|
| 1 | +import typing as ty |
| 2 | +import json |
| 3 | +import attr |
| 4 | +from urllib.request import urlretrieve |
| 5 | +from pathlib import Path |
| 6 | +from functools import reduce |
| 7 | + |
| 8 | +from ..utils.messenger import AuditFlag |
| 9 | +from ..engine import ShellCommandTask |
| 10 | +from ..engine.specs import SpecInfo, ShellSpec, ShellOutSpec, File, attr_fields |
| 11 | +from .helpers_file import is_local_file |
| 12 | + |
| 13 | + |
| 14 | +class BoshTask(ShellCommandTask): |
| 15 | + """Shell Command Task based on the Boutiques descriptor""" |
| 16 | + |
| 17 | + def __init__( |
| 18 | + self, |
| 19 | + zenodo_id=None, |
| 20 | + bosh_file=None, |
| 21 | + audit_flags: AuditFlag = AuditFlag.NONE, |
| 22 | + cache_dir=None, |
| 23 | + input_spec_names: ty.Optional[ty.List] = None, |
| 24 | + messenger_args=None, |
| 25 | + messengers=None, |
| 26 | + name=None, |
| 27 | + output_spec_names: ty.Optional[ty.List] = None, |
| 28 | + rerun=False, |
| 29 | + strip=False, |
| 30 | + **kwargs, |
| 31 | + ): |
| 32 | + """ |
| 33 | + Initialize this task. |
| 34 | +
|
| 35 | + Parameters |
| 36 | + ---------- |
| 37 | + zenodo_id: :obj: str |
| 38 | + Zenodo ID |
| 39 | + bosh_file : : str |
| 40 | + json file with the boutiques descriptors |
| 41 | + audit_flags : :obj:`pydra.utils.messenger.AuditFlag` |
| 42 | + Auditing configuration |
| 43 | + cache_dir : :obj:`os.pathlike` |
| 44 | + Cache directory |
| 45 | + input_spec_names : :obj: list |
| 46 | + Input names for input_spec. |
| 47 | + messenger_args : |
| 48 | + TODO |
| 49 | + messengers : |
| 50 | + TODO |
| 51 | + name : :obj:`str` |
| 52 | + Name of this task. |
| 53 | + output_spec_names : :obj: list |
| 54 | + Output names for output_spec. |
| 55 | + strip : :obj:`bool` |
| 56 | + TODO |
| 57 | +
|
| 58 | + """ |
| 59 | + self.cache_dir = cache_dir |
| 60 | + if (bosh_file and zenodo_id) or not (bosh_file or zenodo_id): |
| 61 | + raise Exception("either bosh or zenodo_id has to be specified") |
| 62 | + elif zenodo_id: |
| 63 | + self.bosh_file = self._download_spec(zenodo_id) |
| 64 | + else: # bosh_file |
| 65 | + self.bosh_file = bosh_file |
| 66 | + |
| 67 | + with self.bosh_file.open() as f: |
| 68 | + self.bosh_spec = json.load(f) |
| 69 | + |
| 70 | + self.input_spec = self._prepare_input_spec(names_subset=input_spec_names) |
| 71 | + self.output_spec = self._prepare_output_spec(names_subset=output_spec_names) |
| 72 | + self.bindings = ["-v", f"{self.bosh_file.parent}:{self.bosh_file.parent}:ro"] |
| 73 | + |
| 74 | + super(BoshTask, self).__init__( |
| 75 | + name=name, |
| 76 | + input_spec=self.input_spec, |
| 77 | + output_spec=self.output_spec, |
| 78 | + executable=["bosh", "exec", "launch"], |
| 79 | + args=["-s"], |
| 80 | + audit_flags=audit_flags, |
| 81 | + messengers=messengers, |
| 82 | + messenger_args=messenger_args, |
| 83 | + cache_dir=self.cache_dir, |
| 84 | + strip=strip, |
| 85 | + rerun=rerun, |
| 86 | + **kwargs, |
| 87 | + ) |
| 88 | + self.strip = strip |
| 89 | + |
| 90 | + def _download_spec(self, zenodo_id): |
| 91 | + """ |
| 92 | + usind boutiques Searcher to find url of zenodo file for a specific id, |
| 93 | + and download the file to self.cache_dir |
| 94 | + """ |
| 95 | + from boutiques.searcher import Searcher |
| 96 | + |
| 97 | + searcher = Searcher(zenodo_id, exact_match=True) |
| 98 | + hits = searcher.zenodo_search().json()["hits"]["hits"] |
| 99 | + if len(hits) == 0: |
| 100 | + raise Exception(f"can't find zenodo spec for {zenodo_id}") |
| 101 | + elif len(hits) > 1: |
| 102 | + raise Exception(f"too many hits for {zenodo_id}") |
| 103 | + else: |
| 104 | + zenodo_url = hits[0]["files"][0]["links"]["self"] |
| 105 | + zenodo_file = self.cache_dir / f"zenodo.{zenodo_id}.json" |
| 106 | + urlretrieve(zenodo_url, zenodo_file) |
| 107 | + return zenodo_file |
| 108 | + |
| 109 | + def _prepare_input_spec(self, names_subset=None): |
| 110 | + """ creating input spec from the zenodo file |
| 111 | + if name_subset provided, only names from the subset will be used in the spec |
| 112 | + """ |
| 113 | + binputs = self.bosh_spec["inputs"] |
| 114 | + self._input_spec_keys = {} |
| 115 | + fields = [] |
| 116 | + for input in binputs: |
| 117 | + name = input["id"] |
| 118 | + if names_subset is None: |
| 119 | + pass |
| 120 | + elif name not in names_subset: |
| 121 | + continue |
| 122 | + else: |
| 123 | + names_subset.remove(name) |
| 124 | + if input["type"] == "File": |
| 125 | + tp = File |
| 126 | + elif input["type"] == "String": |
| 127 | + tp = str |
| 128 | + elif input["type"] == "Number": |
| 129 | + tp = float |
| 130 | + elif input["type"] == "Flag": |
| 131 | + tp = bool |
| 132 | + else: |
| 133 | + tp = None |
| 134 | + # adding list |
| 135 | + if tp and "list" in input and input["list"]: |
| 136 | + tp = ty.List[tp] |
| 137 | + |
| 138 | + mdata = { |
| 139 | + "help_string": input.get("description", None) or input["name"], |
| 140 | + "mandatory": not input["optional"], |
| 141 | + "argstr": input.get("command-line-flag", None), |
| 142 | + } |
| 143 | + fields.append((name, tp, mdata)) |
| 144 | + self._input_spec_keys[input["value-key"]] = "{" + f"{name}" + "}" |
| 145 | + if names_subset: |
| 146 | + raise RuntimeError(f"{names_subset} are not in the zenodo input spec") |
| 147 | + spec = SpecInfo(name="Inputs", fields=fields, bases=(ShellSpec,)) |
| 148 | + return spec |
| 149 | + |
| 150 | + def _prepare_output_spec(self, names_subset=None): |
| 151 | + """ creating output spec from the zenodo file |
| 152 | + if name_subset provided, only names from the subset will be used in the spec |
| 153 | + """ |
| 154 | + boutputs = self.bosh_spec["output-files"] |
| 155 | + fields = [] |
| 156 | + for output in boutputs: |
| 157 | + name = output["id"] |
| 158 | + if names_subset is None: |
| 159 | + pass |
| 160 | + elif name not in names_subset: |
| 161 | + continue |
| 162 | + else: |
| 163 | + names_subset.remove(name) |
| 164 | + path_template = reduce( |
| 165 | + lambda s, r: s.replace(*r), |
| 166 | + self._input_spec_keys.items(), |
| 167 | + output["path-template"], |
| 168 | + ) |
| 169 | + mdata = { |
| 170 | + "help_string": output.get("description", None) or output["name"], |
| 171 | + "mandatory": not output["optional"], |
| 172 | + "output_file_template": path_template, |
| 173 | + } |
| 174 | + fields.append((name, attr.ib(type=File, metadata=mdata))) |
| 175 | + |
| 176 | + if names_subset: |
| 177 | + raise RuntimeError(f"{names_subset} are not in the zenodo output spec") |
| 178 | + spec = SpecInfo(name="Outputs", fields=fields, bases=(ShellOutSpec,)) |
| 179 | + return spec |
| 180 | + |
| 181 | + def _command_args_single(self, state_ind, ind=None): |
| 182 | + """Get command line arguments for a single state""" |
| 183 | + input_filepath = self._bosh_invocation_file(state_ind=state_ind, ind=ind) |
| 184 | + cmd_list = ( |
| 185 | + self.inputs.executable |
| 186 | + + [str(self.bosh_file), input_filepath] |
| 187 | + + self.inputs.args |
| 188 | + + self.bindings |
| 189 | + ) |
| 190 | + return cmd_list |
| 191 | + |
| 192 | + def _bosh_invocation_file(self, state_ind, ind=None): |
| 193 | + """creating bosh invocation file - json file with inputs values""" |
| 194 | + input_json = {} |
| 195 | + for f in attr_fields(self.inputs): |
| 196 | + if f.name in ["executable", "args"]: |
| 197 | + continue |
| 198 | + if self.state and f"{self.name}.{f.name}" in state_ind: |
| 199 | + value = getattr(self.inputs, f.name)[state_ind[f"{self.name}.{f.name}"]] |
| 200 | + else: |
| 201 | + value = getattr(self.inputs, f.name) |
| 202 | + # adding to the json file if specified by the user |
| 203 | + if value is not attr.NOTHING and value != "NOTHING": |
| 204 | + if is_local_file(f): |
| 205 | + value = Path(value) |
| 206 | + self.bindings.extend(["-v", f"{value.parent}:{value.parent}:ro"]) |
| 207 | + value = str(value) |
| 208 | + |
| 209 | + input_json[f.name] = value |
| 210 | + |
| 211 | + filename = self.cache_dir / f"{self.name}-{ind}.json" |
| 212 | + with open(filename, "w") as jsonfile: |
| 213 | + json.dump(input_json, jsonfile) |
| 214 | + |
| 215 | + return str(filename) |
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