequest('/%s/isStageCompatible' % object_id, input_params, always_retry=always_retry, **kwargs) | def workflow_is_stage_compatible(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /workflow-xxxx/isStageCompatible API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Workflows-and-Analyses#API-method%3A-%2Fworkflow-xxxx%2FisStageCompatible | 3.750827 | 3.637201 | 1.03124 |
return DXHTTPRequest('/%s/listProjects' % object_id, input_params, always_retry=always_retry, **kwargs) | def workflow_list_projects(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /workflow-xxxx/listProjects API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Cloning#API-method%3A-%2Fclass-xxxx%2FlistProjects | 3.435024 | 4.095092 | 0.838815 |
return DXHTTPRequest('/%s/moveStage' % object_id, input_params, always_retry=always_retry, **kwargs) | def workflow_move_stage(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /workflow-xxxx/moveStage API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Workflows-and-Analyses#API-method%3A-%2Fworkflow-xxxx%2FmoveStage | 3.45614 | 4.384871 | 0.788197 |
return DXHTTPRequest('/%s/overwrite' % object_id, input_params, always_retry=always_retry, **kwargs) | def workflow_overwrite(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /workflow-xxxx/overwrite API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Workflows-and-Analyses#API-method%3A-%2Fworkflow-xxxx%2Foverwrite | 3.64633 | 4.393746 | 0.829891 |
return DXHTTPRequest('/%s/removeStage' % object_id, input_params, always_retry=always_retry, **kwargs) | def workflow_remove_stage(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /workflow-xxxx/removeStage API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Workflows-and-Analyses#API-method%3A-%2Fworkflow-xxxx%2FremoveStage | 3.482835 | 4.240803 | 0.821268 |
return DXHTTPRequest('/%s/removeTags' % object_id, input_params, always_retry=always_retry, **kwargs) | def workflow_remove_tags(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /workflow-xxxx/removeTags API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Tags#API-method%3A-%2Fclass-xxxx%2FremoveTags | 3.119026 | 3.908909 | 0.797928 |
return DXHTTPRequest('/%s/removeTypes' % object_id, input_params, always_retry=always_retry, **kwargs) | def workflow_remove_types(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /workflow-xxxx/removeTypes API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Types#API-method%3A-%2Fclass-xxxx%2FremoveTypes | 3.209309 | 3.936772 | 0.815213 |
return DXHTTPRequest('/%s/rename' % object_id, input_params, always_retry=always_retry, **kwargs) | def workflow_rename(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /workflow-xxxx/rename API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Name#API-method%3A-%2Fclass-xxxx%2Frename | 3.007368 | 3.94594 | 0.762142 |
return DXHTTPRequest('/%s/validateBatch' % object_id, input_params, always_retry=always_retry, **kwargs) | def workflow_validate_batch(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /workflow-xxxx/validateBatch API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Workflows-and-Analyses#API-method%3A-%2Fworkflow-xxxx%2FvalidateBatch | 3.35405 | 3.964237 | 0.846077 |
return DXHTTPRequest('/%s/setDetails' % object_id, input_params, always_retry=always_retry, **kwargs) | def workflow_set_details(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /workflow-xxxx/setDetails API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Details-and-Links#API-method%3A-%2Fclass-xxxx%2FsetDetails | 3.422015 | 3.566893 | 0.959383 |
return DXHTTPRequest('/%s/setProperties' % object_id, input_params, always_retry=always_retry, **kwargs) | def workflow_set_properties(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /workflow-xxxx/setProperties API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Properties#API-method%3A-%2Fclass-xxxx%2FsetProperties | 3.163846 | 3.838928 | 0.824148 |
return DXHTTPRequest('/%s/setStageInputs' % object_id, input_params, always_retry=always_retry, **kwargs) | def workflow_set_stage_inputs(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /workflow-xxxx/setStageInputs API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Workflows-and-Analyses#API-method%3A-%2Fworkflow-xxxx%2FsetStageInputs | 3.492741 | 3.898901 | 0.895827 |
return DXHTTPRequest('/%s/setVisibility' % object_id, input_params, always_retry=always_retry, **kwargs) | def workflow_set_visibility(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /workflow-xxxx/setVisibility API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Visibility#API-method%3A-%2Fclass-xxxx%2FsetVisibility | 3.681696 | 4.165773 | 0.883797 |
return DXHTTPRequest('/%s/update' % object_id, input_params, always_retry=always_retry, **kwargs) | def workflow_update(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /workflow-xxxx/update API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Workflows-and-Analyses#API-method%3A-%2Fworkflow-xxxx%2Fupdate | 3.528178 | 4.61192 | 0.765013 |
return DXHTTPRequest('/%s/updateStageExecutable' % object_id, input_params, always_retry=always_retry, **kwargs) | def workflow_update_stage_executable(object_id, input_params={}, always_retry=True, **kwargs) | Invokes the /workflow-xxxx/updateStageExecutable API method.
For more info, see: https://wiki.dnanexus.com/API-Specification-v1.0.0/Workflows-and-Analyses#API-method%3A-%2Fworkflow-xxxx%2FupdateStageExecutable | 3.500612 | 3.924764 | 0.891929 |
# If the image is already encoded in Base64, we have nothing to do here
if "src" not in img.attrs or img["src"].startswith("data:"):
return
elif re.match("https?://", img["src"]):
img_data = _load_url(img["src"]).read()
else:
img_data = _load_file(img["src"]).read()
img_... | def _image_to_data(img) | Does the work of encoding an image into Base64 | 3.012202 | 2.790539 | 1.079434 |
if "href" in link.attrs and (re.search("\.css$", link["href"])) or ("rel" in link.attrs and link["rel"] is "stylesheet") or ("type" in link.attrs and link["type"] is "text/css"):
if re.match("https?://", link["href"]):
css_data = _load_url(link["href"]).read()
else:
css_... | def _bake_css(link) | Takes a link element and turns it into an inline style link if applicable | 2.745254 | 2.606675 | 1.053163 |
if "src" in script.attrs:
if re.match("https?://", script["src"]):
script_data = _load_url(script["src"]).read()
else:
script_data = _load_file(script["src"]).read()
script.clear()
if USING_PYTHON2:
script.string = "\n" + script_data + "\n"
... | def _bake_script(script) | Takes a script element and bakes it in only if it contains a remote resource | 2.845523 | 2.636571 | 1.079251 |
if not os.path.exists(path):
parser.error("{} was not found!".format(path))
if USING_PYTHON2:
mode = "r"
else:
mode = "rb"
try:
f = open(path, mode)
return f
except IOError as ex:
parser.error("{path} could not be read due to an I/O error! ({ex})"... | def _load_file(path) | Loads a file from the local filesystem | 3.198411 | 3.073382 | 1.040681 |
try:
response = requests.get(url)
return BytesIO(response.content)
except IOError as ex:
parser.error("{url} could not be loaded remotely! ({ex})".format(url=url, ex=ex)) | def _load_url(url) | Loads a URL resource from a remote server | 4.228206 | 4.184722 | 1.010391 |
if len(soup.find_all("script")) == 0:
soup_str = soup.prettify(formatter=None).strip()
else:
soup_str = str(soup.html)
soup_str = re.sub("&", "&", soup_str)
soup_str = re.sub("<", "<", soup_str)
soup_str = re.sub(">", ">", soup_str)
return soup_str | def _get_bs4_string(soup) | Outputs a BeautifulSoup object as a string that should hopefully be minimally modified | 2.152445 | 2.097747 | 1.026075 |
src = os.path.realpath(src)
path = os.path.dirname(src)
filename = os.path.basename(src)
html = _load_file(src).read()
if imghdr.what("", html):
html = "<html><body><img src='{}'/></body></html>".format(cgi.escape(filename))
# Change to the file's directory so image files with rela... | def bake(src) | Runs the encoder on the given source file | 2.961593 | 3.009067 | 0.984223 |
[project, path, n] = parse_destination(destination)
try:
dxfile = dxpy.upload_string(html, media_type="text/html", project=project, folder=path, hidden=True, name=name or None)
return dxfile.get_id()
except dxpy.DXAPIError as ex:
parser.error("Could not upload HTML report to DNA... | def upload_html(destination, html, name=None) | Uploads the HTML to a file on the server | 4.958365 | 4.998803 | 0.991911 |
[project, path, name] = parse_destination(destination)
files = [dxpy.dxlink(file_id) for file_id in file_ids]
details = {"files": files}
if width:
details["width"] = width
if height:
details["height"] = height
try:
dxrecord = dxpy.new_dxrecord(project=project, folder... | def create_record(destination, file_ids, width=None, height=None) | Creates a master record for the HTML report; this doesn't contain contain the actual HTML, but reports
are required to be records rather than files and we can link more than one HTML file to a report | 3.760163 | 3.556654 | 1.057219 |
try:
out_file = open(filename, "w")
out_file.write(html)
out_file.close()
except IOError as ex:
parser.error("Could not write baked HTML to local file {name}. ({ex})".format(name=filename, ex=ex)) | def save(filename, html) | Creates a baked HTML file on the local system | 3.722192 | 3.163002 | 1.176791 |
if size == 0:
magnitude = 0
level = 0
else:
magnitude = math.floor(math.log(size, 10))
level = int(min(math.floor(magnitude // 3), 4))
return ('%d' if level == 0 else '%.2f') % (float(size) / 2**(level*10)) + ' ' + SIZE_LEVEL[level] | def get_size_str(size) | Formats a byte size as a string.
The returned string is no more than 9 characters long. | 4.0285 | 4.054832 | 0.993506 |
'''
:param thing: something that might be a job-based object reference hash
:param reftype: type that a job-based object reference would be (default is dict)
'''
return isinstance(thing, reftype) and \
((len(thing) == 2 and \
isinstance(thing.get('field'), basestring) and \
... | def is_job_ref(thing, reftype=dict) | :param thing: something that might be a job-based object reference hash
:param reftype: type that a job-based object reference would be (default is dict) | 3.1061 | 2.163688 | 1.435558 |
'''
:param desc: The describe hash of a DNAnexus entity
:type desc: dict
Depending on the class of the entity, this method will print a
formatted and human-readable string containing the data in *desc*.
'''
if desc['class'] in ['project', 'workspace', 'container']:
print_project_des... | def print_desc(desc, verbose=False) | :param desc: The describe hash of a DNAnexus entity
:type desc: dict
Depending on the class of the entity, this method will print a
formatted and human-readable string containing the data in *desc*. | 3.402907 | 2.063038 | 1.649464 |
# If you make this method consume an additional field, you must add it to
# get_ls_l_desc_fields above.
if 'state' in desc:
state_len = len(desc['state'])
if desc['state'] != 'closed':
state_str = YELLOW() + desc['state'] + ENDC()
else:
state_str = GREEN(... | def get_ls_l_desc(desc, include_folder=False, include_project=False) | desc must have at least all the fields given by get_ls_l_desc_fields. | 3.453392 | 3.278782 | 1.053255 |
'''
:param desc: hash of execution's describe output
:param has_children: whether the execution has children to be printed
:param single_result: whether the execution is displayed as a single result or as part of an execution tree
:param is_cached_result: whether the execution should be formatted as... | def get_find_executions_string(desc, has_children, single_result=False, show_outputs=True,
is_cached_result=False) | :param desc: hash of execution's describe output
:param has_children: whether the execution has children to be printed
:param single_result: whether the execution is displayed as a single result or as part of an execution tree
:param is_cached_result: whether the execution should be formatted as a cached re... | 3.792022 | 3.411508 | 1.111538 |
try:
if instance_count_arg is None:
return cls(None)
if isinstance(instance_count_arg, basestring) or isinstance(instance_count_arg, int):
return cls({entrypoint: {"clusterSpec": {"initialInstanceCount": int(instance_count_arg)}}})
if ... | def from_instance_count(cls, instance_count_arg, entrypoint="*") | Returns a SystemRequirementsDict that can be passed as a
"systemRequirements" input to job/new or run/ API calls.
The instance_count_arg should be either a:
* string or int eg. "6" or 8
* dictionary, eg. {"main": 4, "other_function": 2} | 2.932437 | 2.737191 | 1.071331 |
if instance_type_arg is None:
return cls(None)
if isinstance(instance_type_arg, basestring):
# By default, all entry points ("*") should use this instance type
return cls({entrypoint: {"instanceType": instance_type_arg}})
if isinstance(instance_type_a... | def from_instance_type(cls, instance_type_arg, entrypoint="*") | Returns SystemRequirementsDict that can be passed as a
"systemRequirements" input to job/new or run/ API calls.
The instance_type_arg should be either a:
* string, eg. mem1_ssd1_x2
* dictionary, eg. {"main": "mem2_hdd2_x2", "other_function": "mem2_hdd2_x1"} | 3.86225 | 3.702705 | 1.043089 |
if _type not in ('all', 'clusterSpec', 'instanceType'):
raise DXError("Expected '_type' to be either 'all', 'clusterSpec', or 'instanceType'")
if _type == 'all':
return cls(system_requirements)
extracted = defaultdict(dict)
for entrypoint, req in system... | def from_sys_requirements(cls, system_requirements, _type='all') | Returns SystemRequirementsDict encapsulating system requirements.
It can extract only entrypoints with specific fields ('clusterSpec',
'instanceType', etc), depending on the value of _type. | 3.74903 | 2.459376 | 1.524383 |
if d1 is None and d2 is None:
return None
d1 = d1 or {}
d2 = d2 or {}
added = {}
for key in set(list(d1.keys()) + list(d2.keys())):
added[key] = dict(d1.get(key, {}), **(d2.get(key, {})))
return added | def _add_dict_values(self, d1, d2) | Merges the values of two dictionaries, which are expected to be dictionaries, e.g
d1 = {'a': {'x': pqr}}
d2 = {'a': {'y': lmn}, 'b': {'y': rst}}
will return: {'a': {'x': pqr, 'y': lmn}, 'b': {'y': rst}}.
Collisions of the keys of the sub-dictionaries are not checked. | 2.270057 | 2.089733 | 1.086291 |
'''
:rtype: :class:`DXRecord`
:param details: The contents of the record to be created.
:type details: dict
Additional optional parameters not listed: all those under
:func:`dxpy.bindings.DXDataObject.new`, except `details`.
Creates a new remote record object with project set to *project*... | def new_dxrecord(details=None, **kwargs) | :rtype: :class:`DXRecord`
:param details: The contents of the record to be created.
:type details: dict
Additional optional parameters not listed: all those under
:func:`dxpy.bindings.DXDataObject.new`, except `details`.
Creates a new remote record object with project set to *project*
and ret... | 5.285036 | 1.457084 | 3.627133 |
if "init_from" in kwargs:
if kwargs["init_from"] is not None:
if not isinstance(kwargs["init_from"], DXRecord):
raise DXError("Expected instance of DXRecord to init_from")
dx_hash["initializeFrom"] = \
{"id": kwargs["i... | def _new(self, dx_hash, close=False, **kwargs) | :param dx_hash: Standard hash populated in :func:`dxpy.bindings.DXDataObject.new()` containing attributes common to all data object classes.
:type dx_hash: dict
:param init_from: Record from which to initialize the metadata
:type init_from: :class:`DXRecord`
:param close: Whether or not ... | 3.17248 | 2.620682 | 1.210555 |
if isinstance(foo, dict):
for (key, val) in list(foo.items()):
if isinstance(val, dict):
_recursive_cleanup(val)
if val == "" or val == [] or val == {}:
del foo[key] | def _recursive_cleanup(foo) | Aggressively cleans up things that look empty. | 2.293571 | 2.113652 | 1.085122 |
try:
old_cwd = os.getcwd()
os.chdir(destination_directory)
if isinstance(executable, dxpy.DXWorkflow):
_dump_workflow(executable, describe_output)
elif isinstance(executable, dxpy.DXGlobalWorkflow):
# Add inputs, outputs, stages. These fields contain regi... | def dump_executable(executable, destination_directory, omit_resources=False, describe_output={}) | Reconstitutes an app, applet, or a workflow into a directory that would
create a functionally identical executable if "dx build" were run on it.
destination_directory will be the root source directory for the
executable.
:param executable: executable, i.e. app, applet, or workflow, to be dumped
:ty... | 6.39874 | 5.887504 | 1.086834 |
if not isinstance(batchsize, int) or batchsize <= 0 or batchsize > 1000:
raise ValueError("batchsize for resolve_data_objects must be a positive integer not exceeding 1000")
args = {}
if project:
args.update({'project': project})
if folder:
args.update({'folder': folder})
... | def resolve_data_objects(objects, project=None, folder=None, batchsize=1000) | :param objects: Data object specifications, each with fields "name"
(required), "folder", and "project"
:type objects: list of dictionaries
:param project: ID of project context; a data object's project defaults
to this if not specified for that object
:type project: ... | 2.96736 | 2.772943 | 1.070112 |
''' Takes an API method handler (dxpy.api.find*) and calls it with *query*,
and then wraps a generator around its output. Used by the methods below.
Note that this function may only be used for /system/find* methods.
'''
num_results = 0
if "limit" not in query:
query["limit"] = first_p... | def _find(api_method, query, limit, return_handler, first_page_size, **kwargs) | Takes an API method handler (dxpy.api.find*) and calls it with *query*,
and then wraps a generator around its output. Used by the methods below.
Note that this function may only be used for /system/find* methods. | 4.574163 | 2.706125 | 1.6903 |
return find_global_executables(dxpy.api.system_find_apps,
name=name, name_mode=name_mode, category=category,
all_versions=all_versions, published=published,
billed_to=billed_to, created_by=created_by, devel... | def find_apps(name=None, name_mode='exact', category=None,
all_versions=None, published=None,
billed_to=None, created_by=None, developer=None,
created_after=None, created_before=None,
modified_after=None, modified_before=None,
describe=False, limit=N... | This method is identical to :meth:`find_global_executables()` with the API method
used: :meth:`system_find_apps()`. | 1.687725 | 1.523105 | 1.108082 |
return _find_one(find_data_objects, zero_ok=zero_ok, more_ok=more_ok, **kwargs) | def find_one_data_object(zero_ok=False, more_ok=True, **kwargs) | :param zero_ok:
If False (default), :class:`~dxpy.exceptions.DXSearchError` is
raised if the search has 0 results; if True, returns None if the
search has 0 results
:type zero_ok: bool
:param more_ok:
If False, :class:`~dxpy.exceptions.DXSearchError` is raised if
the sear... | 2.702999 | 4.975706 | 0.543239 |
return _find_one(find_projects, zero_ok=zero_ok, more_ok=more_ok, **kwargs) | def find_one_project(zero_ok=False, more_ok=True, **kwargs) | :param zero_ok:
If False (default), :class:`~dxpy.exceptions.DXSearchError` is
raised if the search has 0 results; if True, returns None if the
search has 0 results
:type zero_ok: bool
:param more_ok:
If False, :class:`~dxpy.exceptions.DXSearchError` is raised if
the sear... | 2.778035 | 5.206185 | 0.533603 |
return _find_one(find_apps, zero_ok=zero_ok, more_ok=more_ok, **kwargs) | def find_one_app(zero_ok=False, more_ok=True, **kwargs) | :param zero_ok:
If False (default), :class:`~dxpy.exceptions.DXSearchError` is
raised if the search has 0 results; if True, returns None if the
search has 0 results
:type zero_ok: bool
:param more_ok:
If False, :class:`~dxpy.exceptions.DXSearchError` is raised if
the sear... | 2.747964 | 4.904448 | 0.5603 |
if "limit" not in query:
query["limit"] = min(first_page_size, 1000)
while True:
resp = api_method(org_id, query)
for result in resp["results"]:
yield result
# set up next query
if resp["next"] is not None:
query["starting"] = resp["next"]
... | def _org_find(api_method, org_id, query, first_page_size=100) | Takes an API method handler ``dxpy.api.org_find...`` and calls it with
*org_id* and *query*, then wraps a generator around its output. Used by
:meth:`org_find_members` and :meth:`org_find_projects` below.
:param first_page_size: The number of results that the initial API call will return.
:type first_p... | 2.483693 | 2.966571 | 0.837227 |
query = {}
if level is not None:
query["level"] = level
query["describe"] = describe
return _org_find(dxpy.api.org_find_members, org_id, query) | def org_find_members(org_id=None, level=None, describe=False) | :param org_id: ID of the organization
:type org_id: string
:param level: The membership level in the org that each member in the result set must have (one of "MEMBER" or
"ADMIN")
:type level: string
:param describe: Whether or not to return the response of ``dxpy.api.user_describe`` for each res... | 4.318653 | 3.964571 | 1.089311 |
query = {}
if name is not None:
if name_mode == 'exact':
query['name'] = name
elif name_mode == 'glob':
query['name'] = {'glob': name}
elif name_mode == 'regexp':
query['name'] = {'regexp': name}
else:
raise DXError('org_find_p... | def org_find_projects(org_id=None, name=None, name_mode='exact', ids=None, properties=None, tags=None, describe=False,
public=None, created_after=None, created_before=None, region=None, containsPHI=None) | :param org_id: ID of the organization
:type org_id: string
:param name: Name that each result must have (also see *name_mode* param)
:type name: string
:param name_mode: Method by which to interpret the *name* param ("exact": exact match,
"glob": use "*" and "?" as wildcards, "regexp": interpret... | 1.751187 | 1.688356 | 1.037214 |
return _find(dxpy.api.system_find_orgs, query, limit=None,
return_handler=False, first_page_size=first_page_size) | def find_orgs(query, first_page_size=10) | :param query: The input to the /system/findOrgs API method.
:type query: dict
:param first_page_size: The number of results that the initial
/system/findOrgs API call will return; default 10, max 1000. Subsequent
calls will raise the number of returned results exponentially up to a
max ... | 6.568615 | 6.812107 | 0.964256 |
'''
Create a set of directories, so we could store the input files.
For example, seq1 could be stored under:
/in/seq1/NC_001122.fasta
TODO: this call could fail, we need to report a reasonable error code
Note that we create a directory for every file array, even if
it has zero inputs.
... | def _create_dirs(idir, dirs) | Create a set of directories, so we could store the input files.
For example, seq1 could be stored under:
/in/seq1/NC_001122.fasta
TODO: this call could fail, we need to report a reasonable error code
Note that we create a directory for every file array, even if
it has zero inputs. | 9.986649 | 2.235705 | 4.466889 |
'''
Create a dict of values for the downloaded files. This is similar to the variables created
when running a bash app.
'''
file_key_descs, _ignore = file_load_utils.analyze_bash_vars(
file_load_utils.get_input_json_file(), None)
flattened_dict = {}
def add_if_no_collision(key, va... | def _gen_helper_dict(filtered_inputs) | Create a dict of values for the downloaded files. This is similar to the variables created
when running a bash app. | 3.960624 | 2.867342 | 1.381288 |
'''
Ensure at least ~1.2 GB memory per thread, see PTFM-18767
'''
return min(max_threads, num_cores, max(int(mem_available_mb/1200), 1)) | def _get_num_parallel_threads(max_threads, num_cores, mem_available_mb) | Ensure at least ~1.2 GB memory per thread, see PTFM-18767 | 9.18889 | 2.557507 | 3.592909 |
paragraphs = string.split('\n\n')
refilled_paragraphs = [fill(paragraph) if not paragraph.startswith(ignored_prefix) else paragraph for paragraph in paragraphs]
return '\n\n'.join(refilled_paragraphs).strip('\n') | def refill_paragraphs(string, ignored_prefix=' ') | Refills the given text, where the text is composed of paragraphs
separated by blank lines (i.e. '\n\n'). Lines that begin with
ignored_prefix are not touched; this can be used to keep indented
code snippets from being incorrectly reformatted. | 2.534758 | 2.557941 | 0.990937 |
if args.json:
print(json.dumps(list(results), indent=4))
elif args.brief:
for result in results:
print(result['id'])
else:
if args.func.__name__ in ("find_projects", "org_find_projects"):
_format_find_projects_results(results)
elif args.func.__nam... | def format_find_results(args, results) | Formats the output of ``dx find ...`` commands for `--json` and `--brief` arguments; also formats if no formatting
arguments are given.
Currently used for ``dx find projects``, ``dx find org_projects``, ``dx find org_apps``,
and ``dx find org_members`` | 3.199214 | 2.868321 | 1.115361 |
draw_lines()
draw_histogram()
draw_bar_chart()
destination = "-r /report"
if use_html:
generate_html()
command = "dx-build-report-html {h} {d}".format(h=html_filename, d=destination)
else:
command = "dx-build-report-html {l} {b} {h} {d}".format(l=lines_filename, b=ba... | def main(**kwargs) | Draw a couple of simple graphs and optionally generate an HTML file to upload them | 5.329749 | 4.730925 | 1.126576 |
mu, sigma = 100, 15
x = mu + sigma * numpy.random.randn(10000)
fig = pyplot.figure()
ax = fig.add_subplot(111)
n, bins, patches = ax.hist(x, 50, normed=1, facecolor='green', alpha=0.75)
ax.set_xlabel('Random number generated')
ax.set_ylabel('Probability')
ax.set_xlim(40, 160)
... | def draw_histogram() | Uses sample code from http://matplotlib.org/1.2.1/examples/api/histogram_demo.html | 1.963489 | 1.841484 | 1.066253 |
N = 5
menMeans = (20, 35, 30, 35, 27)
menStd = (2, 3, 4, 1, 2)
ind = numpy.arange(N)
width = 0.35
fig = pyplot.figure()
ax = fig.add_subplot(111)
rects1 = ax.bar(ind, menMeans, width, color='r', yerr=menStd)
womenMeans = (25, 32, 34, 20, 25)
womenStd = (3, 5, 2, 3, 3)
... | def draw_bar_chart() | Uses sample code from http://matplotlib.org/1.2.1/examples/api/barchart_demo.html | 1.429386 | 1.396799 | 1.02333 |
r = numpy.random.randn(200)
fig = pyplot.figure()
ax = fig.add_subplot(111)
ax.plot(r)
ax.grid(True)
pyplot.savefig(lines_filename) | def draw_lines() | Draws a line between a set of random values | 4.117383 | 3.651327 | 1.12764 |
html_file = open(html_filename, "w")
html_file.write("<html><body>")
html_file.write("<h1>Here are some graphs for you!</h1>")
for image in [lines_filename, bars_filename, histogram_filename]:
html_file.write("<div><h2>{0}</h2><img src='{0}' /></div>".format(image))
html_file.write("</b... | def generate_html() | Generate an HTML file incorporating the images produced by this script | 2.836811 | 2.714617 | 1.045013 |
def clean(s):
return u''.join([c if c in ASCII_PRINTABLE else '?' for c in s])
if USING_PYTHON2:
try:
return unicode(o)
except:
try:
s = str(o)
try:
return s.decode("utf-8")
except:
... | def _safe_unicode(o) | Returns an equivalent unicode object, trying harder to avoid
dependencies on the Python default encoding. | 4.888691 | 4.710323 | 1.037867 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.