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Merge pull request #92 from hlasimpk/master
Changes for CCP4online & general fixes
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,173 @@ | ||
| """Code to manage references""" | ||
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| __author__ = "Adam Simpkin, Jens Thomas & Felix Simkovic" | ||
| __date__ = "7 November 2018" | ||
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| from collections import OrderedDict | ||
| import copy | ||
| from enum import Enum | ||
| import os | ||
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| class ReferenceManager(): | ||
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| #Section Names | ||
| class SECTIONS(Enum): | ||
| __order__ = 'GENERAL ROTATION MR REFINEMENT' | ||
| GENERAL = 'General' | ||
| ROTATION = 'Rotation Search' | ||
| MR = 'Molecular Replacement' | ||
| REFINEMENT = 'Refinement' | ||
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| SEC_TAG = 'h3' | ||
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| def __init__(self, d): | ||
| self.references = {} | ||
| self.ordered_labels = [] | ||
| self.citation_file_path = None | ||
| self.section_labels = OrderedDict() | ||
| self.setup_references() | ||
| self.setup_sections(d) | ||
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| def setup_references(self): | ||
| ref_fname = os.path.join(os.environ['CCP4'], "share", "simbad", "static", "simbad.bib") | ||
| if not os.path.isfile(ref_fname): | ||
| msg = "Cannot find BibTex file containing references. " \ | ||
| "Please determine them yourself and cite AMPLE." | ||
| return msg | ||
| article = {} | ||
| entry = False | ||
| with open(ref_fname, "r") as fhin: | ||
| for line in fhin.readlines(): | ||
| line = line.strip() | ||
| if not line: | ||
| continue | ||
| elif line.startswith("@"): | ||
| # Beginning of all BibTex entry blocks | ||
| entry = True | ||
| unique_id = line.replace("@article{", "").replace(",", "") | ||
| article = {'unique_id': unique_id} # Reset the article dictionary | ||
| elif line == "}": | ||
| # End of all BibTex entry blocks | ||
| entry = False | ||
| self.references[article['label']] = article | ||
| elif entry: | ||
| # BibTex entry block | ||
| # Some dirty line handling. | ||
| # Not very bulletproof but should do for now | ||
| line = line.replace("{", "").replace("}", "") | ||
| key, value = [l.strip() for l in line.split("=")] | ||
| value = value.rstrip(",").replace("\"", "") | ||
| # Save the data to the article entry | ||
| article[key] = value | ||
| return | ||
|
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| def setup_sections(self, d): | ||
| # Create default lists | ||
| for section in self.SECTIONS: | ||
| self.section_labels[section] = [] | ||
| # Build up list of program reference labels, ordered by sections | ||
| for section in self.SECTIONS: | ||
| if section == self.SECTIONS.GENERAL: | ||
| self.section_labels[section] = ['SIMBAD', 'CCP4', 'CCTBX'] | ||
| elif section == self.SECTIONS.ROTATION: | ||
| labels = [] | ||
| if d.get('-rot_program') == 'phaser': | ||
| labels.append('PHASER_ROT') | ||
| else: | ||
| labels.append('AMORE') | ||
| self.section_labels[section] = labels | ||
| elif section == self.SECTIONS.MR: | ||
| labels = [] | ||
| if d.get('-mr_program') == 'phaser': | ||
| labels.append('PHASER') | ||
| else: | ||
| labels.append('MOLREP') | ||
| self.section_labels[section] = labels | ||
| elif section == self.SECTIONS.REFINEMENT: | ||
| self.section_labels[self.SECTIONS.REFINEMENT] = ['REFMAC'] | ||
|
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| # Generate ordered list of all relevant reference labels | ||
| for section in self.SECTIONS: | ||
| if section in self.section_labels: | ||
| self.ordered_labels += self.section_labels[section] | ||
| return | ||
|
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| @property | ||
| def methods_as_html(self): | ||
| html = "<p>This section lists the programs and algorithms that were used in this job and the references that should be cited. " + \ | ||
| "Numbers in superscript next to program/reference names refer to the number of the program reference in the overall list of references.</p>" | ||
| for section in self.SECTIONS: | ||
| if section == self.SECTIONS.GENERAL: | ||
| html += '<p>The first 2 references should be cited in all cases.</p>' | ||
| elif section == self.SECTIONS.ROTATION and len(self.section_labels[self.SECTIONS.ROTATION]): | ||
| standfirst = '<p>The rotation searches were carried out with the following programs:</p>' | ||
| html += self._methods_section_html(self.SECTIONS.ROTATION, standfirst) | ||
| elif section == self.SECTIONS.MR and len(self.section_labels[self.SECTIONS.MR]): | ||
| standfirst = '<p>Molecular Replacement was carried out with the following programs:</p>' | ||
| html += self._methods_section_html(self.SECTIONS.MR, standfirst) | ||
| elif section == self.SECTIONS.REFINEMENT and len(self.section_labels[self.SECTIONS.REFINEMENT]): | ||
| standfirst = '<p>Refinement of the MR solutions carried out with the following programs:</p>' | ||
| html += self._methods_section_html(self.SECTIONS.REFINEMENT, standfirst) | ||
| return html | ||
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| def _methods_section_html(self, section, standfirst): | ||
| mysec = self.SECTIONS(section) | ||
| html = '<{}>{}</{}>'.format(self.SEC_TAG, mysec.value, self.SEC_TAG) | ||
| html += standfirst | ||
| html += '<ul>' | ||
| for label in self.section_labels[mysec]: | ||
| html += "<li>{}<sup>{}</sup></li>".format(label, self.ordered_labels.index(label) + 1) | ||
| html += "</ul>" | ||
| return html | ||
|
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| @property | ||
| def citations_as_html(self): | ||
| html = '<{}>References</{}>'.format(self.SEC_TAG, self.SEC_TAG) | ||
| html += '<ol>' | ||
| template_txt = "<li> {author} ({year}). {title}. {journal} {volume}({number}), {pages}. [doi:{doi}]</li>" | ||
| for label in self.ordered_labels: | ||
| ref = copy.copy(self.references[label]) | ||
| ref['author'] = ref['author'].split(" and ")[0].split(",")[0] + " et al." | ||
| ref['pages'] = ref['pages'].replace("--", "-") | ||
| html += template_txt.format(**ref) | ||
| html += '</ol>' | ||
| return html | ||
|
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| @property | ||
| def citations_as_text(self): | ||
| txt = """A number of programs and algorithms were used within the this run of AMPLE. | ||
| The following is a list of citations for this run: | ||
| {0} | ||
| """.format(self.citation_list_as_text) | ||
| if self.citation_file_path: | ||
| txt += """ | ||
| A bibtex file with these references has been saved to the following file: | ||
| {0} | ||
| """.format(self.citation_file_path) | ||
| return txt | ||
|
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| @property | ||
| def citation_list_as_text(self): | ||
| template_txt = "* {author} ({year}). {title}. {journal} {volume}({number}), {pages}. [doi:{doi}]" | ||
| text = "" | ||
| for label in self.ordered_labels: | ||
| ref = copy.copy(self.references[label]) | ||
| ref['author'] = ref['author'].split(" and ")[0].split(",")[0] + " et al." | ||
| ref['pages'] = ref['pages'].replace("--", "-") | ||
| text += template_txt.format(**ref) + os.linesep * 2 | ||
| return text | ||
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| def save_citations_to_file(self, work_dir): | ||
| # ========================================================================= | ||
| # Somewhat a template of how we want to write each article in BibTex format | ||
| # ========================================================================= | ||
| template_bib = "@article{{{unique_id},{sep}author = {{{author}}},{sep}doi = {{{doi}}},{sep}" \ | ||
| "journal = {{{journal}}},{sep}number = {{{number}}},{sep}pages = {{{pages}}},{sep}" \ | ||
| "title = {{{{{title}}}}},{sep}volume = {{{volume}}},{sep}year = {{{year}}},{sep}}}{sep}" | ||
| references_bib = [template_bib.format(sep=os.linesep, **self.references[l]) for l in self.ordered_labels] | ||
| ref_fname = os.path.join(work_dir, "references.bib") | ||
| with open(ref_fname, "w") as fhout: | ||
| fhout.write(os.linesep.join(references_bib)) | ||
| self.citation_file_path = ref_fname | ||
| return ref_fname |
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