From b81abca88538fae3d19ed505ff4e6d4751bb327b Mon Sep 17 00:00:00 2001
From: Gerit Wagner <gerit.wagner@uni-bamberg.de>
Date: Sat, 7 Jun 2025 14:49:20 +0200
Subject: [PATCH 1/2] initial code

---
 colrev/ui_cli/cli.py                          | 12 +++++++
 colrev/ui_cli/cli_file_mode.py                | 31 +++++++++++++++++++
 .../colrev.ui_cli.cli_file_mode.pdf_get.rst   |  6 ++++
 .../colrev.ui_cli.cli_file_mode.rst           | 31 +++++++++++++++++++
 .../dev_docs/_autosummary/colrev.ui_cli.rst   |  1 +
 .../colrev.ui_cli.cli_file_mode.pdf_get.rst   |  6 ++++
 .../dev_docs/colrev.ui_cli.cli_file_mode.rst  | 31 +++++++++++++++++++
 docs/source/dev_docs/colrev.ui_cli.rst        |  1 +
 8 files changed, 119 insertions(+)
 create mode 100644 colrev/ui_cli/cli_file_mode.py
 create mode 100644 docs/source/dev_docs/_autosummary/colrev.ui_cli.cli_file_mode.pdf_get.rst
 create mode 100644 docs/source/dev_docs/_autosummary/colrev.ui_cli.cli_file_mode.rst
 create mode 100644 docs/source/dev_docs/colrev.ui_cli.cli_file_mode.pdf_get.rst
 create mode 100644 docs/source/dev_docs/colrev.ui_cli.cli_file_mode.rst

diff --git a/colrev/ui_cli/cli.py b/colrev/ui_cli/cli.py
index 57c430bd5..2e3a7cacd 100644
--- a/colrev/ui_cli/cli.py
+++ b/colrev/ui_cli/cli.py
@@ -1517,6 +1517,11 @@ def pdfs(
     default=False,
     help="Setup template for custom pdf-get script.",
 )
+@click.option(
+    "--file",
+    type=click.Path(exists=True),
+    help="Path to file(s)",
+)
 @click.option(
     "-v",
     "--verbose",
@@ -1541,6 +1546,7 @@ def pdf_get(
     rename: bool,
     relink_pdfs: bool,
     setup_custom_script: bool,
+    file: Path,
     verbose: bool,
     force: bool,
 ) -> None:
@@ -1549,6 +1555,12 @@ def pdf_get(
     Docs: https://colrev-environment.github.io/colrev/manual/pdf_retrieval/pdf_get.html
     """
 
+    if file:
+        import colrev.ui_cli.cli_file_mode
+
+        colrev.ui_cli.cli_file_mode.pdf_get(file)
+        return
+
     review_manager = get_review_manager(
         ctx,
         {
diff --git a/colrev/ui_cli/cli_file_mode.py b/colrev/ui_cli/cli_file_mode.py
new file mode 100644
index 000000000..b8d934569
--- /dev/null
+++ b/colrev/ui_cli/cli_file_mode.py
@@ -0,0 +1,31 @@
+#!/usr/bin/env python3
+"""File mode operations."""
+from __future__ import annotations
+
+from colrev.constants import Fields
+
+from pathlib import Path
+import colrev.env.local_index
+import colrev.exceptions as colrev_exceptions
+
+def pdf_get(file: Path) -> None:
+    print(f"Download PDFs for: {file}")
+
+    records = colrev.loader.load_utils.load(Path(file))
+    local_index = colrev.env.local_index.LocalIndex(
+        verbose_mode=True
+    )
+
+    for record in records.values():
+        if Fields.FILE in record:
+            continue
+        print(f"Retrieve PDF for record {record[Fields.ID]}.")
+
+        try:
+            retrieved_record = local_index.retrieve(record, include_file=True)
+        except colrev_exceptions.RecordNotInIndexException:
+            continue
+
+        if Fields.FILE in retrieved_record.data:
+            input(retrieved_record.data[Fields.FILE])
+        
\ No newline at end of file
diff --git a/docs/source/dev_docs/_autosummary/colrev.ui_cli.cli_file_mode.pdf_get.rst b/docs/source/dev_docs/_autosummary/colrev.ui_cli.cli_file_mode.pdf_get.rst
new file mode 100644
index 000000000..c53d3aaee
--- /dev/null
+++ b/docs/source/dev_docs/_autosummary/colrev.ui_cli.cli_file_mode.pdf_get.rst
@@ -0,0 +1,6 @@
+colrev.ui\_cli.cli\_file\_mode.pdf\_get
+=======================================
+
+.. currentmodule:: colrev.ui_cli.cli_file_mode
+
+.. autofunction:: pdf_get
\ No newline at end of file
diff --git a/docs/source/dev_docs/_autosummary/colrev.ui_cli.cli_file_mode.rst b/docs/source/dev_docs/_autosummary/colrev.ui_cli.cli_file_mode.rst
new file mode 100644
index 000000000..ec9f278f6
--- /dev/null
+++ b/docs/source/dev_docs/_autosummary/colrev.ui_cli.cli_file_mode.rst
@@ -0,0 +1,31 @@
+colrev.ui\_cli.cli\_file\_mode
+==============================
+
+.. automodule:: colrev.ui_cli.cli_file_mode
+
+   
+   
+   
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+      :toctree:
+      :nosignatures:
+   
+      pdf_get
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+
+
diff --git a/docs/source/dev_docs/_autosummary/colrev.ui_cli.rst b/docs/source/dev_docs/_autosummary/colrev.ui_cli.rst
index e022ee9f8..ae2ca962f 100644
--- a/docs/source/dev_docs/_autosummary/colrev.ui_cli.rst
+++ b/docs/source/dev_docs/_autosummary/colrev.ui_cli.rst
@@ -28,6 +28,7 @@ colrev.ui\_cli
 
    colrev.ui_cli.add_package_to_settings
    colrev.ui_cli.cli
+   colrev.ui_cli.cli_file_mode
    colrev.ui_cli.cli_status_printer
    colrev.ui_cli.cli_validation
    colrev.ui_cli.dedupe_errors
diff --git a/docs/source/dev_docs/colrev.ui_cli.cli_file_mode.pdf_get.rst b/docs/source/dev_docs/colrev.ui_cli.cli_file_mode.pdf_get.rst
new file mode 100644
index 000000000..c53d3aaee
--- /dev/null
+++ b/docs/source/dev_docs/colrev.ui_cli.cli_file_mode.pdf_get.rst
@@ -0,0 +1,6 @@
+colrev.ui\_cli.cli\_file\_mode.pdf\_get
+=======================================
+
+.. currentmodule:: colrev.ui_cli.cli_file_mode
+
+.. autofunction:: pdf_get
\ No newline at end of file
diff --git a/docs/source/dev_docs/colrev.ui_cli.cli_file_mode.rst b/docs/source/dev_docs/colrev.ui_cli.cli_file_mode.rst
new file mode 100644
index 000000000..ec9f278f6
--- /dev/null
+++ b/docs/source/dev_docs/colrev.ui_cli.cli_file_mode.rst
@@ -0,0 +1,31 @@
+colrev.ui\_cli.cli\_file\_mode
+==============================
+
+.. automodule:: colrev.ui_cli.cli_file_mode
+
+   
+   
+   
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+      :toctree:
+      :nosignatures:
+   
+      pdf_get
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+
+
diff --git a/docs/source/dev_docs/colrev.ui_cli.rst b/docs/source/dev_docs/colrev.ui_cli.rst
index 056703f3d..a61194ef6 100644
--- a/docs/source/dev_docs/colrev.ui_cli.rst
+++ b/docs/source/dev_docs/colrev.ui_cli.rst
@@ -28,6 +28,7 @@
 
    colrev.ui_cli.add_package_to_settings
    colrev.ui_cli.cli
+   colrev.ui_cli.cli_file_mode
    colrev.ui_cli.cli_status_printer
    colrev.ui_cli.cli_validation
    colrev.ui_cli.dedupe_errors

From 55c8484c4cc01b3cdcbbc55d634a59833a3ff01e Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sat, 7 Jun 2025 12:50:15 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 colrev/ui_cli/cli_file_mode.py                | 10 +++-----
 .../colrev.ui_cli.cli_file_mode.pdf_get.rst   |  2 +-
 .../colrev.ui_cli.cli_file_mode.rst           | 25 +++++--------------
 .../colrev.ui_cli.cli_file_mode.pdf_get.rst   |  2 +-
 .../dev_docs/colrev.ui_cli.cli_file_mode.rst  | 25 +++++--------------
 5 files changed, 18 insertions(+), 46 deletions(-)

diff --git a/colrev/ui_cli/cli_file_mode.py b/colrev/ui_cli/cli_file_mode.py
index b8d934569..f089a68d1 100644
--- a/colrev/ui_cli/cli_file_mode.py
+++ b/colrev/ui_cli/cli_file_mode.py
@@ -2,19 +2,18 @@
 """File mode operations."""
 from __future__ import annotations
 
-from colrev.constants import Fields
-
 from pathlib import Path
+
 import colrev.env.local_index
 import colrev.exceptions as colrev_exceptions
+from colrev.constants import Fields
+
 
 def pdf_get(file: Path) -> None:
     print(f"Download PDFs for: {file}")
 
     records = colrev.loader.load_utils.load(Path(file))
-    local_index = colrev.env.local_index.LocalIndex(
-        verbose_mode=True
-    )
+    local_index = colrev.env.local_index.LocalIndex(verbose_mode=True)
 
     for record in records.values():
         if Fields.FILE in record:
@@ -28,4 +27,3 @@ def pdf_get(file: Path) -> None:
 
         if Fields.FILE in retrieved_record.data:
             input(retrieved_record.data[Fields.FILE])
-        
\ No newline at end of file
diff --git a/docs/source/dev_docs/_autosummary/colrev.ui_cli.cli_file_mode.pdf_get.rst b/docs/source/dev_docs/_autosummary/colrev.ui_cli.cli_file_mode.pdf_get.rst
index c53d3aaee..e91d384ad 100644
--- a/docs/source/dev_docs/_autosummary/colrev.ui_cli.cli_file_mode.pdf_get.rst
+++ b/docs/source/dev_docs/_autosummary/colrev.ui_cli.cli_file_mode.pdf_get.rst
@@ -3,4 +3,4 @@ colrev.ui\_cli.cli\_file\_mode.pdf\_get
 
 .. currentmodule:: colrev.ui_cli.cli_file_mode
 
-.. autofunction:: pdf_get
\ No newline at end of file
+.. autofunction:: pdf_get
diff --git a/docs/source/dev_docs/_autosummary/colrev.ui_cli.cli_file_mode.rst b/docs/source/dev_docs/_autosummary/colrev.ui_cli.cli_file_mode.rst
index ec9f278f6..dbbf7d2b6 100644
--- a/docs/source/dev_docs/_autosummary/colrev.ui_cli.cli_file_mode.rst
+++ b/docs/source/dev_docs/_autosummary/colrev.ui_cli.cli_file_mode.rst
@@ -3,29 +3,16 @@ colrev.ui\_cli.cli\_file\_mode
 
 .. automodule:: colrev.ui_cli.cli_file_mode
 
-   
-   
-   
 
-   
-   
-   .. rubric:: Functions
 
-   .. autosummary::
-      :toctree:
-      :nosignatures:
-   
-      pdf_get
-   
-   
 
-   
-   
-   
 
-   
-   
-   
 
 
+   .. rubric:: Functions
 
+   .. autosummary::
+      :toctree:
+      :nosignatures:
+
+      pdf_get
diff --git a/docs/source/dev_docs/colrev.ui_cli.cli_file_mode.pdf_get.rst b/docs/source/dev_docs/colrev.ui_cli.cli_file_mode.pdf_get.rst
index c53d3aaee..e91d384ad 100644
--- a/docs/source/dev_docs/colrev.ui_cli.cli_file_mode.pdf_get.rst
+++ b/docs/source/dev_docs/colrev.ui_cli.cli_file_mode.pdf_get.rst
@@ -3,4 +3,4 @@ colrev.ui\_cli.cli\_file\_mode.pdf\_get
 
 .. currentmodule:: colrev.ui_cli.cli_file_mode
 
-.. autofunction:: pdf_get
\ No newline at end of file
+.. autofunction:: pdf_get
diff --git a/docs/source/dev_docs/colrev.ui_cli.cli_file_mode.rst b/docs/source/dev_docs/colrev.ui_cli.cli_file_mode.rst
index ec9f278f6..dbbf7d2b6 100644
--- a/docs/source/dev_docs/colrev.ui_cli.cli_file_mode.rst
+++ b/docs/source/dev_docs/colrev.ui_cli.cli_file_mode.rst
@@ -3,29 +3,16 @@ colrev.ui\_cli.cli\_file\_mode
 
 .. automodule:: colrev.ui_cli.cli_file_mode
 
-   
-   
-   
 
-   
-   
-   .. rubric:: Functions
 
-   .. autosummary::
-      :toctree:
-      :nosignatures:
-   
-      pdf_get
-   
-   
 
-   
-   
-   
 
-   
-   
-   
 
 
+   .. rubric:: Functions
 
+   .. autosummary::
+      :toctree:
+      :nosignatures:
+
+      pdf_get