Feature: Sim Amend Revision

designsafe/apps/api/tasks.py

@@ -669,6 +669,7 @@ def amend_publication_data(self, project_id, amendments=None, authors=None, revi
     """
     from designsafe.apps.projects.managers import publication as PublicationManager
     from designsafe.libs.fedora.fedora_operations import amend_project_fedora, ingest_project_experimental
+    from designsafe.libs.fedora.sim_operations import ingest_project_sim
     try:
         amended_pub = PublicationManager.amend_publication(project_id, amendments, authors, revision)
         PublicationManager.amend_datacite_doi(amended_pub)
@@ -677,6 +678,8 @@ def amend_publication_data(self, project_id, amendments=None, authors=None, revi
            amend_project_fedora(project_id, version=revision)
         if amended_pub.project.value.projectType == 'experimental':
             ingest_project_experimental(project_id, version=revision, amend=True)
+        if amended_pub.project.value.projectType == 'simulation':
+            ingest_project_sim(project_id, version=revision, amend=True)
     except Exception as exc:
         logger.error('Proj Id: %s. %s', project_id, exc, exc_info=True)
         raise self.retry(exc=exc)
@@ -773,6 +776,10 @@ def save_to_fedora(self, project_id, revision=None):
             from designsafe.libs.fedora.fedora_operations import ingest_project_experimental
             ingest_project_experimental(project_id, version=revision)
             return
+        if pub.project.value.projectType == 'simulation':
+            from designsafe.libs.fedora.sim_operations import ingest_project_sim
+            ingest_project_sim(project_id, version=revision)
+            return
 
         _root = os.path.join('/corral-repl/tacc/NHERI/published', project_id)
         fedora_base = 'http://fedoraweb01.tacc.utexas.edu:8080/fcrepo/rest/publications_01'

designsafe/libs/fedora/fedora_operations.py

@@ -76,6 +76,9 @@
     "references": {
         "@id": "http://purl.org/dc/elements/1.1/references"
     },
+    "isReferencedBy": {
+        "@id": "http://purl.org/dc/elements/1.1/isReferencedBy"
+    },
     "relation": {
         "@id": "http://purl.org/dc/elements/1.1/relation"
     },

designsafe/libs/fedora/sim_operations.py

@@ -0,0 +1,305 @@
+import requests
+from requests import HTTPError
+from django.conf import settings
+import json
+import magic
+import os
+import hashlib
+from urllib import parse
+from io import StringIO
+from requests.adapters import HTTPAdapter
+from requests.packages.urllib3.util.retry import Retry
+from designsafe.apps.data.models.elasticsearch import IndexedPublication
+from django.contrib.auth import get_user_model
+from designsafe.apps.api.publications.operations import _get_user_by_username
+from designsafe.libs.fedora.fedora_operations import format_metadata_for_fedora, fedora_post, fedora_update, create_fc_version, upload_manifest, generate_manifest
+import logging
+logger = logging.getLogger(__name__)
+
+
+def walk_sim(project_id, version=None):
+    from urllib import parse
+    doc = IndexedPublication.from_id(project_id, revision=version)
+
+    relation_map = []
+    full_author_list = []
+
+    project_meta = format_metadata_for_fedora(project_id, version=version)
+    if version:
+        project_id = '{}v{}'.format(project_id, str(version))
+    license = project_meta.get('license', None)
+    print(project_id)
+
+    project_map = {
+        'uuid': doc.project.uuid,
+        'container_path': project_id,
+        'fedora_mapping': {**project_meta, 'generated': [], 'license': None},
+        'fileObjs': []
+    }
+
+    sims_list = doc.simulations
+    for sim in sims_list:
+        # Do stuff with experiment.
+        sim_container_path = "{}/{}".format(project_id, parse.quote(sim.value.title))
+        print('simulation ' + sim.value.title)
+        sim_doi = sim.doi
+        project_map['fedora_mapping']['generated'].append('Experiment: {}'.format(sim_doi))
+
+        sim_map = {
+            'uuid': sim.uuid,
+            'container_path': sim_container_path,
+            'fedora_mapping': {**format_sim(sim), 'license': license, 'wasGeneratedBy': project_id, 'generated': []},
+            'fileObjs': getattr(sim, 'fileObjs', [])
+        }
+
+        full_author_list += sim_map['fedora_mapping']['creator']
+
+
+        reports = filter(
+            lambda report: sim.uuid in report.value.simulations,
+            getattr(doc, 'reports', []))
+        for report in reports:
+            # Do stuff with report.
+            report_container_path = "{}/{}".format(sim_container_path, parse.quote(report.value.title))
+            print('\treport ' + report.value.title)
+            sim_map['fedora_mapping']['generated'].append('Report: {}'.format(report.value.title))
+
+            report_map = {
+                'uuid': report.uuid,
+                'fileObjs': report.fileObjs,
+                'container_path': report_container_path,
+                'fedora_mapping': {**format_report(report), 'wasGeneratedBy': 'Simulation: {}'.format(sim_doi)}
+            }
+            relation_map.append(report_map)
+
+
+        analysis_list = filter(
+            lambda analysis: sim.uuid in analysis.value.simulations,
+            getattr(doc, 'analysiss', []))
+        for analysis in analysis_list:
+            # Do stuff with report.
+            analysis_container_path = "{}/{}".format(sim_container_path, parse.quote(analysis.value.title))
+            print('\tanalysis ' + analysis.value.title)
+            sim_map['fedora_mapping']['generated'].append('Analysis: {}'.format(analysis.value.title))
+
+            analysis_map = {
+                'uuid': analysis.uuid,
+                'fileObjs': analysis.fileObjs,
+                'container_path': analysis_container_path,
+                'fedora_mapping': {**format_analysis(analysis), 'wasGeneratedBy': 'Simulation: {}'.format(sim_doi)}
+            }
+            relation_map.append(analysis_map)
+
+
+        models = filter(
+            lambda model: sim.uuid in model.value.simulations,
+            getattr(doc, 'models', [])
+        )
+        for model in models:
+            # Do stuff with model.
+            model_container_path = "{}/{}".format(sim_container_path, parse.quote(model.value.title))
+            print('\tmodel ' + model.value.title)
+            sim_map['fedora_mapping']['generated'].append('Simulation Model: {}'.format(model.value.title))
+
+            model_map = {
+                'uuid': model.uuid,
+                'fileObjs': model.fileObjs,
+                'container_path': model_container_path,
+                'fedora_mapping': {**format_model(model), 'wasGeneratedBy': 'Simulation: {}'.format(sim_doi)}
+            }
+
+            inputs = filter(
+            lambda input: model.uuid in input.value.modelConfigs,
+            getattr(doc, 'inputs', [])
+            )
+
+            for input in inputs:
+                input_container_path = "{}/{}".format(model_container_path, parse.quote(input.value.title))
+                print('\t\tinput ' + input.value.title)
+                sim_map['fedora_mapping']['generated'].append('Simulation Input: {}'.format(input.value.title))
+                input_map = {
+                    'uuid': input.uuid,
+                    'fileObjs': input.fileObjs,
+                    'container_path': input_container_path,
+                    'fedora_mapping': {**format_input(input), 
+                                       'wasGeneratedBy': 'Simulation: {}'.format(sim_doi), 
+                                       'wasDerivedFrom': 'Simulation Model: {}'.format(model.value.title),
+                                       'wasInfluencedBy': []}
+                }
+
+                outputs = filter(
+                lambda output: input.uuid in output.value.simInputs,
+                getattr(doc, 'outputs', [])
+                ) 
+
+                for output in outputs:
+                    output_container_path = "{}/{}".format(input_container_path, parse.quote(output.value.title))
+                    print('\t\t\toutput ' + output.value.title)
+                    sim_map['fedora_mapping']['generated'].append('Simulation Input: {}'.format(output.value.title))
+                    input_map['fedora_mapping']['wasInfluencedBy'].append('Simulation Output: {}'.format(output.value.title))
+                    output_map = {
+                        'uuid': output.uuid,
+                        'fileObjs': output.fileObjs,
+                        'container_path': output_container_path,
+                        'fedora_mapping': {**format_output(output), 
+                                        'wasGeneratedBy': 'Simulation: {}'.format(sim_doi), 
+                                        'wasDerivedFrom': ['Simulation Model: {}'.format(model.value.title), 'Simulation Input: {}'.format(input.value.title)],
+                                        }
+                    }
+
+                    relation_map.append(output_map)
+
+                relation_map.append(input_map)
+
+            relation_map.append(model_map)
+
+        relation_map.append(sim_map)
+
+    project_map['fedora_mapping']['creator'] = list(set(full_author_list))
+    relation_map.append(project_map)
+    return relation_map[::-1]
+
+
+def format_sim(sim):
+    """
+    Map experiment to Datacite fields for Fedora.
+    """
+    meta = sim.value
+
+    sim_type = meta.simulationType
+    if sim_type == 'other':
+        sim_type = getattr(meta, 'simulationTypeOther', 'other')
+
+
+    publication_date = str(sim.created)
+
+    try:
+        authors = sim.authors
+        creator = list(map(lambda author: "{lname}, {fname}".format(**author.to_dict()), authors))
+    except AttributeError:
+        creator = list(map(lambda username: _get_user_by_username(sim, username), meta.authors))
+
+    try:
+        dois = list(meta.dois)
+    except AttributeError:
+        dois = [sim.doi]
+
+
+    referenced_by = []
+    part_of = []
+    references = []
+
+    refs = getattr(meta, 'referencedData', [])
+    for ref in refs:
+        if ref['hrefType'] == 'URL':
+            ref_val = f"{ref['title']} ({ref['doi']})"
+        elif ref['hrefType'] == 'DOI':
+            ref_val = ref['doi']
+        references.append(ref_val)
+
+
+    related_work = getattr(meta, 'relatedWork', [])
+    for work in related_work:
+        if work['hrefType'] == 'URL':
+            work_val = f"{work['title']} ({work['href']})"
+        elif work['hrefType'] == 'DOI':
+            work_val = work['href']
+
+        if work['type'] == 'Linked Project':
+            part_of.append(work_val)
+
+        if work['type'] == 'Linked Dataset':
+            part_of.append(work_val)
+
+        if work['type'] == 'Context':
+            references.append(work_val)
+
+        if work['type'] == 'Cited By':
+            referenced_by.append(work_val)
+
+
+
+
+    return {
+        'type': sim_type,
+        'identifier': dois + [sim.uuid],
+        'creator': creator,
+        'title': meta.title,
+        'description': meta.description,
+        'available': publication_date,
+        'publisher': 'Designsafe',
+        'isReferencedBy': referenced_by,
+        'isPartOf': part_of,
+        'references': references
+    }
+
+
+def format_report(report):
+    return {
+        'type': 'report',
+        'title': report.value.title,
+        'description': report.value.description,
+        'tags': getattr(report.value, 'tags', [])
+    }
+
+def format_analysis(analysis):
+    return {
+        'type': 'analysis',
+        'title': analysis.value.title,
+        'description': analysis.value.description,
+        'tags': getattr(analysis.value, 'tags', [])
+    }
+
+def format_model(model):
+    return {
+        'type': 'simulation model',
+        'title': model.value.title,
+        'description': model.value.description,
+        'tags': getattr(model.value, 'tags', [])
+    }
+
+def format_input(input):
+    return {
+        'type': 'simulation input',
+        'title': input.value.title,
+        'description': input.value.description,
+        'tags': getattr(input.value, 'tags', [])
+    }
+
+def format_output(output):
+    return {
+        'type': 'simulation output',
+        'title': output.value.title,
+        'description': output.value.description,
+        'tags': getattr(output.value, 'tags', [])
+    }
+
+
+def generate_manifest_sim(project_id, version=None):
+    walk_result = walk_sim(project_id, version=version)
+    return generate_manifest(walk_result, project_id, version)
+
+
+def upload_manifest_sim(project_id, version=None):
+    manifest_dict = generate_manifest_sim(project_id, version=version)
+    return upload_manifest(manifest_dict, project_id, version)
+
+
+def ingest_project_sim(project_id, version=None, amend=False):
+    """
+    Ingest a project into Fedora by creating a record in the repo, updating it
+    with the published metadata, and uploading its files.
+    """
+    container_path = project_id
+    if version:
+        container_path = '{}v{}'.format(container_path, str(version))
+
+    walk_result = walk_sim(project_id, version=version)
+    for entity in walk_result:
+        if amend:
+            create_fc_version(entity['container_path'])
+        fedora_post(entity['container_path'])
+        fedora_update(entity['container_path'], entity['fedora_mapping'])
+
+    if not amend:
+        upload_manifest_sim(project_id, version=version)

designsafe/static/scripts/data-depot/components/projects/index.js

@@ -16,10 +16,11 @@ import {
 import {
     VersionExperimentSelectionComponent,
     VersionFieldReconSelectionComponent,
+    VersionSimulationSelectionComponent,
     VersionCitationComponent
 } from './pipeline-version/pipeline-version.component';
 import { VersionChangesComponent } from './pipeline-version/pipeline-version-changes.component';
-import { AmendExperimentComponent, AmendFieldReconComponent } from './pipeline-amend/pipeline-amend.component';
+import { AmendExperimentComponent, AmendFieldReconComponent, AmendSimulationComponent } from './pipeline-amend/pipeline-amend.component';
 import { AmendOtherComponent } from './pipeline-amend/pipeline-amend-other.component';
 import { AmendCitationComponent } from './pipeline-amend/pipeline-amend-citation.component';
 import {
@@ -91,11 +92,13 @@ ddProjectsComponents.component('pipelineStart', PipelineStartComponent);
 ddProjectsComponents.component('amendOther', AmendOtherComponent);
 ddProjectsComponents.component('amendExperiment', AmendExperimentComponent);
 ddProjectsComponents.component('amendFieldRecon', AmendFieldReconComponent);
+ddProjectsComponents.component('amendSimulation', AmendSimulationComponent);
 ddProjectsComponents.component('amendCitation', AmendCitationComponent);
 ddProjectsComponents.component('versionOtherSelection', VersionOtherSelectionComponent);
 ddProjectsComponents.component('versionOtherCitation', VersionOtherCitationComponent);
 ddProjectsComponents.component('versionExperimentSelection', VersionExperimentSelectionComponent);
 ddProjectsComponents.component('versionFieldReconSelection', VersionFieldReconSelectionComponent);
+ddProjectsComponents.component('versionSimulationSelection', VersionSimulationSelectionComponent);
 ddProjectsComponents.component('versionCitation', VersionCitationComponent);
 ddProjectsComponents.component('versionChanges', VersionChangesComponent);
 ddProjectsComponents.component('pipelineSelectExp', PipelineSelectionExpComponent);

designsafe/static/scripts/data-depot/components/projects/pipeline-amend/amend-citation.template.html

@@ -12,6 +12,7 @@
     <div class="pipeline-header">
         <h3>Confirm Author Order</h3>
         <strong>You are required to confirm the list of Authors on your Citation(s) before continuing.</strong>
+        Click Save to confirm.
         Your citation(s) will be updated to match what is shown in the preview.
         <div ng-if="$ctrl.ui.loading">
             <h3 class="text-center">