Update CLI commands

Update 'reconcile' command
* Add 'bitstreams' to context object

Update 'additems' command
* Deprecate 'field_map' and 'file_type' args
* Remove unused S3 client
* Add conditions for retrieving 'bitstream_file_paths' from context or provided metadata_csv
* Pull out DSpaceCollection.post_items into CLI command

Author: jonavellecuerdo

Pipfile.lock

@@ -16,27 +16,34 @@ Note: Previously, the repository comprised of self-contained scripts that could
 ### Reconciling files with metadata CSV
 
 ```bash
-pipenv run dsaps --url $DSPACE_URL -e $DSPACE_EMAIL -p $DSPACE_PASSWORD reconcile -m <metadata-csv> -o /output -d <content-directory> -t <file-type>
+pipenv run dsaps --config-file $CONFIG_FILE --url $DSPACE_URL -e $DSPACE_EMAIL -p $DSPACE_PASSWORD reconcile -m <metadata-csv> -o /output -d <content-directory>
 ```
 
 ### Creating a new collection within a DSpace community
 
 ```bash
-pipenv run dsaps --url $DSPACE_URL -e $DSPACE_EMAIL -p $DSPACE_PASSWORD newcollection -c <community-handle> -n <collection-name>
+pipenv run dsaps --config-file $CONFIG_FILE --url $DSPACE_URL -e $DSPACE_EMAIL -p $DSPACE_PASSWORD newcollection -c <community-handle> -n <collection-name>
 ```
 
 ### Adding items to a DSpace collection
 
 The command below shows `newcollection` and `additems` being run in conjunction with each other. Note that the invocation must call `newcollection` first. In practice, this is the command that is usually run:
 
 ```bash
-pipenv run dsaps --url $DSPACE_URL -e $DSPACE_EMAIL -p $DSPACE_PASSWORD newcollection -c <community-handle> -n <collection-name> additems -m <metadata-csv> -f config/<field-mapping>.json -d <s3-bucket-name> -t <file-type> 
+pipenv run dsaps --config-file $CONFIG_FILE --url $DSPACE_URL -e $DSPACE_EMAIL -p $DSPACE_PASSWORD newcollection -c <community-handle> -n <collection-name> additems -m <metadata-csv> -d <s3-bucket-path> 
 ``` 
 
 ## Environment 
 
 ### Required
 
+```shell
+# The file path to the source configuration JSON with settings for bitstream retrieval and field mappings.
+CONFIG_FILE=
+```
+
+### Optional
+
 ```shell
 # The url for the DSpace REST API
 DSPACE_URL=
@@ -58,14 +65,16 @@ All CLI commands can be run with `pipenv run <COMMAND>`.
 Usage: -c [OPTIONS] COMMAND1 [ARGS]... [COMMAND2 [ARGS]...]...
 
 Options:
+  --config-file TEXT   File path to source configuration JSON with settings
+                       for bitstream retrieval and field mappings.  [required]
   --url TEXT           The url for the DSpace REST API. Defaults to env var
-                       DSPACE_URL if not set.  [required]
+                       DSPACE_URL if not set.
   -e, --email TEXT     The email associated with the DSpace user account used
                        for authentication. Defaults to env var DSPACE_EMAIL if
-                       not set.  [required]
+                       not set.
   -p, --password TEXT  The password associated with the DSpace user account
                        used for authentication. Defaults to env var
-                       DSPACE_PASSWORD if not set.  [required]
+                       DSPACE_PASSWORD if not set.
   --help               Show this message and exit.
 
 Commands:
@@ -87,10 +96,10 @@ Usage: -c reconcile [OPTIONS]
       file with a corresponding file in the content directory.
 
       * no_files.csv: File identifiers for entries in metadata CSV file
-      without a corresponding file in the content directory.
+      without a     corresponding file in the content directory.
 
       * no_metadata.csv: File identifiers for files in the content directory
-      without a corresponding entry in the metadata CSV file.
+      without a     corresponding entry in the metadata CSV file.
 
       * updated-<metadata-csv>.csv: Entries from the metadata CSV file with a
       corresponding file in the content directory.
@@ -101,8 +110,6 @@ Options:
   -o, --output-directory TEXT   The filepath where output files are written.
   -d, --content-directory TEXT  The name of the S3 bucket containing files for
                                 DSpace uploads.  [required]
-  -t, --file-type TEXT          The file type for DSpace uploads (i.e., the
-                                file extension, excluding the dot).
   --help                        Show this message and exit.
 ```
 
@@ -127,20 +134,18 @@ Usage: -c additems [OPTIONS]
 
   Add items to a DSpace collection.
 
-  The method relies on a CSV file with metadata for uploads, a JSON document
-  that maps metadata to a DSpace schema, and a directory containing the files
-  to be uploaded.
+  The updated metadata CSV file from running 'reconcile' is used for this
+  process. The method will first add an item to the specified DSpace
+  collection. The bitstreams (i.e., files) associated with the item are read
+  from the metadata CSV file, and uploaded to the newly created item on
+  DSpace.
 
 Options:
-  -m, --metadata-csv FILE       The filepath to a CSV file containing metadata
-                                for Dspace uploads.  [required]
-  -f, --field-map FILE          The filepath to a JSON document that maps
-                                columns in the metadata CSV file to a DSpace
-                                schema.  [required]
+  -m, --metadata-csv FILE       File path to a CSV file describing the
+                                metadata and bitstreams for DSpace uploads.
+                                [required]
   -d, --content-directory TEXT  The name of the S3 bucket containing files for
                                 DSpace uploads.  [required]
-  -t, --file-type TEXT          The file type for DSpace uploads (i.e., the
-                                file extension, excluding the dot).
   -r, --ingest-report           Create ingest report for updating other
                                 systems.
   -c, --collection-handle TEXT  The handle identifying a DSpace collection

README.md

@@ -3,7 +3,7 @@
         "bitstream_folders": [
             "objects"
         ],
-        "id_regex": ".*-(.*?-.*)\\..*$"
+        "id_regex": ".*-(\\d*?-\\d*).*$"
     },
     "mapping": {
         "item_identifier": {

config/aspace.json

@@ -1,6 +1,5 @@
 import csv
 import datetime
-import json
 import logging
 import os
 
@@ -10,9 +9,8 @@
 import click
 import structlog
 
-from dsaps import helpers
+from dsaps import dspace, helpers
 from dsaps.s3 import S3Client
-from dsaps.dspace import DSpaceClient, DSpaceCollection
 
 
 logger = structlog.get_logger()
@@ -28,7 +26,10 @@ def validate_path(ctx, param, value):
 
 @click.group(chain=True)
 @click.option(
-    "--config-file", required=True, help="File path to source configuration JSON."
+    "--config-file",
+    envvar="CONFIG_FILE",
+    required=True,
+    help="File path to source configuration JSON with settings for bitstream retrieval and field mappings.",
 )
 @click.option(
     "--url",
@@ -83,10 +84,11 @@ def main(ctx, config_file, url, email, password):
     logger.info("Running process")
     source_config = helpers.load_source_config(config_file)
     if url:
-        dspace_client = DSpaceClient(url)
+        dspace_client = dspace.DSpaceClient(url)
         dspace_client.authenticate(email, password)
         ctx.obj["dspace_client"] = dspace_client
-    ctx.obj["config"] = source_config
+    ctx.obj["source_config"] = source_config
+    logger.info("Initializing S3 client")
     ctx.obj["s3_client"] = S3Client.get_client()
     ctx.obj["start_time"] = perf_counter()
 
@@ -97,27 +99,14 @@ def main(ctx, config_file, url, email, password):
     "--metadata-csv",
     required=True,
     type=click.Path(exists=True, file_okay=True, dir_okay=False),
-    help="The filepath to a CSV file containing metadata for Dspace uploads.",
-)
-@click.option(
-    "-f",
-    "--field-map",
-    required=True,
-    type=click.Path(exists=True, file_okay=True, dir_okay=False),
-    help="The filepath to a JSON document that maps columns in the metadata CSV file to a DSpace schema.",
+    help="File path to a CSV file describing the metadata and bitstreams for DSpace uploads.",
 )
 @click.option(
     "-d",
     "--content-directory",
     required=True,
     help="The name of the S3 bucket containing files for DSpace uploads.",
 )
-@click.option(
-    "-t",
-    "--file-type",
-    help="The file type for DSpace uploads (i.e., the file extension, excluding the dot).",
-    default="*",
-)
 @click.option(
     "-r",
     "--ingest-report",
@@ -134,41 +123,51 @@ def main(ctx, config_file, url, email, password):
 def additems(
     ctx,
     metadata_csv,
-    field_map,
     content_directory,
-    file_type,
     ingest_report,
     collection_handle,
 ):
     """Add items to a DSpace collection.
 
-    The method relies on a CSV file with metadata for uploads, a JSON document that maps
-    metadata to a DSpace schema, and a directory containing the files to be uploaded.
+    The updated metadata CSV file from running 'reconcile' is used for this process.
+    The method will first add an item to the specified DSpace collection. The bitstreams
+    (i.e., files) associated with the item are read from the metadata CSV file, and
+    uploaded to the newly created item on DSpace.
     """
-    s3_client = ctx.obj["s3_client"]
+    mapping = ctx.obj["source_config"]["mapping"]
     dspace_client = ctx.obj["dspace_client"]
 
     if "collection_uuid" not in ctx.obj and collection_handle is None:
         raise click.UsageError(
-            "collection_handle option must be used or "
-            "additems must be run after newcollection "
-            "command."
+            "Option '--collection-handle' must be used or "
+            "run 'additems' after 'newcollection' command."
         )
     elif "collection_uuid" in ctx.obj:
         collection_uuid = ctx.obj["collection_uuid"]
     else:
         collection_uuid = dspace_client.get_uuid_from_handle(collection_handle)
-    with open(metadata_csv, "r") as csvfile, open(field_map, "r") as jsonfile:
+
+    if metadata_csv is None:
+        raise click.UsageError("Option '--metadata-csv' must be used.")
+
+    dspace_collection = dspace.Collection(uuid=collection_uuid)
+
+    with open(metadata_csv, "r") as csvfile:
         metadata = csv.DictReader(csvfile)
-        mapping = json.load(jsonfile)
-        collection = DSpaceCollection.create_metadata_for_items_from_csv(
-            metadata, mapping
+        dspace_collection = dspace_collection.add_items(metadata, mapping)
+
+    for item in dspace_collection.items:
+        logger.info(f"Posting item: {item}")
+        item_uuid, item_handle = dspace_client.post_item_to_collection(
+            collection_uuid, item
         )
-    for item in collection.items:
-        item.bitstreams_in_directory(content_directory, s3_client, file_type)
-    collection.uuid = collection_uuid
-    for item in collection.post_items(dspace_client):
-        logger.info(item.file_identifier)
+        item.uuid = item_uuid
+        item.handle = item_handle
+        logger.info(f"Item posted: {item_uuid}")
+        for bitstream in item.bitstreams:
+            logger.info(f"Posting bitstream: {bitstream}")
+            dspace_client.post_bitstream(item.uuid, bitstream)
+
     logger.info(
         "Total elapsed: %s",
         str(timedelta(seconds=perf_counter() - ctx.obj["start_time"])),
@@ -192,7 +191,9 @@ def additems(
 def newcollection(ctx, community_handle, collection_name):
     """Create a new DSpace collection within a community."""
     dspace_client = ctx.obj["dspace_client"]
-    collection_uuid = dspace_client.post_coll_to_comm(community_handle, collection_name)
+    collection_uuid = dspace_client.post_collection_to_community(
+        community_handle, collection_name
+    )
     ctx.obj["collection_uuid"] = collection_uuid
 
 
@@ -235,22 +236,21 @@ def reconcile(ctx, metadata_csv, output_directory, content_directory):
         * updated-<metadata-csv>.csv: Entries from the metadata CSV file with a
         corresponding file in the content directory.
     """
-    source_settings = ctx.obj["config"]["settings"]
-    s3_client = ctx.obj["s3_client"]
-    files_dict = helpers.get_files_from_s3(
+    source_settings = ctx.obj["source_config"]["settings"]
+    bitstreams = helpers.get_files_from_s3(
         s3_path=content_directory,
-        s3_client=s3_client,
+        s3_client=ctx.obj["s3_client"],
         bitstream_folders=source_settings.get("bitstream_folders"),
         id_regex=source_settings["id_regex"],
     )
     metadata_ids = helpers.create_metadata_id_list(metadata_csv)
-    metadata_matches = helpers.match_metadata_to_files(files_dict.keys(), metadata_ids)
-    file_matches = helpers.match_files_to_metadata(files_dict.keys(), metadata_ids)
+    metadata_matches = helpers.match_metadata_to_files(bitstreams.keys(), metadata_ids)
+    file_matches = helpers.match_files_to_metadata(bitstreams.keys(), metadata_ids)
     no_files = set(metadata_ids) - set(metadata_matches)
-    no_metadata = set(files_dict.keys()) - set(file_matches)
+    no_metadata = set(bitstreams.keys()) - set(file_matches)
     helpers.create_csv_from_list(no_metadata, f"{output_directory}no_metadata")
     helpers.create_csv_from_list(no_files, f"{output_directory}no_files")
     helpers.create_csv_from_list(metadata_matches, f"{output_directory}metadata_matches")
     helpers.update_metadata_csv(
-        metadata_csv, output_directory, metadata_matches, files_dict
+        metadata_csv, output_directory, metadata_matches, bitstreams
     )