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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,160 @@ | ||
| import logging | ||
| import os | ||
| from .const import * | ||
| from .conductor import _get_yaml_path | ||
|
|
||
| _LOGGER = logging.getLogger(__name__) | ||
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| def write_sample_yaml_prj(namespaces): | ||
| """ | ||
| Plugin: saves sample representation with project reference to YAML. | ||
| This plugin can be parametrized by providing the path value/template in | ||
| 'pipeline.var_templates.sample_yaml_prj_path'. This needs to be a complete and | ||
| absolute path to the file where sample YAML representation is to be | ||
| stored. | ||
| :param dict namespaces: variable namespaces dict | ||
| :return dict: sample namespace dict | ||
| """ | ||
| sample = namespaces["sample"] | ||
| sample.to_yaml( | ||
| _get_yaml_path(namespaces, SAMPLE_YAML_PRJ_PATH_KEY, "_sample_prj"), | ||
| add_prj_ref=True, | ||
| ) | ||
| return {"sample": sample} | ||
|
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| def write_custom_template(namespaces): | ||
| """ | ||
| Plugin: Populates a user-provided jinja template | ||
| Parameterize by providing pipeline.var_templates.custom_template | ||
| """ | ||
|
|
||
| def load_template(pipeline): | ||
| with open(namespaces["pipeline"]["var_templates"]["custom_template"], "r") as f: | ||
| x = f.read() | ||
| t = jinja2.Template(x) | ||
| return t | ||
|
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||
| err_msg = ( | ||
| "Custom template plugin requires a template in var_templates.custom_template" | ||
| ) | ||
| if "var_templates" not in namespaces["pipeline"].keys(): | ||
| _LOGGER.error(err_msg) | ||
| return None | ||
|
|
||
| if "custom_template" not in namespaces["pipeline"]["var_templates"].keys(): | ||
| _LOGGER.error(err_msg) | ||
| return None | ||
|
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| import jinja2 | ||
|
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||
| tpl = load_template(namespaces["pipeline"]) | ||
| content = tpl.render(namespaces) | ||
| pth = _get_yaml_path(namespaces, "custom_template_output", "config") | ||
| namespaces["sample"]["custom_template_output"] = pth | ||
| with open(pth, "wb") as fh: | ||
| # print(content) | ||
| fh.write(content.encode()) | ||
|
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| return {"sample": namespaces["sample"]} | ||
|
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|
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| def write_sample_yaml_cwl(namespaces): | ||
| """ | ||
| Plugin: Produce a cwl-compatible yaml representation of the sample | ||
| Also adds the 'cwl_yaml' attribute to sample objects, which points | ||
| to the file produced. | ||
| This plugin can be parametrized by providing the path value/template in | ||
| 'pipeline.var_templates.sample_cwl_yaml_path'. This needs to be a complete and | ||
| absolute path to the file where sample YAML representation is to be | ||
| stored. | ||
| :param dict namespaces: variable namespaces dict | ||
| :return dict: updated variable namespaces dict | ||
| """ | ||
| from eido import read_schema | ||
| from ubiquerg import is_url | ||
|
|
||
| def _get_schema_source( | ||
| schema_source, piface_dir=namespaces["looper"]["piface_dir"] | ||
| ): | ||
| # Stolen from piface object; should be a better way to do this... | ||
| if is_url(schema_source): | ||
| return schema_source | ||
| elif not os.path.isabs(schema_source): | ||
| schema_source = os.path.join(piface_dir, schema_source) | ||
| return schema_source | ||
|
|
||
| # To be compatible as a CWL job input, we need to handle the | ||
| # File and Directory object types directly. | ||
| sample = namespaces["sample"] | ||
| sample.sample_yaml_cwl = _get_yaml_path( | ||
| namespaces, SAMPLE_CWL_YAML_PATH_KEY, "_sample_cwl" | ||
| ) | ||
|
|
||
| if "input_schema" in namespaces["pipeline"]: | ||
| schema_path = _get_schema_source(namespaces["pipeline"]["input_schema"]) | ||
| file_list = [] | ||
| for ischema in read_schema(schema_path): | ||
| if "files" in ischema["properties"]["samples"]["items"]: | ||
| file_list.extend(ischema["properties"]["samples"]["items"]["files"]) | ||
|
|
||
| for file_attr in file_list: | ||
| _LOGGER.debug("CWL-ing file attribute: {}".format(file_attr)) | ||
| file_attr_value = sample[file_attr] | ||
| # file paths are assumed relative to the sample table; | ||
| # but CWL assumes they are relative to the yaml output file, | ||
| # so we convert here. | ||
| file_attr_rel = os.path.relpath( | ||
| file_attr_value, os.path.dirname(sample.sample_yaml_cwl) | ||
| ) | ||
| sample[file_attr] = {"class": "File", "path": file_attr_rel} | ||
|
|
||
| directory_list = [] | ||
| for ischema in read_schema(schema_path): | ||
| if "directories" in ischema["properties"]["samples"]["items"]: | ||
| directory_list.extend( | ||
| ischema["properties"]["samples"]["items"]["directories"] | ||
| ) | ||
|
|
||
| for dir_attr in directory_list: | ||
| _LOGGER.debug("CWL-ing directory attribute: {}".format(dir_attr)) | ||
| dir_attr_value = sample[dir_attr] | ||
| # file paths are assumed relative to the sample table; | ||
| # but CWL assumes they are relative to the yaml output file, | ||
| # so we convert here. | ||
| sample[dir_attr] = {"class": "Directory", "location": dir_attr_value} | ||
| else: | ||
| _LOGGER.warning( | ||
| "No 'input_schema' defined, producing a regular " | ||
| "sample YAML representation" | ||
| ) | ||
| _LOGGER.info("Writing sample yaml to {}".format(sample.sample_yaml_cwl)) | ||
| sample.to_yaml(sample.sample_yaml_cwl) | ||
| return {"sample": sample} | ||
|
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||
|
|
||
| def write_sample_yaml(namespaces): | ||
| """ | ||
| Plugin: saves sample representation to YAML. | ||
| This plugin can be parametrized by providing the path value/template in | ||
| 'pipeline.var_templates.sample_yaml_path'. This needs to be a complete and | ||
| absolute path to the file where sample YAML representation is to be | ||
| stored. | ||
| :param dict namespaces: variable namespaces dict | ||
| :return dict: sample namespace dict | ||
| """ | ||
| sample = namespaces["sample"] | ||
| sample["sample_yaml_path"] = _get_yaml_path( | ||
| namespaces, SAMPLE_YAML_PATH_KEY, "_sample" | ||
| ) | ||
| sample.to_yaml(sample["sample_yaml_path"], add_prj_ref=False) | ||
| return {"sample": sample} |