sipstore: create SIPs on record create/update

Signed-off-by: Pamfilos Fokianos <pamfilosf@gmail.com>

Author: pamfilos

.gitignore

@@ -64,3 +64,6 @@ target/
 
 # Jetbrains editor project folder
 .idea/
+
+# SIPStore
+archive/

cernopendata/config.py

@@ -435,3 +435,6 @@
         **params
     )
 ]
+
+SIPSTORE_CHECKSUM_ALGORITHM = 'adler32'
+

cernopendata/modules/fixtures/cli.py

@@ -37,13 +37,19 @@
 from invenio_pidstore.models import PersistentIdentifier
 from invenio_records_files.api import Record
 from invenio_records_files.models import RecordsBuckets
+from invenio_sipstore.models import SIPMetadataType
 from sqlalchemy.orm.attributes import flag_modified
 
 from cernopendata.modules.records.minters.docid import \
     cernopendata_docid_minter
 from cernopendata.modules.records.minters.recid import \
     cernopendata_recid_minter
 
+from .sip_utils import (
+    handle_sipstore_record_file_index,
+    handle_sipstore_record_file,
+    sip_record,
+)
 
 def get_jsons_from_dir(dir):
     """Get JSON files inside a dir."""
@@ -55,8 +61,9 @@ def get_jsons_from_dir(dir):
     return res
 
 
-def handle_record_files(data, bucket, files, skip_files):
+def handle_record_files(data, bucket, files, skip_files, skip_sips):
     """Handles record files."""
+    sip_files = []
     for file in files:
         if skip_files:
             break
@@ -89,45 +96,80 @@ def handle_record_files(data, bucket, files, skip_files):
                                  str(e)))
             continue
 
+        if not skip_sips:
+            if file.get("type", None) == "index.json":
+                sip_files += handle_sipstore_record_file_index(f)
 
-def create_record(schema, data, files, skip_files):
+    return sip_files
+
+
+def handle_sip_files(files, skip_files, skip_sips):
+    """Handles record files."""
+    sip_files = []
+    for file in files:
+        if skip_files:
+            break
+        assert 'uri' in file
+        assert 'size' in file
+        assert 'checksum' in file
+        f = FileInstance.get_by_uri(file.get("uri"))
+
+        if f and not skip_sips:
+            if file.get("type", None) == "index.json":
+                sip_files += handle_sipstore_record_file_index(f)
+
+    return sip_files
+
+
+def create_record(schema, data, files, skip_files, skip_sips):
     """Creates a new record."""
     id = uuid.uuid4()
-    cernopendata_recid_minter(id, data)
+    pid = cernopendata_recid_minter(id, data)
+
     data['$schema'] = schema
     record = Record.create(data, id_=id)
     if not skip_files:
         bucket = Bucket.create()
-        handle_record_files(data, bucket, files, skip_files)
+        sip_files_content = handle_record_files(
+            data, bucket, files, skip_files, skip_sips)
+
         RecordsBuckets.create(
             record=record.model, bucket=bucket)
 
-    return record
+    return pid, record, sip_files_content
 
 
-def update_record(pid, schema, data, files, skip_files):
+def update_record(pid, schema, data, files, skip_files, skip_sips):
     """Updates the given record."""
     record = Record.get_record(pid.object_uuid)
-    with db.session.begin_nested():
-        if record.files and not skip_files:
-            bucket_id = record.files.bucket
-            bucket = Bucket.get(bucket_id.id)
-            for o in ObjectVersion.get_by_bucket(bucket).all():
-                o.remove()
-                o.file.delete()
-            RecordsBuckets.query.filter_by(
-                record=record.model,
-                bucket=bucket
-            ).delete()
-            bucket_id.remove()
-    db.session.commit()
+    # with db.session.begin_nested():
+    #     if record.files and not skip_files:
+    #         bucket_id = record.files.bucket
+    #         bucket = Bucket.get(bucket_id.id)
+    #         for o in ObjectVersion.get_by_bucket(bucket).all():
+    #             o.remove()
+    #             o.file.delete()
+    #         RecordsBuckets.query.filter_by(
+    #             record=record.model,
+    #             bucket=bucket
+    #         ).delete()
+    #         bucket_id.remove()
+    # db.session.commit()
+
     record.update(data)
+    sip_files_content = []
     if not skip_files:
-        bucket = Bucket.create()
-        handle_record_files(data, bucket, files, skip_files)
-        RecordsBuckets.create(
-            record=record.model, bucket=bucket)
-    return record
+        sip_files_content = handle_sip_files(
+                files,
+                skip_files,
+                skip_sips
+            )
+        # bucket = Bucket.create()
+        # sip_files_content = handle_record_files(
+        # data, bucket, files, skip_files, skip_sips)
+        # RecordsBuckets.create(
+        #     record=record.model, bucket=bucket)
+    return record, sip_files_content
 
 
 def create_doc(data, schema):
@@ -156,6 +198,8 @@ def fixtures():
 @fixtures.command()
 @click.option('--skip-files', is_flag=True, default=False,
               help='Skip loading of files')
+@click.option('--skip-sips', is_flag=True, default=False,
+              help='Skip create/update of SIPs')
 @click.option('files', '--file', '-f', multiple=True,
               type=click.Path(exists=True),
               help='Path to the file(s) to be loaded. If not provided, all'
@@ -165,8 +209,9 @@ def fixtures():
 @click.option('--mode', required=True, type=click.Choice(
     ['insert', 'replace', 'insert-or-replace']))
 @with_appcontext
-def records(skip_files, files, profile, mode):
+def records(skip_files, skip_sips,  files, profile, mode):
     """Load all records."""
+
     if profile:
         import cProfile
         import pstats
@@ -187,31 +232,34 @@ def records(skip_files, files, profile, mode):
     else:
         record_json = glob.glob(os.path.join(data, '*.json'))
 
+
     for filename in record_json:
         # name = filename.split('/')[-1]
         # if name.startswith('opera'):
         #     click.echo('Skipping opera records ...')
         #     continue
+
         click.echo('Loading records from {0} ...'.format(filename))
         with open(filename, 'rb') as source:
             for data in json.load(source):
-
                 if not data:
                     click.echo('IGNORING a possibly broken or corrupted '
                                'record entry in file {0} ...'.format(filename))
                     continue
 
                 files = data.get('files', [])
 
+                pid = None
                 if mode == 'insert-or-replace':
                     try:
                         pid = PersistentIdentifier.get('recid', data['recid'])
                         if pid:
-                            record = update_record(
-                                pid, schema, data, files, skip_files)
+                            record, sip_files_content = update_record(
+                                pid, schema, data, files, skip_files, skip_sips)
                             action = 'updated'
                     except PIDDoesNotExistError:
-                        record = create_record(schema, data, files, skip_files)
+                        pid, record, sip_files_content = create_record(
+                            schema, data, files, skip_files, skip_sips)
                         action = 'inserted'
                 elif mode == 'insert':
                     try:
@@ -223,7 +271,8 @@ def records(skip_files, files, profile, mode):
                                     data.get('recid')), err=True)
                             return
                     except PIDDoesNotExistError:
-                        record = create_record(schema, data, files, skip_files)
+                        pid, record, sip_files_content = create_record(
+                            schema, data, files, skip_files, skip_sips)
                         action = 'inserted'
                 else:
                     try:
@@ -234,13 +283,20 @@ def records(skip_files, files, profile, mode):
                             'cannot replace it.'.format(
                                 data.get('recid')), err=True)
                         return
-                    record = update_record(
-                        pid, schema, data, files, skip_files)
+                    record, sip_files_content = update_record(
+                        pid, schema, data, files, skip_files, skip_sips)
                     action = 'updated'
 
+
+
                 if not skip_files:
                     record.files.flush()
                 record.commit()
+
+                if not skip_sips:
+                    sip_record(pid, record, sip_files_content, action)
+                    # sip_record(pid, record, ''.join(sip_files_content), action)
+
                 db.session.commit()
                 click.echo(
                     'Record recid {0} {1}.'.format(
@@ -462,3 +518,49 @@ def pids():
             db.session.add(record)
             db.session.commit()
             db.session.expunge_all()
+
+
+
+@fixtures.command()
+@with_appcontext
+def sipmetadata():
+    """Load sipmetadata types."""
+    data = [
+     {
+         "title": "CERN Open Data Record JSON",
+         "name": "record-json",
+         "format": "json",
+         "schema": current_app.extensions['invenio-jsonschemas'] \
+                    .path_to_url('records/record-v1.0.0.json')
+     },
+     {
+         "title": "CERN Open Data Docs JSON",
+         "name": "docs-json",
+         "format": "json",
+         "schema": current_app.extensions['invenio-jsonschemas'] \
+                    .path_to_url('records/docs-v1.0.0.json')
+     },
+     {
+         "title": "CERN Open Data Glossary JSON",
+         "name": "glossary-json",
+         "format": "json",
+         "schema": current_app.extensions['invenio-jsonschemas'] \
+                    .path_to_url('records/glossary-term-v1.0.0.json')
+     },
+     {
+         "title": "BagIt Archiver metadata",
+         "name": "bagit",
+         "format": "json",
+         "schema": current_app.extensions['invenio-jsonschemas'] \
+                    .path_to_url('sipstore/bagit-v1.0.0.json')
+     }
+    ]
+
+    click.secho('Loading SIP metadata types...', fg='blue')
+    with click.progressbar(data) as types:
+     with db.session.begin_nested():
+         for type in types:
+             db.session.add(SIPMetadataType(**type))
+     db.session.commit()
+    click.secho('SIP metadata types loaded!', fg='green')
+

cernopendata/modules/fixtures/data/example_records/test_sip_record_1.json

@@ -0,0 +1,83 @@
+[
+  {
+    "abstract": {
+      "description": "Sample event set from /BTag/Run2011A-12Oct2013-v1/AOD primary dataset in json format readable from the browser-based 3d event display"
+    },
+    "accelerator": "CERN-LHC",
+    "authors": [
+      {
+        "name": "McCauley, Thomas"
+      }
+    ],
+    "collections": [
+      "CMS-Derived-Datasets"
+    ],
+    "collision_information": {
+      "energy": "7TeV",
+      "type": "pp"
+    },
+    "date_created": [
+      "2011"
+    ],
+    "date_published": "2016",
+    "distribution": {
+      "formats": [
+        "ig"
+      ],
+      "number_events": 25
+    },
+    "doi": "10.7483/OPENDATA.CMS.BK3T.NKC6",
+    "experiment": "CMS",
+    "files": [
+      {
+        "checksum": "sha1:a100d93d3b27def7954fa5827e9717ab4ec407cc",
+        "size": 2411180,
+        "uri": "root://eospublic.cern.ch//eos/opendata/cms/Run2011A/BTag/IG/12Oct2013-v1/BTag.ig"
+      }
+    ],
+    "methodology": {
+      "description": "These files contain the objects to be displayed with the online event display. No event selection, apart accepting only the validated runs, is applied. The software to produce these files is available in:",
+      "links": [
+        {
+          "recid": "550"
+        }
+      ]
+    },
+    "note": {
+      "description": "No selection or quality criteria have been applied on the individual physics objects, apart from accepting only the validated runs"
+    },
+    "publisher": "CERN Open Data Portal",
+    "recid": "614",
+    "relations": [
+      {
+        "doi": "10.7483/OPENDATA.CMS.N372.QF6S",
+        "recid": "15",
+        "title": "/BTag/Run2011A-12Oct2013-v1/AOD",
+        "type": "isChildOf"
+      }
+    ],
+    "run_period": [
+      "Run2011A"
+    ],
+    "system_details": {
+      "global_tag": "FT_53_LV5_AN1::All",
+      "release": "CMSSW_5_3_30"
+    },
+    "title": "Event display file derived from /BTag/Run2011A-12Oct2013-v1/AOD",
+    "type": {
+      "primary": "Dataset",
+      "secondary": [
+        "Derived"
+      ]
+    },
+    "usage": {
+      "description": "The data can be accessed from the file menu of the online event display",
+      "links": [
+        {
+          "description": "Explore and visualise events",
+          "url": "/visualise/events/CMS"
+        }
+      ]
+    }
+  }
+]