Add extract single file (#123)

* Add extract single file * Disable duplicate-code check, seems not controllable: pylint-dev/pylint#214 * Tidy some excessive sets of positional args
zimeon · Oct 21, 2024 · 065c8e3 · 065c8e3
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diff --git a/.github/workflows/action.yml b/.github/workflows/action.yml
@@ -33,7 +33,7 @@ jobs:
           pydocstyle *.py ocfl tests
       - name: Lint with pylint
         run: |
-          pylint --disable=line-too-long,raise-missing-from,fixme,redefined-builtin,invalid-name,consider-using-f-string,too-many-instance-attributes,too-many-return-statements,too-many-branches,too-many-arguments,too-many-locals,too-many-statements,too-many-nested-blocks,broad-exception-raised,superfluous-parens *.py ocfl
+          pylint --disable=line-too-long,raise-missing-from,fixme,redefined-builtin,invalid-name,consider-using-f-string,too-many-instance-attributes,too-many-return-statements,too-many-branches,too-many-arguments,too-many-locals,too-many-statements,too-many-nested-blocks,broad-exception-raised,superfluous-parens,duplicate-code *.py ocfl
           pylint --disable=line-too-long,fixme,invalid-name,consider-using-f-string,too-many-statements,duplicate-code tests
       - name: Test with pytest
         run: |

diff --git a/docs/demo_build_v1_0_spec_examples.md b/docs/demo_build_v1_0_spec_examples.md
@@ -100,7 +100,7 @@ This is inventory should match the example with 3 versions in <https://ocfl.io/1
   "type": "https://ocfl.io/1.0/spec/#inventory",
   "versions": {
     "v1": {
-      "created": "2024-10-21T14:04:00.192769Z",
+      "created": "2024-10-21T17:57:00.954822Z",
       "state": {
         "7dcc352f96c56dc...c31": [
           "foo/bar.xml"
@@ -114,7 +114,7 @@ This is inventory should match the example with 3 versions in <https://ocfl.io/1
       }
     },
     "v2": {
-      "created": "2024-10-21T14:04:00.193378Z",
+      "created": "2024-10-21T17:57:00.955241Z",
       "state": {
         "4d27c86b026ff70...b53": [
           "foo/bar.xml"
@@ -126,7 +126,7 @@ This is inventory should match the example with 3 versions in <https://ocfl.io/1
       }
     },
     "v3": {
-      "created": "2024-10-21T14:04:00.193732Z",
+      "created": "2024-10-21T17:57:00.955552Z",
       "state": {
         "4d27c86b026ff70...b53": [
           "foo/bar.xml"

diff --git a/docs/demo_build_v1_1_spec_examples.md b/docs/demo_build_v1_1_spec_examples.md
@@ -100,7 +100,7 @@ This is inventory should match the example with 3 versions in <https://ocfl.io/1
   "type": "https://ocfl.io/1.1/spec/#inventory",
   "versions": {
     "v1": {
-      "created": "2024-10-21T14:04:00.709527Z",
+      "created": "2024-10-21T17:57:01.757332Z",
       "state": {
         "7dcc352f96c56dc...c31": [
           "foo/bar.xml"
@@ -114,7 +114,7 @@ This is inventory should match the example with 3 versions in <https://ocfl.io/1
       }
     },
     "v2": {
-      "created": "2024-10-21T14:04:00.710212Z",
+      "created": "2024-10-21T17:57:01.757764Z",
       "state": {
         "4d27c86b026ff70...b53": [
           "foo/bar.xml"
@@ -126,7 +126,7 @@ This is inventory should match the example with 3 versions in <https://ocfl.io/1
       }
     },
     "v3": {
-      "created": "2024-10-21T14:04:00.710604Z",
+      "created": "2024-10-21T17:57:01.758072Z",
       "state": {
         "4d27c86b026ff70...b53": [
           "foo/bar.xml"

diff --git a/docs/demo_ocfl_object_script.md b/docs/demo_ocfl_object_script.md
@@ -35,7 +35,7 @@ Without an `--objdir` argument the script just writes out the inventory for the
   "type": "https://ocfl.io/1.1/spec/#inventory",
   "versions": {
     "v1": {
-      "created": "2024-10-21T14:03:55.460006Z",
+      "created": "2024-10-21T17:56:53.127967Z",
       "state": {
         "43a43fe8a8a082d3b5343dfaf2fd0c8b8e370675b1f376e92e9994612c33ea255b11298269d72f797399ebb94edeefe53df243643676548f584fb8603ca53a0f": [
           "a_file.txt"
@@ -69,23 +69,23 @@ Without an `--objdir` argument the script just writes out the inventory for each
   "type": "https://ocfl.io/1.1/spec/#inventory",
   "versions": {
     "v1": {
-      "created": "2024-10-21T14:03:55.607383Z",
+      "created": "2024-10-21T17:56:53.371204Z",
       "state": {
         "43a43fe8a8a082d3b5343dfaf2fd0c8b8e370675b1f376e92e9994612c33ea255b11298269d72f797399ebb94edeefe53df243643676548f584fb8603ca53a0f": [
           "a_file.txt"
         ]
       }
     },
     "v2": {
-      "created": "2024-10-21T14:03:55.607784Z",
+      "created": "2024-10-21T17:56:53.371363Z",
       "state": {
         "296e72b8fd5f7f0ac1473993600ae34953d5dab646f17e7b182b8648aff830d7bf01b56490777cb3e72b33fcc1ae520506badea1032252d1a55fd7362e269975": [
           "a_file.txt"
         ]
       }
     },
     "v3": {
-      "created": "2024-10-21T14:03:55.607960Z",
+      "created": "2024-10-21T17:56:53.371494Z",
       "state": {
         "43a43fe8a8a082d3b5343dfaf2fd0c8b8e370675b1f376e92e9994612c33ea255b11298269d72f797399ebb94edeefe53df243643676548f584fb8603ca53a0f": [
           "a_file.txt"
@@ -119,7 +119,7 @@ INFO:root:Built object http://example.org/obj2 at tmp/obj2 with 3 versions
 
 ## 5. Test extract of version.
 
-### 5.1 Extract v1 of an OCFL v1.0 object
+### 5.1 Extract v1 of content in an OCFL v1.0 object
 
 Version 1 object with location specified in `--objdir` and the first version specified in `--objver`, extract into tmp/v1:
 
@@ -134,21 +134,32 @@ and the extracted files are:
 ```
 > find tmp/v1 -print
 tmp/v1
-tmp/v1/empty.txt
 tmp/v1/image.tiff
+tmp/v1/empty.txt
 tmp/v1/foo
 tmp/v1/foo/bar.xml
 ```
 
 
-### 5.2 Extract v2 of content in the same OCFL v1.1 object
+### 5.2 Extract v2 of content in an OCFL v1.1 object
 
 ```
 > python ocfl-object.py extract --objver v2 --objdir fixtures/1.1/good-objects/spec-ex-full --dstdir tmp/v2 -v
 INFO:root:Extracted v2 into tmp/v2
 Extracted content for v2 in tmp/v2
 ```
 
+and the extracted files are:
+
+```
+> find tmp/v2 -print
+tmp/v2
+tmp/v2/empty2.txt
+tmp/v2/empty.txt
+tmp/v2/foo
+tmp/v2/foo/bar.xml
+```
+
 
 ### 5.3 Extract head version (v3) of content in the same OCFL v1.1 object
 
@@ -158,6 +169,48 @@ INFO:root:Extracted v3 into tmp/head
 Extracted content for v3 in tmp/head
 ```
 
+and the extracted files are:
+
+```
+> find tmp/v3 -print
+find: ‘tmp/v3’: No such file or directory
+```
+
+(last command exited with return code 1)
+
+
+### 5.4 Extract foo/bar.xml of v3 into a new directory
+
+```
+> python ocfl-object.py extract --objver v3 --objdir fixtures/1.1/good-objects/spec-ex-full --logical-path foo/bar.xml --dstdir tmp/files -v
+Extracted foo/bar.xml in v3 to tmp/files
+```
+
+and the extracted file is:
+
+```
+> find tmp/files -print
+tmp/files
+tmp/files/bar.xml
+```
+
+
+### 5.5 Extract image.tiff of v3 (default) into the same directory
+
+```
+> python ocfl-object.py extract --objdir fixtures/1.1/good-objects/spec-ex-full --logical-path image.tiff --dstdir tmp/files -v
+Extracted image.tiff in v3 to tmp/files
+```
+
+and the directory now contains two extracted files:
+
+```
+> find tmp/files -print
+tmp/files
+tmp/files/image.tiff
+tmp/files/bar.xml
+```
+
 
 ## 6. Test error conditions.
 

diff --git a/docs/demo_ocfl_script.md b/docs/demo_ocfl_script.md
@@ -59,8 +59,8 @@ ERROR:root:Add object failed because path ark%3A123%2Fabc exists
 
 ```
 > python ocfl.py list --root=extra_fixtures/good-storage-roots/simple-root
-http%3A%2F%2Fexample.org%2Fminimal_mixed_digests -- id=http://example.org/minimal_mixed_digests
 ark%3A123%2Fabc -- id=ark:123/abc
+http%3A%2F%2Fexample.org%2Fminimal_mixed_digests -- id=http://example.org/minimal_mixed_digests
 ark%3A%2F12345%2Fbcd987 -- id=ark:/12345/bcd987
 Found 3 OCFL Objects under root extra_fixtures/good-storage-roots/simple-root
 ```

diff --git a/docs/demo_ocfl_sidecar_script.md b/docs/demo_ocfl_sidecar_script.md
@@ -20,15 +20,15 @@ ocfl-sidecar.py is part of ocfl-py version 1.9.0
 
 ```
 > mkdir -v tmp/obj
-tmp/obj
+mkdir: created directory 'tmp/obj'
 ```
 
 
 ### 2.2 Copy in an inventory from an example
 
 ```
 > cp -v fixtures/1.0/good-objects/minimal_one_version_one_file/inventory.json tmp/obj
-fixtures/1.0/good-objects/minimal_one_version_one_file/inventory.json -> tmp/obj/inventory.json
+'fixtures/1.0/good-objects/minimal_one_version_one_file/inventory.json' -> 'tmp/obj/inventory.json'
 ```
 
 
@@ -68,47 +68,47 @@ Written sidecar file tmp/obj/inventory.json.sha256
 
 ```
 > mkdir -v tmp/obj1
-tmp/obj1
+mkdir: created directory 'tmp/obj1'
 ```
 
 
 ### 3.2 Set up directory as object 2 root
 
 ```
 > mkdir -v tmp/obj2
-tmp/obj2
+mkdir: created directory 'tmp/obj2'
 ```
 
 
 ### 3.3 Set up directory as object 3 root
 
 ```
 > mkdir -v tmp/obj3
-tmp/obj3
+mkdir: created directory 'tmp/obj3'
 ```
 
 
 ### 3.4 Copy in an inventory from an example for object 1
 
 ```
 > cp -v fixtures/1.1/good-objects/minimal_uppercase_digests/inventory.json tmp/obj1
-fixtures/1.1/good-objects/minimal_uppercase_digests/inventory.json -> tmp/obj1/inventory.json
+'fixtures/1.1/good-objects/minimal_uppercase_digests/inventory.json' -> 'tmp/obj1/inventory.json'
 ```
 
 
 ### 3.5 Copy in an inventory from an example for object 2
 
 ```
 > cp -v fixtures/1.1/good-objects/minimal_mixed_digests/inventory.json tmp/obj2
-fixtures/1.1/good-objects/minimal_mixed_digests/inventory.json -> tmp/obj2/inventory.json
+'fixtures/1.1/good-objects/minimal_mixed_digests/inventory.json' -> 'tmp/obj2/inventory.json'
 ```
 
 
 ### 3.6 Copy in an inventory from an example for object 3
 
 ```
 > cp -v fixtures/1.1/good-objects/minimal_no_content/inventory.json tmp/obj3
-fixtures/1.1/good-objects/minimal_no_content/inventory.json -> tmp/obj3/inventory.json
+'fixtures/1.1/good-objects/minimal_no_content/inventory.json' -> 'tmp/obj3/inventory.json'
 ```
 
 

diff --git a/docs/demo_using_bagit_bags.md b/docs/demo_using_bagit_bags.md
@@ -10,11 +10,11 @@ Imagine that we have a Bagit bag [`tests/testdata/bags/uaa_v1`](https://github.c
 
 ```
 > python ocfl-object.py create --objdir tmp/obj --srcbag tests/testdata/bags/uaa_v1 -v
-INFO:bagit:Verifying checksum for file /Users/sw272/src/ocfl-py/tests/testdata/bags/uaa_v1/data/my_content/dracula.txt
-INFO:bagit:Verifying checksum for file /Users/sw272/src/ocfl-py/tests/testdata/bags/uaa_v1/data/my_content/poe.txt
-INFO:bagit:Verifying checksum for file /Users/sw272/src/ocfl-py/tests/testdata/bags/uaa_v1/bagit.txt
-INFO:bagit:Verifying checksum for file /Users/sw272/src/ocfl-py/tests/testdata/bags/uaa_v1/bag-info.txt
-INFO:bagit:Verifying checksum for file /Users/sw272/src/ocfl-py/tests/testdata/bags/uaa_v1/manifest-sha512.txt
+INFO:bagit:Verifying checksum for file /home/runner/work/ocfl-py/ocfl-py/tests/testdata/bags/uaa_v1/data/my_content/dracula.txt
+INFO:bagit:Verifying checksum for file /home/runner/work/ocfl-py/ocfl-py/tests/testdata/bags/uaa_v1/data/my_content/poe.txt
+INFO:bagit:Verifying checksum for file /home/runner/work/ocfl-py/ocfl-py/tests/testdata/bags/uaa_v1/bagit.txt
+INFO:bagit:Verifying checksum for file /home/runner/work/ocfl-py/ocfl-py/tests/testdata/bags/uaa_v1/bag-info.txt
+INFO:bagit:Verifying checksum for file /home/runner/work/ocfl-py/ocfl-py/tests/testdata/bags/uaa_v1/manifest-sha512.txt
 INFO:root:Created OCFL object info:bb123cd4567 in tmp/obj
 ```
 
@@ -55,13 +55,13 @@ If we have a bag [`tests/testdata/bags/uaa_v2`](https://github.com/zimeon/ocfl-p
 
 ```
 > python ocfl-object.py update --objdir tmp/obj --srcbag tests/testdata/bags/uaa_v2 -v
-INFO:bagit:Verifying checksum for file /Users/sw272/src/ocfl-py/tests/testdata/bags/uaa_v2/data/my_content/a_second_copy_of_dracula.txt
-INFO:bagit:Verifying checksum for file /Users/sw272/src/ocfl-py/tests/testdata/bags/uaa_v2/data/my_content/dracula.txt
-INFO:bagit:Verifying checksum for file /Users/sw272/src/ocfl-py/tests/testdata/bags/uaa_v2/data/my_content/poe-nevermore.txt
-INFO:bagit:Verifying checksum for file /Users/sw272/src/ocfl-py/tests/testdata/bags/uaa_v2/data/my_content/another_directory/a_third_copy_of_dracula.txt
-INFO:bagit:Verifying checksum for file /Users/sw272/src/ocfl-py/tests/testdata/bags/uaa_v2/bagit.txt
-INFO:bagit:Verifying checksum for file /Users/sw272/src/ocfl-py/tests/testdata/bags/uaa_v2/bag-info.txt
-INFO:bagit:Verifying checksum for file /Users/sw272/src/ocfl-py/tests/testdata/bags/uaa_v2/manifest-sha512.txt
+INFO:bagit:Verifying checksum for file /home/runner/work/ocfl-py/ocfl-py/tests/testdata/bags/uaa_v2/data/my_content/a_second_copy_of_dracula.txt
+INFO:bagit:Verifying checksum for file /home/runner/work/ocfl-py/ocfl-py/tests/testdata/bags/uaa_v2/data/my_content/dracula.txt
+INFO:bagit:Verifying checksum for file /home/runner/work/ocfl-py/ocfl-py/tests/testdata/bags/uaa_v2/data/my_content/poe-nevermore.txt
+INFO:bagit:Verifying checksum for file /home/runner/work/ocfl-py/ocfl-py/tests/testdata/bags/uaa_v2/data/my_content/another_directory/a_third_copy_of_dracula.txt
+INFO:bagit:Verifying checksum for file /home/runner/work/ocfl-py/ocfl-py/tests/testdata/bags/uaa_v2/bagit.txt
+INFO:bagit:Verifying checksum for file /home/runner/work/ocfl-py/ocfl-py/tests/testdata/bags/uaa_v2/bag-info.txt
+INFO:bagit:Verifying checksum for file /home/runner/work/ocfl-py/ocfl-py/tests/testdata/bags/uaa_v2/manifest-sha512.txt
 INFO:root:Will update info:bb123cd4567 v1 -> v2
 INFO:root:Updated OCFL object info:bb123cd4567 in tmp/obj by adding v2
 ```
@@ -96,12 +96,12 @@ Similarly we can `--update` with [`tests/testdata/bags/uaa_v3`](https://github.c
 
 ```
 > python ocfl-object.py update --objdir tmp/obj --srcbag tests/testdata/bags/uaa_v3 -v
-INFO:bagit:Verifying checksum for file /Users/sw272/src/ocfl-py/tests/testdata/bags/uaa_v3/data/my_content/dracula.txt
-INFO:bagit:Verifying checksum for file /Users/sw272/src/ocfl-py/tests/testdata/bags/uaa_v3/data/my_content/poe-nevermore.txt
-INFO:bagit:Verifying checksum for file /Users/sw272/src/ocfl-py/tests/testdata/bags/uaa_v3/data/my_content/another_directory/a_third_copy_of_dracula.txt
-INFO:bagit:Verifying checksum for file /Users/sw272/src/ocfl-py/tests/testdata/bags/uaa_v3/bagit.txt
-INFO:bagit:Verifying checksum for file /Users/sw272/src/ocfl-py/tests/testdata/bags/uaa_v3/bag-info.txt
-INFO:bagit:Verifying checksum for file /Users/sw272/src/ocfl-py/tests/testdata/bags/uaa_v3/manifest-sha512.txt
+INFO:bagit:Verifying checksum for file /home/runner/work/ocfl-py/ocfl-py/tests/testdata/bags/uaa_v3/data/my_content/dracula.txt
+INFO:bagit:Verifying checksum for file /home/runner/work/ocfl-py/ocfl-py/tests/testdata/bags/uaa_v3/data/my_content/poe-nevermore.txt
+INFO:bagit:Verifying checksum for file /home/runner/work/ocfl-py/ocfl-py/tests/testdata/bags/uaa_v3/data/my_content/another_directory/a_third_copy_of_dracula.txt
+INFO:bagit:Verifying checksum for file /home/runner/work/ocfl-py/ocfl-py/tests/testdata/bags/uaa_v3/bagit.txt
+INFO:bagit:Verifying checksum for file /home/runner/work/ocfl-py/ocfl-py/tests/testdata/bags/uaa_v3/bag-info.txt
+INFO:bagit:Verifying checksum for file /home/runner/work/ocfl-py/ocfl-py/tests/testdata/bags/uaa_v3/manifest-sha512.txt
 INFO:root:Will update info:bb123cd4567 v2 -> v3
 INFO:root:Updated OCFL object info:bb123cd4567 in tmp/obj by adding v3
 ```
@@ -140,13 +140,13 @@ Finally, we can `--update` again with [`tests/testdata/bags/uaa_v4`](https://git
 
 ```
 > python ocfl-object.py update --objdir tmp/obj --srcbag tests/testdata/bags/uaa_v4 -v
-INFO:bagit:Verifying checksum for file /Users/sw272/src/ocfl-py/tests/testdata/bags/uaa_v4/data/my_content/dracula.txt
-INFO:bagit:Verifying checksum for file /Users/sw272/src/ocfl-py/tests/testdata/bags/uaa_v4/data/my_content/dunwich.txt
-INFO:bagit:Verifying checksum for file /Users/sw272/src/ocfl-py/tests/testdata/bags/uaa_v4/data/my_content/poe-nevermore.txt
-INFO:bagit:Verifying checksum for file /Users/sw272/src/ocfl-py/tests/testdata/bags/uaa_v4/data/my_content/another_directory/a_third_copy_of_dracula.txt
-INFO:bagit:Verifying checksum for file /Users/sw272/src/ocfl-py/tests/testdata/bags/uaa_v4/bagit.txt
-INFO:bagit:Verifying checksum for file /Users/sw272/src/ocfl-py/tests/testdata/bags/uaa_v4/bag-info.txt
-INFO:bagit:Verifying checksum for file /Users/sw272/src/ocfl-py/tests/testdata/bags/uaa_v4/manifest-sha512.txt
+INFO:bagit:Verifying checksum for file /home/runner/work/ocfl-py/ocfl-py/tests/testdata/bags/uaa_v4/data/my_content/dracula.txt
+INFO:bagit:Verifying checksum for file /home/runner/work/ocfl-py/ocfl-py/tests/testdata/bags/uaa_v4/data/my_content/dunwich.txt
+INFO:bagit:Verifying checksum for file /home/runner/work/ocfl-py/ocfl-py/tests/testdata/bags/uaa_v4/data/my_content/poe-nevermore.txt
+INFO:bagit:Verifying checksum for file /home/runner/work/ocfl-py/ocfl-py/tests/testdata/bags/uaa_v4/data/my_content/another_directory/a_third_copy_of_dracula.txt
+INFO:bagit:Verifying checksum for file /home/runner/work/ocfl-py/ocfl-py/tests/testdata/bags/uaa_v4/bagit.txt
+INFO:bagit:Verifying checksum for file /home/runner/work/ocfl-py/ocfl-py/tests/testdata/bags/uaa_v4/bag-info.txt
+INFO:bagit:Verifying checksum for file /home/runner/work/ocfl-py/ocfl-py/tests/testdata/bags/uaa_v4/manifest-sha512.txt
 INFO:root:Will update info:bb123cd4567 v3 -> v4
 INFO:root:Updated OCFL object info:bb123cd4567 in tmp/obj by adding v4
 ```
@@ -161,8 +161,8 @@ Taking the newly created OCFL object `/tmp/obj` we can `--extract` the `v4` cont
 INFO:root:Extracted v4 into tmp/extracted_v4
 INFO:bagit:Creating bag for directory tmp/extracted_v4
 INFO:bagit:Creating data directory
-INFO:bagit:Moving my_content to /privatetmp/extracted_v4/tmp7apb1l_h/my_content
-INFO:bagit:Moving /privatetmp/extracted_v4/tmp7apb1l_h to data
+INFO:bagit:Moving my_content to tmp/extracted_v4/tmpvzloz7i3/my_content
+INFO:bagit:Moving tmp/extracted_v4/tmpvzloz7i3 to data
 INFO:bagit:Using 1 processes to generate manifests: sha512
 INFO:bagit:Generating manifest lines for file data/my_content/dracula.txt
 INFO:bagit:Generating manifest lines for file data/my_content/dunwich.txt