From 1661596a1a1dd9a10cc038d5c2cdd0e9d61a16f1 Mon Sep 17 00:00:00 2001
From: Mike Boyle <michael.oliver.boyle@gmail.com>
Date: Sat, 28 Sep 2024 00:36:02 -0400
Subject: [PATCH] Add functions to process SimulationAnnex into `Simulations`
 data

---
 sxs/simulations/local.py | 147 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 147 insertions(+)
 create mode 100644 sxs/simulations/local.py

diff --git a/sxs/simulations/local.py b/sxs/simulations/local.py
new file mode 100644
index 0000000..6f096bc
--- /dev/null
+++ b/sxs/simulations/local.py
@@ -0,0 +1,147 @@
+from pathlib import Path
+from .. import sxs_id, Metadata, sxs_directory
+from ..utilities import sxs_identifier_re
+from ..zenodo import path_to_invenio as p2i
+
+def file_upload_allowed(file, directory_listing):
+    """Return True if the file should be uploaded
+    
+    A file should be uploaded if
+        * it is named "metadata.json" or "Horizons.h5"
+        * it is named "Strain_*.json" or "ExtraWaveforms.json" and the corresponding
+          ".h5" file is in the directory listing
+        * it is named "Strain_*.h5" or "ExtraWaveforms.h5" and the corresponding
+          ".json" file is in the directory listing
+    
+    """
+    # Check `file.name` to ignore the directory
+    if file.name in ["metadata.json", "Horizons.h5"]:
+        return True
+    if file.name.startswith("Strain_") or file.name.startswith("ExtraWaveforms"):
+        # Ensure that both `.h5` and `.json` exist for all such files
+        if file.suffix == ".json":
+            return file.with_suffix(".h5") in directory_listing
+        elif file.suffix == ".h5":
+            return file.with_suffix(".json") in directory_listing
+        else:
+            return False
+    return False
+
+
+def files_to_upload(directory, annex_dir="."):
+    """Return a list of files to upload
+
+    The files to upload are those that are in the directory listing
+    and pass the `file_upload_allowed` function.
+
+    """
+    full_directory = annex_dir / Path(directory)
+    files = []
+    for lev in full_directory.resolve().glob("Lev*"):
+        directory_listing = list(lev.iterdir())
+        files.extend([
+            file for file in directory_listing
+            if file_upload_allowed(file, directory_listing)
+        ])
+    return sorted(files, key=lambda x: str(x).lower())
+
+
+def extract_id_from_common_metadata(file, annex_dir):
+    """Extract the SXS ID from a common-metadata.txt file
+    
+    If the ID doesn't exist, return the directory path, relative to
+    the `annex_dir`.
+    """
+    file = Path(file)
+    annex_dir = Path(annex_dir)
+    key = str(file.resolve().parent.relative_to(annex_dir.resolve()))
+    with file.open("r") as f:
+        for line in f.readlines():
+            line = line.strip()
+            if "alternative-names" in line:
+                if (m := sxs_identifier_re.search(line)):
+                    key = m["sxs_identifier"]
+                    break
+    return key
+
+
+def local_simulations(annex_dir):
+    """
+    Walk the annex directory to find and process all simulations
+
+    For each `common-metadata.txt` file found:
+        - Ensures that at least one directory starting with "Lev"
+          exists; if not, the process is skipped.
+        - Defines a key for the metadata, which is either:
+            - The SXS ID contained in that file's "alternative-names"
+              field, if present.
+            - The directory path relative to `annex_dir`.
+        - Chooses the highest "Lev" directory and extracts the
+          metadata.
+        - Finds all files to upload in the directory; if none are
+          found, the process is skipped.
+        - Adds the "files" dictionary to the metadata, pointing to
+          each file that would be uploaded if the simulation were
+          published.
+
+    Args:
+        annex_dir (str or Path): The path to the annex directory to be
+        processed.
+
+    Returns:
+        dict: A dictionary containing the processed simulations
+        metadata.
+    """
+    from os import walk
+
+    simulations = {}
+    annex_dir = Path(annex_dir).resolve()
+
+    # The `walk` method can be made *much* faster than the `glob` method
+    for dirpath, dirnames, filenames in walk(annex_dir, topdown=True):
+        dirpath = Path(dirpath)
+
+        # Ignore hidden directories
+        if dirpath.name.startswith("."):
+            dirnames[:] = []
+            continue
+
+        if "common-metadata.txt" in filenames:
+            if not any(d.startswith("Lev") for d in dirnames):
+                continue
+
+            key = extract_id_from_common_metadata(dirpath / "common-metadata.txt", annex_dir)
+
+            # Find the highest Lev directory and extract the metadata
+            highest_lev = sorted(
+                [d for d in dirnames if d.startswith("Lev")]
+            )[-1]
+            metadata = Metadata.load(dirpath / highest_lev / "metadata")
+
+            metadata["files"] = {
+                p2i(file.relative_to(dirpath)): {"link": str(file)}
+                for file in files_to_upload(dirpath, annex_dir)
+            }
+
+            simulations[key] = metadata
+
+            dirnames[:] = []  # Don't keep looking for common-metadata.txt files under this directory
+
+    return simulations
+
+
+def write_local_simulations(annex_dir):
+    """Write the local simulations to a file for use when loading `Simulations`
+
+    Args:
+        annex_dir (str or Path): The path to the annex directory to be
+        processed.
+
+    Returns:
+        None
+    """
+    from json import dump
+
+    simulations = local_simulations(annex_dir)
+    with open(sxs_directory("cache") / "local_simulations.json", "w") as f:
+        dump(simulations, f, indent=2, separators=(",", ": "), ensure_ascii=True)