hrm_omero.misc

  1"""Miscellaneous functions used across the package."""
  2
  3import os
  4
  5from loguru import logger as log
  6
  7
  8class OmeroId:
  9
 10    """Representation of a (group-qualified) OMERO object ID.
 11
 12    The purpose of this class is to facilitate parsing and access of the
 13    ubiquitious target IDs denoting objects in OMERO. The constructor takes
 14    the common string of the form `G:[gid]:[type]:[iid]` as an input and sets
 15    the properties `group`, `obj_type` and `obj_id` accordingly after validating
 16    their contents for having reasonable values.
 17
 18    Attributes
 19    ----------
 20    group : str
 21        The OMERO group ID as an int-like `str`.
 22    obj_type : str
 23        The OMERO object type, e.g. `Experimenter`, `Image`, ...
 24    obj_id : str
 25        The OMERO object ID as an int-like `str`.
 26    """
 27
 28    def __init__(self, id_str):
 29        self.group = None
 30        self.obj_type = None
 31        self.obj_id = None
 32        self.parse_id_str(id_str)
 33
 34    def parse_id_str(self, id_str):
 35        """Parse and validate an ID string of the form `G:[gid]:[type]:[oid]`
 36
 37        The method will parse the given string and set the object's `group`, `obj_type`
 38        and `obj_id` values accordingly. In case for `id_str` the special value `ROOT`
 39        was supplied, `group` and `obj_id` will be set to `-1` whereas `obj_type` will
 40        be set to `BaseTree`.
 41
 42        Parameters
 43        ----------
 44        id_str : str
 45            The ID of an OMERO object, e.g.
 46            * `G:23:Image:42`
 47            * `G:4:Dataset:765487`
 48            * special case `ROOT`, same as `G:-1:BaseTree:-1`
 49
 50        Raises
 51        ------
 52        ValueError
 53            Raised in case a malformed `id_str` was given.
 54        """
 55        log.trace(f"Parsing ID string: [{id_str}]")
 56        if id_str == "ROOT":
 57            self.group = -1
 58            self.obj_type = "BaseTree"
 59            self.obj_id = -1
 60            log.debug(f"Converted special ID 'ROOT' to [{str(self)}].")
 61            return
 62
 63        try:
 64            group_type, group_id, obj_type, obj_id = id_str.split(":")
 65            int(group_id)  # raises a TypeError if cast to int fails
 66            int(obj_id)  # raises a TypeError if cast to int fails
 67            if group_type != "G":
 68                raise ValueError(f"Invalid group qualifier '{group_type}'.")
 69            if obj_type not in [
 70                "Image",
 71                "Dataset",
 72                "Project",
 73                "Experimenter",
 74                "ExperimenterGroup",
 75            ]:
 76                raise ValueError(f"Invalid object type '{obj_type}'.")
 77            if int(obj_id) < 1:
 78                raise ValueError(f"Invalid object ID '{obj_id}'.")
 79        except (ValueError, TypeError) as err:
 80            # pylint: disable-msg=raise-missing-from
 81            msg = f"Malformed id_str '{id_str}', expecting `G:[gid]:[type]:[oid]`."
 82            raise ValueError(msg, err)
 83
 84        log.debug(f"Validated ID string: group={group_id}, {obj_type}={obj_id}")
 85        self.group = group_id
 86        self.obj_type = obj_type
 87        self.obj_id = obj_id
 88
 89    def __str__(self):
 90        return f"G:{self.group}:{self.obj_type}:{self.obj_id}"
 91
 92
 93def printlog(level, message):
 94    """Simple wrapper to push a message to stdout and logging.
 95
 96    Note that something very similiar (or identical) could be achieved by adding a log
 97    handler that emits to stdout.
 98
 99    Parameters
100    ----------
101    level : str
102        The log level of the message as defined by loguru.
103    message : str
104        The message to be printed and logged.
105    """
106    print(message)
107    log.log(level, message)
108
109
110def changemodes(basepath, elements, dmode=0o775, fmode=0o664):
111    """Recursive `chmod` function in the spirit of `os.makedirs()`.
112
113    Parameters
114    ----------
115    basepath : str
116        The base path where to look for the given elements.
117    elements : list(str)
118        A list of file and directory names relative to `basepath`.
119    dmode : int, optional
120        The mode to use for directories, by default `0o775`
121    fmode : int, optional
122        The mode to use for files, by default `0o664`
123    """
124    for item in elements:
125        path = os.path.join(basepath, item)
126
127        if os.path.isdir(path):
128            log.trace(f"Adjusting permissions on [{path}] to [{dmode:o}]...")
129            os.chmod(path, mode=dmode)
130        else:
131            log.trace(f"Adjusting permissions on [{path}] to [{fmode:o}]...")
132            os.chmod(path, mode=fmode)
133
134        for dirpath, dirnames, filenames in os.walk(path):
135            for dname in dirnames:
136                log.trace(f"Adjusting permissions on [{dname}] to [{dmode:o}]...")
137                os.chmod(os.path.join(dirpath, dname), mode=dmode)
138            for fname in filenames:
139                log.trace(f"Adjusting permissions on [{fname}] to [{fmode:o}]...")
140                os.chmod(os.path.join(dirpath, fname), mode=fmode)