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Merge pull request #36 from unity-sds/mcduffie
Add notebook for interacting with Dockstore API to publish an application
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‎jupyter-notebooks/tutorials/dockstore_publish.ipynb

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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 1,
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"id": "702d6a78-9eef-418a-b624-43ee8ee98643",
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"metadata": {},
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"outputs": [],
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"source": [
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"import os\n",
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"import sys"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"id": "6f3a0abe-3a42-455d-b365-0f0039455570",
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"metadata": {},
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"outputs": [],
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"source": [
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"sys.path.append(os.path.expanduser(\"~/unity-py\"))"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"id": "0d63d3d2-0f6e-4303-b37d-8394e0e1411c",
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"metadata": {},
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"outputs": [],
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"source": [
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"from unity_py.services.application_service import *"
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]
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},
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{
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"cell_type": "markdown",
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"id": "42bfa738-fc42-421a-b2cf-44b1204e32eb",
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"metadata": {},
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"source": [
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"## Configuration"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"id": "11b285a3-2b97-4cd1-9115-05beb47de12a",
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"metadata": {},
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"outputs": [],
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"source": [
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"dockstore_api_uri = \"http://uads-test-dockstore-deploy-lb-1762603872.us-west-2.elb.amazonaws.com:9998/api\""
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]
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"id": "2f1108d3-b0cb-49ec-9c87-d86515b102f9",
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"metadata": {},
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"outputs": [],
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"source": [
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"token = !cat ~/.dockstore/config | grep token | awk '{print $2}'\n",
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"token = token[0]"
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]
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},
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{
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"cell_type": "markdown",
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"id": "7e128d17-f0a4-4698-8ab1-4d68f0da0316",
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"metadata": {},
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"source": [
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"## Catalog Interface\n"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"id": "b9dae047-4ac0-478c-87b7-b8011d09465c",
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"metadata": {},
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"outputs": [],
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"source": [
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"app_catalog = DockstoreAppCatalog(dockstore_api_uri, token)"
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]
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},
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{
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"cell_type": "markdown",
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"id": "919b88c1-4e85-446e-801e-0ee76d264525",
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"metadata": {},
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"source": [
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"## Existing User Applications"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 7,
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"id": "4ca327d3-35fe-4455-8eae-a9d56a88c423",
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"metadata": {
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"tags": []
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},
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"outputs": [],
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"source": [
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"for app in app_catalog.application_list(for_user=True):\n",
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" print(f\"{app.id} {app.name} {app.source_repository}\")"
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]
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},
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{
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"cell_type": "markdown",
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"id": "29b1516d-e67e-48d7-a2fc-e4293317f46a",
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"metadata": {},
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"source": [
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"## New Application"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 8,
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"id": "fcbe7a9c-6893-424d-822a-f1c1a1b10773",
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"metadata": {},
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"outputs": [],
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"source": [
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"name = \"sounder_sips_l1a\"\n",
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"source_repository = \"[email protected]:unity-sds/sounder-sips-application.git\"\n",
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"workflow_path = \"/cwl/l1a_workflow.cwl\""
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]
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},
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{
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"cell_type": "code",
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"execution_count": 9,
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"id": "f2a48297-ca47-43b6-929e-484159876607",
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"metadata": {},
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"outputs": [],
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"source": [
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"new_app = ApplicationPackage(name, source_repository, workflow_path)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 10,
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"id": "eed8a991-dadb-48e9-91b2-fb93abfbf1f8",
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"ApplicationPackage(name='sounder_sips_l1a', source_repository='[email protected]:unity-sds/sounder-sips-application.git', workflow_path='/cwl/l1a_workflow.cwl', id=None, is_published=False, description='', workflow_type='CWL')"
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]
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},
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"execution_count": 10,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"new_app"
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]
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},
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{
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"cell_type": "markdown",
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"id": "1f94da3e-727a-456e-ab13-32edf688ddba",
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"metadata": {},
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"source": [
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"## Publish Application"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 11,
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"id": "f3ea1bb2-00ff-46d6-9a18-ef23a5bd93f0",
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"metadata": {},
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"outputs": [],
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"source": [
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"reg_app = app_catalog.register(new_app)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 12,
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"id": "360a929a-bbbf-4a51-8433-b72f7424f7b7",
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"DockstoreApplicationPackage(name='sounder_sips_l1a', source_repository='[email protected]:unity-sds/sounder-sips-application.git', workflow_path='/cwl/l1a_workflow.cwl', id='50', is_published=False, description='Processes Sounder SIPS L0 products into L1A products', workflow_type='CWL', dockstore_info={'type': 'BioWorkflow', 'descriptorType': 'CWL', 'aliases': {}, 'author': 'James McDuffie', 'checker_id': None, 'conceptDoi': None, 'dbCreateDate': 1670623272833, 'dbUpdateDate': 1670623276387, 'defaultTestParameterFilePath': '/test.json', 'defaultVersion': 'main', 'description': 'Processes Sounder SIPS L0 products into L1A products', 'descriptorTypeSubclass': 'NOT_APPLICABLE', 'email': '[email protected]', 'forumUrl': None, 'full_workflow_path': 'github.com/unity-sds/sounder-sips-application/sounder_sips_l1a', 'gitUrl': '[email protected]:unity-sds/sounder-sips-application.git', 'has_checker': False, 'id': 50, 'input_file_formats': [], 'isChecker': False, 'is_published': False, 'labels': [], 'lastUpdated': 1670623272828, 'last_modified': 2004663152, 'last_modified_date': 1668451974000, 'licenseInformation': {'licenseName': 'Other'}, 'mode': 'FULL', 'organization': 'unity-sds', 'output_file_formats': [], 'parent_id': None, 'path': 'github.com/unity-sds/sounder-sips-application', 'repository': 'sounder-sips-application', 'sourceControl': 'github.com', 'source_control_provider': 'GITHUB', 'starredUsers': [], 'topic': 'This repository represents the containerization of the Sounder SIPS SPSS repository into a Unity Application Package.', 'topicAutomatic': 'This repository represents the containerization of the Sounder SIPS SPSS repository into a Unity Application Package.', 'topicId': None, 'topicManual': None, 'topicSelection': 'AUTOMATIC', 'userIdToOrcidPutCode': None, 'users': [{'avatarUrl': 'https://avatars.githubusercontent.com/u/3554574?v=4', 'curator': False, 'id': 2, 'isAdmin': False, 'name': 'mcduffie', 'orcid': None, 'privacyPolicyVersion': 'PRIVACY_POLICY_VERSION_2_5', 'privacyPolicyVersionAcceptanceDate': 1660239673886, 'setupComplete': False, 'tosacceptanceDate': 1660239673886, 'tosversion': 'TOS_VERSION_2', 'userProfiles': None, 'username': 'mcduffie', 'usernameChangeRequired': False}], 'workflowName': 'sounder_sips_l1a', 'workflowVersions': [{'aliases': None, 'author': 'James McDuffie', 'authors': [{'affiliation': None, 'email': '[email protected]', 'name': 'James McDuffie', 'role': None}], 'commitID': 'a1e2cf4b07504820129cd8ed7554134b4534f79d', 'dbUpdateDate': 1670623276387, 'description': 'Processes Sounder SIPS L0 products into L1A products', 'descriptionSource': 'DESCRIPTOR', 'dirtyBit': False, 'doiStatus': 'NOT_REQUESTED', 'doiURL': None, 'email': '[email protected]', 'frozen': False, 'hidden': False, 'id': 73, 'images': None, 'input_file_formats': [], 'last_modified': 1668451974000, 'legacyVersion': True, 'name': 'main', 'orcidAuthors': None, 'output_file_formats': [], 'reference': 'main', 'referenceType': 'BRANCH', 'subClass': None, 'synced': True, 'valid': True, 'validations': None, 'verified': False, 'verifiedSource': None, 'verifiedSources': [], 'versionEditor': None, 'versionMetadata': {'description': 'Processes Sounder SIPS L0 products into L1A products', 'id': 73, 'parsedInformationSet': [{'descriptorLanguage': 'CWL', 'hasHTTPImports': False, 'hasLocalImports': True}], 'publicAccessibleTestParameterFile': None, 'userIdToOrcidPutCode': {}}, 'workflow_path': '/cwl/l1a_workflow.cwl', 'workingDirectory': 'cwl'}], 'workflow_path': '/cwl/l1a_workflow.cwl'})"
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]
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},
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"execution_count": 12,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"reg_app"
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]
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},
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{
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"cell_type": "markdown",
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"id": "704a1308-796f-4591-adf1-a98b35a20b26",
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"metadata": {
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"tags": []
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},
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"source": [
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"## Delete Application (Cleanup)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 13,
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"id": "307ee2df-c596-4170-81bb-faff193c86b7",
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"metadata": {},
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"outputs": [],
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"source": [
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"del_app = app_catalog.unregister(reg_app, delete=True)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 14,
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"id": "f76c6475-ca8e-46be-bf1e-1608cd628f9d",
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"DockstoreApplicationPackage(name='sounder_sips_l1a', source_repository='[email protected]:unity-sds/sounder-sips-application.git', workflow_path='/cwl/l1a_workflow.cwl', id=None, is_published=False, description='Processes Sounder SIPS L0 products into L1A products', workflow_type='CWL', dockstore_info=None)"
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]
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},
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"execution_count": 14,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"del_app"
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.10.6"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

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