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Merge pull request #444 from bioimage-io/partner_module
create bioimageio.spec.partner
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,3 @@ | ||
| { | ||
| "version": "0.4.5post12" | ||
| "version": "0.4.5post13" | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| """bioimageio.spec extensions for BioImage.IO community partners""" | ||
| # todo: consider moving to its own module, e.g. bioimageio.partner | ||
| # todo: if not moving to its own module, add the dependency to a 'partner' extra in setup.py |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,169 @@ | ||
| # type: ignore | ||
| """ImJoy plugin parser module.""" | ||
| import copy | ||
| import json | ||
| import uuid | ||
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| import requests | ||
| from lxml import etree | ||
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| from bioimageio.spec.shared import yaml | ||
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| tag_types = ["config", "script", "link", "window", "style", "docs", "attachment"] | ||
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| CONFIGURABLE_FIELDS = [ | ||
| "env", | ||
| "requirements", | ||
| "dependencies", | ||
| "icon", | ||
| "ui", | ||
| "type", | ||
| "flags", | ||
| "labels", | ||
| "cover", | ||
| "base_frame", | ||
| "base_worker", | ||
| "passive", | ||
| ] | ||
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| class dotdict(dict): # pylint: disable=invalid-name | ||
| """Access dictionary attributes with dot.notation.""" | ||
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| __getattr__ = dict.get | ||
| __setattr__ = dict.__setitem__ | ||
| __delattr__ = dict.__delitem__ | ||
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| def __deepcopy__(self, memo=None): | ||
| """Make a deep copy.""" | ||
| return dotdict(copy.deepcopy(dict(self), memo=memo)) | ||
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| def parse_imjoy_plugin(source, overwrite_config=None): | ||
| """Parse ImJoy plugin file and return a dict with all the fields.""" | ||
| root = etree.HTML("<html>" + source + "</html>") | ||
| plugin_comp = dotdict() | ||
| for tag_type in tag_types: | ||
| elms = root.xpath(f".//{tag_type}") | ||
| values = [] | ||
| for elm in elms: | ||
| values.append( | ||
| dotdict( | ||
| attrs=dotdict(elm.attrib), | ||
| content=elm.text, | ||
| ) | ||
| ) | ||
| plugin_comp[tag_type] = values | ||
| if plugin_comp.config[0].attrs.lang == "yaml": | ||
| config = yaml.load(plugin_comp.config[0].content) | ||
| elif plugin_comp.config[0].attrs.lang == "json": | ||
| config = json.loads(plugin_comp.config[0].content) | ||
| else: | ||
| raise Exception("Unsupported config language: " + plugin_comp.config[0].attrs.lang) | ||
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| overwrite_config = overwrite_config or {} | ||
| config["tag"] = overwrite_config.get("tag") or (config.get("tags") and config.get("tags")[0]) | ||
| config["hot_reloading"] = overwrite_config.get("hot_reloading") | ||
| config["scripts"] = [] | ||
| # try to match the script with current tag | ||
| for elm in plugin_comp.script: | ||
| if elm.attrs.tag == config["tag"]: | ||
| config["script"] = elm.content | ||
| # exclude script with mismatched tag | ||
| if not elm.attrs.tag or elm.attrs.tag == config["tag"]: | ||
| config["scripts"].append(elm) | ||
| if not config.get("script") and len(plugin_comp.script) > 0: | ||
| config["script"] = plugin_comp.script[0].content | ||
| config["lang"] = plugin_comp.script[0].attrs.lang | ||
| config["links"] = plugin_comp.link or None | ||
| config["windows"] = plugin_comp.window or None | ||
| config["styles"] = plugin_comp.style or None | ||
| config["docs"] = plugin_comp.docs[0] if plugin_comp.docs else config.get("docs") | ||
| config["attachments"] = plugin_comp.attachment or None | ||
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| config["_id"] = overwrite_config.get("_id") or config.get("name").replace(" ", "_") | ||
| config["uri"] = overwrite_config.get("uri") | ||
| config["origin"] = overwrite_config.get("origin") | ||
| config["namespace"] = overwrite_config.get("namespace") | ||
| config["code"] = source | ||
| config["id"] = config.get("name").strip().replace(" ", "_") + "_" + str(uuid.uuid4()) | ||
| config["runnable"] = config.get("runnable", True) | ||
| config["requirements"] = config.get("requirements") or [] | ||
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| for field in CONFIGURABLE_FIELDS: | ||
| obj = config.get(field) | ||
| if obj and isinstance(obj, dict) and not isinstance(obj, list): | ||
| if config.get("tag"): | ||
| config[field] = obj.get(config.get("tag")) | ||
| if not obj.get(config.get("tag")): | ||
| print("WARNING: " + field + " do not contain a tag named: " + config.get("tag")) | ||
| else: | ||
| raise Exception("You must use 'tags' with configurable fields.") | ||
| config["lang"] = config.get("lang") or "javascript" | ||
| return config | ||
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| def convert_config_to_rdf(plugin_config, source_url=None) -> dict: | ||
| """Convert imjoy plugin config to RDF format.""" | ||
| rdf = { | ||
| "type": "application", | ||
| } | ||
| if source_url: | ||
| rdf["source"] = source_url | ||
| fields = [ | ||
| "icon", | ||
| "name", | ||
| "version", | ||
| "api_version", | ||
| "description", | ||
| "license", | ||
| "requirements", | ||
| "dependencies", | ||
| "env", | ||
| "passive", | ||
| "services", | ||
| ] | ||
| for field in fields: | ||
| if field in plugin_config: | ||
| rdf[field] = plugin_config[field] | ||
| tags = plugin_config.get("labels", []) + plugin_config.get("flags", []) | ||
| if "bioengine" not in tags: | ||
| tags.append("bioengine") | ||
| rdf["tags"] = tags | ||
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| docs = plugin_config.get("docs") | ||
| if isinstance(docs, dict): | ||
| rdf["documentation"] = docs.get("content") | ||
| elif isinstance(docs, str): | ||
| rdf["documentation"] = docs | ||
| rdf["covers"] = plugin_config.get("cover") | ||
| # make sure we have a list | ||
| if not rdf["covers"]: | ||
| rdf["covers"] = [] | ||
| elif not isinstance(rdf["covers"], list): | ||
| rdf["covers"] = [rdf["covers"]] | ||
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| rdf["badges"] = plugin_config.get("badge") | ||
| if not rdf["badges"]: | ||
| rdf["badges"] = [] | ||
| elif not isinstance(rdf["badges"], list): | ||
| rdf["badges"] = [rdf["badges"]] | ||
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| authors = plugin_config.get("author") | ||
| if authors: | ||
| if isinstance(authors, str): | ||
| authors = {"name": authors} | ||
| if not isinstance(authors, list): | ||
| authors = [authors] | ||
| rdf["authors"] = authors | ||
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| return rdf | ||
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| def get_plugin_as_rdf(source_url) -> dict: | ||
| """Get imjoy plugin config in RDF format.""" | ||
| req = requests.get(source_url) | ||
| source = req.text | ||
| plugin_config = parse_imjoy_plugin(source) | ||
| rdf = convert_config_to_rdf(plugin_config, source_url) | ||
| return rdf |
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