Merge branch 'develop' into fix/cache

Reviewed-on: https://www.kuhl-mann.de/git/git/jkuhl/corrlib/pulls/6

corrlib/find.py

@@ -5,7 +5,7 @@ import json
 import pandas as pd
 import numpy as np
 from .input.implementations import codes
-from .tools import k2m
+from .tools import k2m, get_file
 # this will implement the search functionality
 
 
@@ -143,21 +143,22 @@ def find_record(path, ensemble, correlator_name, code, project=None, parameters=
     db = path + '/backlogger.db'
     if code not in codes:
         raise ValueError("Code " + code + "unknown, take one of the following:" + ", ".join(codes))
-    if os.path.exists(db):
+    get_file(path, "backlogger.db")
-        dl.get(db, dataset=path)
     results = _db_lookup(db, ensemble, correlator_name,code, project, parameters=parameters, created_before=created_before, created_after=created_after, updated_before=updated_before, updated_after=updated_after, revision=revision)
     if code == "sfcf":
         results = sfcf_filter(results, **kwargs)
-    print("Found " + str(len(results)) + " results")
+    print("Found " + str(len(results)) + " result" + ("s" if len(results)>1 else ""))
     return results.reset_index()
 
 
-def find_project(db, name):
+def find_project(path, name):
-    return _project_lookup_by_alias(db, name)
+    get_file(path, "backlogger.db")
+    return _project_lookup_by_alias(os.path.join(path, "backlogger.db"), name)
 
 
 def list_projects(path):
     db = path + '/backlogger.db'
+    get_file(path, "backlogger.db")
     conn = sqlite3.connect(db)
     c = conn.cursor()
     c.execute("SELECT id,aliases FROM projects")

corrlib/main.py

@@ -5,7 +5,7 @@ import os
 from .git_tools import move_submodule
 import shutil
 from .find import _project_lookup_by_id
-from .tools import list2str, str2list
+from .tools import list2str, str2list, get_file
 from typing import Union
 
 
@@ -24,13 +24,15 @@ def create_project(path: str, uuid: str, owner: Union[str, None]=None, tags: Uni
     code: str (optional)
         The code that was used to create the measurements.
     """
-    conn = sqlite3.connect(path + "/backlogger.db")
+    db = path + "/backlogger.db"
+    get_file(path, "backlogger.db")
+    conn = sqlite3.connect(db)
     c = conn.cursor()
     known_projects = c.execute("SELECT * FROM projects WHERE id=?", (uuid,))
     if known_projects.fetchone():
         raise ValueError("Project already imported, use update_project() instead.")
 
-    dl.unlock(path + "/backlogger.db", dataset=path)
+    dl.unlock(db, dataset=path)
     alias_str = None
     if aliases is not None:
         alias_str = list2str(aliases)
@@ -40,11 +42,12 @@ def create_project(path: str, uuid: str, owner: Union[str, None]=None, tags: Uni
     c.execute("INSERT INTO projects (id, aliases, customTags, owner, code, created_at, updated_at) VALUES (?, ?, ?, ?, ?, datetime('now'), datetime('now'))", (uuid, alias_str, tag_str, owner, code))
     conn.commit()
     conn.close()
-    dl.save(path + "/backlogger.db", message="Added entry for project " + uuid + " to database", dataset=path)
+    dl.save(db, message="Added entry for project " + uuid + " to database", dataset=path)
 
 
-def update_project_data(db, uuid, prop, value = None):
+def update_project_data(path, uuid, prop, value = None):
-    conn = sqlite3.connect(db)
+    get_file(path, "backlogger.db")
+    conn = sqlite3.connect(os.path.join(path, "backlogger.db"))
     c = conn.cursor()
     c.execute(f"UPDATE projects SET '{prop}' = '{value}' WHERE id == '{uuid}'")
     conn.commit()
@@ -54,6 +57,7 @@ def update_project_data(db, uuid, prop, value = None):
 
 def update_aliases(path: str, uuid: str, aliases: list[str]):
     db = os.path.join(path, "backlogger.db")
+    get_file(path, "backlogger.db")
     known_data = _project_lookup_by_id(db, uuid)[0]
     known_aliases = known_data[1]
 
@@ -73,7 +77,7 @@ def update_aliases(path: str, uuid: str, aliases: list[str]):
     if not len(new_alias_list) == len(known_alias_list):
         alias_str = list2str(new_alias_list)
         dl.unlock(db, dataset=path)
-        update_project_data(db, uuid, "aliases", alias_str)
+        update_project_data(path, uuid, "aliases", alias_str)
         dl.save(db, dataset=path)
     return
 
@@ -117,11 +121,13 @@ def import_project(path: str, url: str, owner: Union[str, None]=None, tags: Unio
     if not uuid:
         raise ValueError("The dataset does not have a uuid!")
     if not os.path.exists(path + "/projects/" + uuid):
-        dl.unlock(path + "/backlogger.db", dataset=path)
+        db = path + "/backlogger.db"
+        get_file(path, "backlogger.db")
+        dl.unlock(db, dataset=path)
         create_project(path, uuid, owner, tags, aliases, code)
         move_submodule(path, 'projects/tmp', 'projects/' + uuid)
         os.mkdir(path + '/import_scripts/' + uuid)
-        dl.save([path + "/backlogger.db", path + '/projects/' + uuid], message="Import project from " + url, dataset=path)
+        dl.save([db, path + '/projects/' + uuid], message="Import project from " + url, dataset=path)
     else:
         dl.drop(tmp_path, reckless='kill')
         shutil.rmtree(tmp_path)    
@@ -134,3 +140,11 @@ def import_project(path: str, url: str, owner: Union[str, None]=None, tags: Unio
             
     # make this more concrete
     return uuid
+
+
+def drop_project_data(path: str, uuid: str, path_in_project: str = ""):
+    """
+    Drop (parts of) a prject to free up diskspace
+    """
+    dl.drop(path + "/projects/" + uuid + "/" + path_in_project)
+

corrlib/meas_io.py

@@ -7,7 +7,7 @@ import json
 from typing import Union, Optional
 from pyerrors import Obs, Corr, load_object, dump_object
 from hashlib import sha256, sha1
-from .tools import cached, record2name_key, name_key2record, make_version_hash
+from .tools import cached, get_file, record2name_key, name_key2record, make_version_hash
 from .cache_io import is_in_cache, cache_path, cache_dir, get_version_hash
 
 
@@ -28,6 +28,7 @@ def write_measurement(path, ensemble, measurement, uuid, code, parameter_file: O
         The uuid of the project.
     """
     db = os.path.join(path, 'backlogger.db')
+    get_file(path, "backlogger.db")
     dl.unlock(db, dataset=path)
     conn = sqlite3.connect(db)
     c = conn.cursor()
@@ -159,8 +160,9 @@ def load_records(path: str, record_paths: list[str], preloaded = {}) -> list[Uni
 
 
 def preload(path: str, file: str):
-    dl.get(os.path.join(path, file), dataset=path)
+    get_file(path, file)
     filedict = pj.load_json_dict(os.path.join(path, file))
+    print("> read file")
     return filedict
 
 
@@ -168,6 +170,7 @@ def drop_record(path: str, meas_path: str):
     file_in_archive, sub_key = record2name_key(meas_path)
     file = os.path.join(path, file_in_archive)
     db = os.path.join(path, 'backlogger.db')
+    get_file(path, 'backlogger.db')
     dl.unlock(db, dataset=path)
     conn = sqlite3.connect(db)
     c = conn.cursor()

corrlib/tools.py

@@ -1,5 +1,6 @@
-import hashlib
 import os
+import datalad.api as dl
+import hashlib
 
 def str2list(string):
     return string.split(",")
@@ -16,20 +17,3 @@ def m2k(m):
 
 def k2m(k):
     return (1/(2*k))-4
-
-
-def record2name_key(record_path: str):
-    file = record_path.split("::")[0]
-    key = record_path.split("::")[1]
-    return file, key
-
-
-def name_key2record(name: str, key: str):
-    return name + "::" + key
-
-
-def make_version_hash(path, record):
-    file, key = record2name_key(record)
-    with open(os.path.join(path, file), 'rb') as fp:
-        file_hash = hashlib.file_digest(fp, 'sha1').hexdigest()
-    return file_hash

corrlib/version.py

@@ -1 +1 @@
-__version__ = "0.1.4"
+__version__ = "0.2.3"

examples/example_import.toml

@@ -0,0 +1,28 @@
+['project']
+url = "git@kuhl-mann.de:lattice/cA_data.git"
+code = "sfcf"
+[measurements]
+[measurements.a]
+    path = "/path/to/measurement"
+    ensemble = "A1k1"
+    param_file = "/path/to/file"
+    version = "1.1"
+    prefix = "pref"
+    cfg_seperator = "n"
+    names = ['list', 'of', 'names']
+[measurements.b]
+    path = "/path/to/measurement"
+    ensemble = "A1k1"
+    param_file = "/path/to/file"
+    version = "1.1"
+    prefix = "pref"
+    cfg_seperator = "n"
+    names = ['list', 'of', 'names']
+[measurements.c]
+    path = "/path/to/measurement"
+    ensemble = "A1k1"
+    param_file = "/path/to/file"
+    version = "1.1"
+    prefix = "pref"
+    cfg_seperator = "n"
+    names = ['list', 'of', 'names']

pyproject.toml

@@ -0,0 +1,6 @@
+[build-system]
+requires = ["setuptools >= 63.0.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.ruff.lint]
+ignore = ["F403"]

tests/import_project_test.py

@@ -0,0 +1,17 @@
+import corrlib.toml as t
+
+
+def test_toml_check_measurement_data():
+    measurements = {
+                    "a":
+                        {
+                            "path": "/path/to/measurement",
+                            "ensemble": "A1k1",
+                            "param_file": "/path/to/file",
+                            "version": "1.1",
+                            "prefix": "pref",
+                            "cfg_seperator": "n",
+                            "names": ['list', 'of', 'names']
+                        }
+                    }
+    t.check_measurement_data(measurements)