From a80218ecf033d0a48d87dc54302cbde295e65aff Mon Sep 17 00:00:00 2001
From: Daniel <d.hornung@indiscale.com>
Date: Thu, 11 May 2023 17:51:17 +0200
Subject: [PATCH] WIP: Rename caosdb -> linkahead
---
.../bloxberg/bloxberg.py | 10 ++--
src/linkaheadadvancedtools/cfoods/h5.py | 2 +-
src/linkaheadadvancedtools/crawler.py | 14 +++---
src/linkaheadadvancedtools/export_related.py | 2 +-
src/linkaheadadvancedtools/loadFiles.py | 46 +++++++++----------
.../models/data_model.py | 6 +--
src/linkaheadadvancedtools/models/parser.py | 10 ++--
src/linkaheadadvancedtools/scifolder/utils.py | 2 +-
.../serverside/examples/example_script.py | 4 +-
.../serverside/generic_analysis.py | 2 +-
.../serverside/helper.py | 20 ++++----
11 files changed, 59 insertions(+), 59 deletions(-)
diff --git a/src/linkaheadadvancedtools/bloxberg/bloxberg.py b/src/linkaheadadvancedtools/bloxberg/bloxberg.py
index a774a8b9..43b4cb17 100644
--- a/src/linkaheadadvancedtools/bloxberg/bloxberg.py
+++ b/src/linkaheadadvancedtools/bloxberg/bloxberg.py
@@ -75,12 +75,12 @@ A dict with the following keys:
Parameters
----------
-entity : caosdb.Entity
+entity : linkahead.Entity
The entity to be certified
Returns
-------
-out : caosdb.Record
+out : linkahead.Record
A BloxbergCertificate Record with all the necessary Properties.
"""
# Calculate hash
@@ -126,7 +126,7 @@ This method does nothing if the verification passes, else it raises an exception
Parameters
----------
-certificate : caosdb.Record
+certificate : linkahead.Record
The BloxbergCertificate Record which shall be verified.
"""
@@ -138,7 +138,7 @@ The BloxbergCertificate Record which shall be verified.
Parameters
----------
-certificate : caosdb.Record
+certificate : linkahead.Record
The BloxbergCertificate Record for which the JSON is generated.
filename : str
@@ -162,7 +162,7 @@ def certify_entity(entity, json_filename=None):
Parameters
----------
-entity : caosdb.Entity
+entity : linkahead.Entity
The Entity to be certified.
json_filename : str
diff --git a/src/linkaheadadvancedtools/cfoods/h5.py b/src/linkaheadadvancedtools/cfoods/h5.py
index 2615040f..be0cd1c0 100644
--- a/src/linkaheadadvancedtools/cfoods/h5.py
+++ b/src/linkaheadadvancedtools/cfoods/h5.py
@@ -172,7 +172,7 @@ class H5CFood(AbstractFileCFood):
self.to_be_inserted = db.Container()
self.insert_missing_structure(self.structure)
- # TODO this is a workaround due to the fact that the caosdb library
+ # TODO this is a workaround due to the fact that the LinkAhead library
# changes the objects in the Container if it is inserted. The graph
# structure is flattened. I.e. references to other entity objects are
# replaced with their IDs. However this code depends on this graph.
diff --git a/src/linkaheadadvancedtools/crawler.py b/src/linkaheadadvancedtools/crawler.py
index dc4e52e6..4a522153 100644
--- a/src/linkaheadadvancedtools/crawler.py
+++ b/src/linkaheadadvancedtools/crawler.py
@@ -526,16 +526,16 @@ ____________________\n""".format(i+1, len(pending_changes)) + str(el[3]))
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1">
<title>Crawler</title>
- <link rel="stylesheet" href="{url}/webinterface/css/webcaosdb.css"/>
+ <link rel="stylesheet" href="{url}/webinterface/css/weblinkahead.css"/>
<link rel="stylesheet" href="{url}/webinterface/css/bootstrap.css">
<script src="{url}/webinterface/js/jquery.js"></script>
<script src="{url}/webinterface/js/utif.js"></script>
<script src="{url}/webinterface/js/loglevel.js"></script>
<script src="{url}/webinterface/js/bootstrap.js"></script>
<script src="{url}/webinterface/js/ext_table_preview.js"></script>
- <script src="{url}/webinterface/js/webcaosdb.js"></script>
+ <script src="{url}/webinterface/js/weblinkahead.js"></script>
<script src="{url}/webinterface/js/plotly.js"></script>
- <script src="{url}/webinterface/js/caosdb.js"></script>
+ <script src="{url}/webinterface/js/linkahead.js"></script>
<script src="{url}/webinterface/js/state-machine.js"></script>
<script src="{url}/webinterface/js/showdown.js"></script>
<script src="{url}/webinterface/js/preview.js"></script>
@@ -608,7 +608,7 @@ ____________________\n""".format(i+1, len(pending_changes)) + str(el[3]))
filename: path to the html site that allow the authorization
"""
- caosdb_config = db.configuration.get_config()
+ linkahead_config = db.configuration.get_config()
text = """Dear Curator,
there where changes that need your authorization. Please check the following
carefully and if the changes are ok, click on the following link:
@@ -616,12 +616,12 @@ carefully and if the changes are ok, click on the following link:
{url}/Shared/{filename}
{changes}
- """.format(url=caosdb_config["Connection"]["url"],
+ """.format(url=linkahead_config["Connection"]["url"],
filename=filename,
changes="\n".join(changes))
try:
- fro = caosdb_config["advancedtools"]["crawler.from_mail"]
- to = caosdb_config["advancedtools"]["crawler.to_mail"]
+ fro = linkahead_config["advancedtools"]["crawler.from_mail"]
+ to = linkahead_config["advancedtools"]["crawler.to_mail"]
except KeyError:
logger.error("Server Configuration is missing a setting for "
"sending mails. The administrator should check "
diff --git a/src/linkaheadadvancedtools/export_related.py b/src/linkaheadadvancedtools/export_related.py
index 62a777ae..ad8aa192 100755
--- a/src/linkaheadadvancedtools/export_related.py
+++ b/src/linkaheadadvancedtools/export_related.py
@@ -128,7 +128,7 @@ def export(cont, directory="."):
xml = etree.tounicode(cont.to_xml(
local_serialization=True), pretty_print=True)
- with open(os.path.join(directory, "caosdb_data.xml"), "w") as fi:
+ with open(os.path.join(directory, "linkahead_data.xml"), "w") as fi:
fi.write(xml)
diff --git a/src/linkaheadadvancedtools/loadFiles.py b/src/linkaheadadvancedtools/loadFiles.py
index d57ac33c..ec8f1800 100755
--- a/src/linkaheadadvancedtools/loadFiles.py
+++ b/src/linkaheadadvancedtools/loadFiles.py
@@ -50,15 +50,15 @@ def convert_size(size):
return '%s %s' % (s, size_name[i])
-def combine_ignore_files(caosdbignore, localignore, dirname=None):
- """appends the contents of localignore to caosdbignore and saves the result
+def combine_ignore_files(linkaheadignore, localignore, dirname=None):
+ """appends the contents of localignore to linkaheadignore and saves the result
and returns the name
"""
tmp = NamedTemporaryFile(delete=False, mode="w",
- dir=dirname, prefix=".caosdbignore")
- with open(caosdbignore, "r") as base:
+ dir=dirname, prefix=".linkaheadignore")
+ with open(linkaheadignore, "r") as base:
tmp.write(base.read())
with open(localignore, "r") as local:
tmp.write(local.read())
@@ -66,15 +66,15 @@ def combine_ignore_files(caosdbignore, localignore, dirname=None):
return tmp.name
-def compile_file_list(caosdbignore, localpath):
+def compile_file_list(linkaheadignore, localpath):
"""creates a list of files that contain all files under localpath except
- those excluded by caosdbignore
+ those excluded by linkaheadignore
"""
from gitignore_parser import parse_gitignore
- matches = parse_gitignore(caosdbignore)
- current_ignore = caosdbignore
+ matches = parse_gitignore(linkaheadignore)
+ current_ignore = linkaheadignore
non_ignored_files = []
ignore_files = []
for root, dirs, files in os.walk(localpath):
@@ -88,14 +88,14 @@ def compile_file_list(caosdbignore, localpath):
current_ignore = ignore_files[-1][1]
matches = parse_gitignore(current_ignore)
else:
- current_ignore = caosdbignore
+ current_ignore = linkaheadignore
matches = parse_gitignore(current_ignore)
# create a new local ignore file
- if ".caosdbignore" in files:
+ if ".linkaheadignore" in files:
current_ignore = combine_ignore_files(current_ignore,
os.path.join(
- root, ".caosdbignore"),
+ root, ".linkaheadignore"),
# due to the logic of gitignore_parser the file
# has to be written to this folder
dirname=root)
@@ -128,12 +128,12 @@ def create_re_for_file_list(files, localroot, remoteroot):
return "^("+regexp[1:]+")$"
-def loadpath(path, include, exclude, prefix, dryrun, forceAllowSymlinks, caosdbignore=None,
+def loadpath(path, include, exclude, prefix, dryrun, forceAllowSymlinks, linkaheadignore=None,
localpath=None):
- if caosdbignore:
+ if linkaheadignore:
# create list of files and create regular expression for small chunks
- filelist = compile_file_list(caosdbignore, localpath)
+ filelist = compile_file_list(linkaheadignore, localpath)
fulllist = filelist
index = 0
@@ -146,7 +146,7 @@ def loadpath(path, include, exclude, prefix, dryrun, forceAllowSymlinks, caosdbi
else:
includes = [include]
- # if no caosdbignore file is used, this iterates over a single include
+ # if no linkaheadignore file is used, this iterates over a single include
for include in includes:
if dryrun:
logger.info("Performin a dryrun!")
@@ -194,14 +194,14 @@ def main(argv=None):
parser.add_argument("-p", "--prefix", dest="prefix",
help="store files with this prefix into the server's"
" file system.")
- parser.add_argument("-c", "--caosdbignore", help="""
-Path to a caosdbignore file that defines which files shall be included and which do not.
+ parser.add_argument("-c", "--linkaheadignore", help="""
+Path to a linkaheadignore file that defines which files shall be included and which do not.
The syntax is the same as in a gitignore file. You must also provide the localpath option
since the check is done locally.
"""
)
parser.add_argument("-l", "--localpath", help="Path to the root directory on this machine. "
- "This is needed if a caosdbignore file is used since the check is done "
+ "This is needed if a linkaheadignore file is used since the check is done "
"locally")
parser.add_argument("-i", "--include", dest="include",
help="""
@@ -236,12 +236,12 @@ exclude is given preference over include.
"directory tree.", action="store_true")
args = parser.parse_args()
- if args.caosdbignore and (args.exclude or args.include):
+ if args.linkaheadignore and (args.exclude or args.include):
raise ValueError(
- "Do not use a caosdbignore file and in- or exclude simultaneously!")
+ "Do not use a linkaheadignore file and in- or exclude simultaneously!")
- if args.caosdbignore and not args.localpath:
- raise ValueError("To use caosdbignore you must supply a local path!")
+ if args.linkaheadignore and not args.localpath:
+ raise ValueError("To use linkaheadignore you must supply a local path!")
if args.localpath and (args.exclude or args.include):
raise ValueError(
@@ -262,7 +262,7 @@ exclude is given preference over include.
prefix=args.prefix,
dryrun=args.dryrun,
forceAllowSymlinks=args.forceAllowSymlinks,
- caosdbignore=args.caosdbignore,
+ linkaheadignore=args.linkaheadignore,
localpath=args.localpath,
)
diff --git a/src/linkaheadadvancedtools/models/data_model.py b/src/linkaheadadvancedtools/models/data_model.py
index c9e344c6..d207ff73 100644
--- a/src/linkaheadadvancedtools/models/data_model.py
+++ b/src/linkaheadadvancedtools/models/data_model.py
@@ -33,7 +33,7 @@ import linkahead as db
from linkahead.apiutils import compare_entities, describe_diff
-CAOSDB_INTERNAL_PROPERTIES = [
+LINKAHEAD_INTERNAL_PROPERTIES = [
"description",
"name",
"unit",
@@ -45,7 +45,7 @@ class DataModel(dict):
When constructing a data model the LinkAhead representation can easily be
created using the classes RecordType and Propery, storing them in a
- Container and inserting it in CaoSDB. However, this has one drawback: You
+ Container and inserting it in Linkahead. However, this has one drawback: You
cannot simply change someting and update the container. The container will
insist on having valid ids for all contained Entities.
@@ -136,7 +136,7 @@ class DataModel(dict):
any_change = False
for ent in existing_entities:
- if ent.name in CAOSDB_INTERNAL_PROPERTIES:
+ if ent.name in LINKAHEAD_INTERNAL_PROPERTIES:
# Workaround for the usage of internal properties like name
# in via the extern keyword:
ref = db.Property(name=ent.name).retrieve()
diff --git a/src/linkaheadadvancedtools/models/parser.py b/src/linkaheadadvancedtools/models/parser.py
index 981455c5..803fc7fa 100644
--- a/src/linkaheadadvancedtools/models/parser.py
+++ b/src/linkaheadadvancedtools/models/parser.py
@@ -47,11 +47,11 @@ from warnings import warn
import jsonschema
import linkahead as db
-from .data_model import CAOSDB_INTERNAL_PROPERTIES, DataModel
+from .data_model import LINKAHEAD_INTERNAL_PROPERTIES, DataModel
# Keywords which are allowed in data model descriptions.
KEYWORDS = ["parent", # deprecated, use inherit_from_* instead:
- # https://gitlab.com/caosdb/caosdb-advanced-user-tools/-/issues/36
+ # https://gitlab.com/linkahead/linkahead-advanced-user-tools/-/issues/36
"importance",
"datatype", # for example TEXT, INTEGER or REFERENCE
"unit",
@@ -254,7 +254,7 @@ class Parser(object):
ymlmodel["extern"] = []
for name in ymlmodel["extern"]:
- if name in CAOSDB_INTERNAL_PROPERTIES:
+ if name in LINKAHEAD_INTERNAL_PROPERTIES:
self.model[name] = db.Property(name=name).retrieve()
continue
for role in ("Property", "RecordType", "Record", "File"):
@@ -547,7 +547,7 @@ class Parser(object):
iterate over properties and check whether it is a base datatype of a
name that was defined in the model (or extern part)
- the string representations are replaced with caosdb objects
+ the string representations are replaced with LinkAhead objects
"""
@@ -771,7 +771,7 @@ class JsonSchemaParser(Parser):
if "type" in elt and elt["type"] == "integer":
raise NotImplementedError(
"Integer-enums are not allowd until "
- "https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/issues/224 "
+ "https://gitlab.indiscale.com/caosdb/src/LinkAhead-server/-/issues/224 "
"has been fixed."
)
rt = db.RecordType(name=name)
diff --git a/src/linkaheadadvancedtools/scifolder/utils.py b/src/linkaheadadvancedtools/scifolder/utils.py
index 34cbcf36..c25d2643 100644
--- a/src/linkaheadadvancedtools/scifolder/utils.py
+++ b/src/linkaheadadvancedtools/scifolder/utils.py
@@ -174,7 +174,7 @@ def get_xls_header(filepath):
"""
This function reads an xlsx file and creates a dictionary analogue to the
one created by the yaml headers in README.md files read with the get_header
- function of caosdb-advancedtools.
+ function of linkahead-advancedtools.
As xlsx files lack the hierarchical structure, the information that can be
provided is less complex. See the possibility to use the xlsx files as a
less powerfull version for people who are not comfortable with the
diff --git a/src/linkaheadadvancedtools/serverside/examples/example_script.py b/src/linkaheadadvancedtools/serverside/examples/example_script.py
index fe401cb3..ff1e5559 100755
--- a/src/linkaheadadvancedtools/serverside/examples/example_script.py
+++ b/src/linkaheadadvancedtools/serverside/examples/example_script.py
@@ -72,14 +72,14 @@ def send_mail(changes: [db.Entity], receipient: str):
receipient: The person who shall receive the mail.
"""
- caosdb_config = db.configuration.get_config()
+ linkahead_config = db.configuration.get_config()
text = """Dear Curator,
The following changes where done automatically.
{changes}
""".format(changes="\n".join(changes))
try:
- fro = caosdb_config["advancedtools"]["automated_updates.from_mail"]
+ fro = linkahead_config["advancedtools"]["automated_updates.from_mail"]
except KeyError:
logger.error("Server Configuration is missing a setting for "
"sending mails. The administrator should check "
diff --git a/src/linkaheadadvancedtools/serverside/generic_analysis.py b/src/linkaheadadvancedtools/serverside/generic_analysis.py
index a0ff479d..fc1df3c6 100644
--- a/src/linkaheadadvancedtools/serverside/generic_analysis.py
+++ b/src/linkaheadadvancedtools/serverside/generic_analysis.py
@@ -18,7 +18,7 @@
# along with this program. If not, see <https://www.gnu.org/licenses/>.
#
#
-# See: https://gitlab.indiscale.com/caosdb/src/caosdb-advanced-user-tools/-/issues/55
+# See: https://gitlab.indiscale.com/caosdb/src/linkahead-advanced-user-tools/-/issues/55
# This source file is work in progress and currently untested.
diff --git a/src/linkaheadadvancedtools/serverside/helper.py b/src/linkaheadadvancedtools/serverside/helper.py
index 0a6f32a0..246f308f 100644
--- a/src/linkaheadadvancedtools/serverside/helper.py
+++ b/src/linkaheadadvancedtools/serverside/helper.py
@@ -165,7 +165,7 @@ def recordtype_is_child_of(rt, parent):
Parameters
----------
- rt : caosdb.Entity
+ rt : linkahead.Entity
The child RecordType.
parent : str or int
The parent's name or id.
@@ -193,7 +193,7 @@ def init_data_model(entities):
Parameters
----------
- entities : iterable of caosdb.Entity
+ entities : iterable of linkahead.Entity
The data model entities which are to be checked for existence.
Raises
@@ -338,7 +338,7 @@ def send_mail(from_addr, to, subject, body, cc=None, bcc=None,
send_mail_bin=None):
""" Send an email via the configured send_mail client.
- The relevant options in the pycaosdb.ini are:
+ The relevant options in the pylinkahead.ini are:
[Misc]
sendmail = ...
@@ -364,8 +364,8 @@ def send_mail(from_addr, to, subject, body, cc=None, bcc=None,
------
subprocess.CalledProcessError
If the sendmail client returned with a non-zero code.
- caosdb.ConfigurationException
- If the caosdb configuration has no `Misc.sendmail` configured while the
+ linkahead.ConfigurationException
+ If the linkahead configuration has no `Misc.sendmail` configured while the
`send_mail_bin` parameter is None.
"""
@@ -388,14 +388,14 @@ def send_mail(from_addr, to, subject, body, cc=None, bcc=None,
if send_mail_bin is not None:
sendmail = send_mail_bin
else:
- caosdb_config = db.configuration.get_config()
+ linkahead_config = db.configuration.get_config()
- if "Misc" not in caosdb_config or "sendmail" not in caosdb_config["Misc"]:
+ if "Misc" not in linkahead_config or "sendmail" not in linkahead_config["Misc"]:
err_msg = ("No sendmail executable configured. "
"Please configure `Misc.sendmail` "
- "in your pycaosdb.ini.")
+ "in your pylinkahead.ini.")
raise db.ConfigurationError(err_msg)
- sendmail = caosdb_config["Misc"]["sendmail"]
+ sendmail = linkahead_config["Misc"]["sendmail"]
# construct sendmail command
# options explained (from `man sendmail`):
@@ -437,7 +437,7 @@ def get_file_via_download(ent, logger=logging.getLogger(__name__)):
try:
# TODO remove the following treatment of size=0 when the
# following issue is resolved:
- # https://gitlab.com/caosdb/caosdb-server/-/issues/107
+ # https://gitlab.com/linkahead/linkahead-server/-/issues/107
if ent.size > 0:
val_file = ent.download()
--
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