def get_repository_latex_pdfs(sample_type):
"""Get the Latex static PDFs directory"""
latex_dir = get_repository_latex()
if sample_type == 'oralskin':
pdfs_dir = get_path(latex_dir, 'pdfs-oralskin')
elif sample_type == 'fecal':
pdfs_dir = get_path(latex_dir, 'pdfs-gut')
elif sample_type == 'mod1':
pdfs_dir = get_path(latex_dir, 'pdfs-mod1')
else:
raise ValueError("Unknown sample type: %s" % sample_type)
check_file(pdfs_dir)
return pdfs_dir
def get_repository_latex_pdfs(sample_type):
"""Get the Latex static PDFs directory"""
latex_dir = get_repository_latex()
if sample_type == 'oralskin':
pdfs_dir = get_path(latex_dir, 'pdfs-oralskin')
elif sample_type == 'fecal':
pdfs_dir = get_path(latex_dir, 'pdfs-gut')
elif sample_type == 'mod1':
pdfs_dir = get_path(latex_dir, 'pdfs-mod1')
else:
raise ValueError("Unknown sample type: %s" % sample_type)
check_file(pdfs_dir)
return pdfs_dir
def bootstrap_result(rel_existing_path, static_paths, base_cmd_fmt,
to_pdf_fmt, sample_id, name):
"""Stage for results
sample_id : an id
name : None or str
rel_existing_path : a function that gets an existing path
static_paths : a dict of paths
base_cmd_fmt : base format for the commands to execute
to_pdf_fmt : base format for the call to construct the latex PDF
"""
if name is None:
unidentified = rel_existing_path('unidentified')
def bootstrap_path(x):
return os.path.join(unidentified, x)
else:
identified = rel_existing_path('identified')
def bootstrap_path(x):
return os.path.join(identified, x)
template_path = rel_existing_path('template_files')
indiv_dir = bootstrap_path(sample_id)
pdf_dir = os.path.join(indiv_dir, 'pdfs-gut')
def tex_path(x):
return os.path.join(indiv_dir, x)
def fig_pdf_path(x):
return os.path.join(pdf_dir, x)
def template_files_path(x):
return os.path.join(template_path, x)
fig1_src = template_files_path("Figure_1.%s_huge.pdf" % sample_id)
fig2_src = template_files_path("Figure_2.%s_huge.pdf" % sample_id)
fig3_src = template_files_path("Figure_3.%s_huge.pdf" % sample_id)
fig4_src = template_files_path("Figure_4_%s.pdf" % sample_id)
fig6_src = template_files_path("Figure_6_%s.txt" % sample_id)
macros_src = template_files_path("macros_%s.tex" % sample_id)
fig1_dst = fig_pdf_path("figure1.pdf")
fig2_dst = fig_pdf_path("figure2.pdf")
fig3_dst = fig_pdf_path("figure3.pdf")
fig4_dst = fig_pdf_path("figure4.pdf")
fig6_dst = tex_path("%s_taxa.txt" % sample_id)
macros_dst = tex_path("macros_gut.tex")
template_dst = tex_path('%s.tex' % sample_id)
check_file(fig1_src, e=MissingFigure)
check_file(fig2_src, e=MissingFigure)
check_file(fig3_src, e=MissingFigure)
check_file(fig4_src, e=MissingFigure)
check_file(fig6_src, e=MissingFigure)
check_file(macros_src, e=MissingFigure)
cmds = []
cmds.append('mkdir -p %s' % pdf_dir)
cmds.append('cp %s %s' % (fig1_src, fig1_dst))
cmds.append('cp %s %s' % (fig2_src, fig2_dst))
cmds.append('cp %s %s' % (fig3_src, fig3_dst))
cmds.append('cp %s %s' % (fig4_src, fig4_dst))
cmds.append('cp %s %s' % (fig6_src, fig6_dst))
cmds.append('cp %s %s' % (macros_src, macros_dst))
cmds.append('cp %s %s' % (static_paths['template'], template_dst))
cmds.append('cp %s %s' % (static_paths['aglogo'], pdf_dir))
cmds.append('cp %s %s' % (static_paths['fig1_legend'], pdf_dir))
cmds.append('cp %s %s' % (static_paths['fig2_legend'], pdf_dir))
cmds.append('cp %s %s' % (static_paths['fig2_2ndlegend'], pdf_dir))
cmds.append('cp %s %s' % (static_paths['fig3_legend'], pdf_dir))
cmds.append('cp %s %s' % (static_paths['fig4_overlay'], pdf_dir))
cmds.append('cp %s %s' % (static_paths['fig1_ovals'], pdf_dir))
cmds.append('cp %s %s' % (static_paths['fig2_ovals'], pdf_dir))
cmds.append('cp %s %s' % (static_paths['ball_legend'], pdf_dir))
cmds.append('cp %s %s' % (static_paths['title'], pdf_dir))
name_fmt = "echo '\n\def\yourname{%s}\n' >> %s"
if name is None:
cmds.append(name_fmt % ("unidentified", macros_dst))
else:
cmds.append(name_fmt % (name, macros_dst))
indiv_cmd = base_cmd_fmt % (static_paths['working_dir'], '; '.join(cmds))
latex_cmd = to_pdf_fmt % {'path': indiv_dir, 'input': template_dst}
return (indiv_cmd, latex_cmd)
def get_path(d, f):
"""Check and get a path, or throw IOError"""
path = os.path.join(d, f)
check_file(path)
return path
def bootstrap_result(rel_existing_path, static_paths, base_cmd_fmt, to_pdf_fmt,
sample_id, name):
"""Stage for results
sample_id : an id
name : None or str
rel_existing_path : a function that gets an existing path
static_paths : a dict of paths
base_cmd_fmt : base format for the commands to execute
to_pdf_fmt : base format for the call to construct the latex PDF
"""
if name is None:
unidentified = rel_existing_path('unidentified')
def bootstrap_path(x):
return os.path.join(unidentified, x)
else:
identified = rel_existing_path('identified')
def bootstrap_path(x):
return os.path.join(identified, x)
template_path = rel_existing_path('template_files')
indiv_dir = bootstrap_path(sample_id)
pdf_dir = os.path.join(indiv_dir, 'pdfs-gut')
def tex_path(x):
return os.path.join(indiv_dir, x)
def fig_pdf_path(x):
return os.path.join(pdf_dir, x)
def template_files_path(x):
return os.path.join(template_path, x)
fig1_src = template_files_path("Figure_1.%s_huge.pdf" % sample_id)
fig2_src = template_files_path("Figure_2.%s_huge.pdf" % sample_id)
fig3_src = template_files_path("Figure_3.%s_huge.pdf" % sample_id)
fig4_src = template_files_path("Figure_4_%s.pdf" % sample_id)
fig6_src = template_files_path("Figure_6_%s.txt" % sample_id)
macros_src = template_files_path("macros_%s.tex" % sample_id)
fig1_dst = fig_pdf_path("figure1.pdf")
fig2_dst = fig_pdf_path("figure2.pdf")
fig3_dst = fig_pdf_path("figure3.pdf")
fig4_dst = fig_pdf_path("figure4.pdf")
fig6_dst = tex_path("%s_taxa.txt" % sample_id)
macros_dst = tex_path("macros_gut.tex")
template_dst = tex_path('%s.tex' % sample_id)
check_file(fig1_src, e=MissingFigure)
check_file(fig2_src, e=MissingFigure)
check_file(fig3_src, e=MissingFigure)
check_file(fig4_src, e=MissingFigure)
check_file(fig6_src, e=MissingFigure)
check_file(macros_src, e=MissingFigure)
cmds = []
cmds.append('mkdir -p %s' % pdf_dir)
cmds.append('cp %s %s' % (fig1_src, fig1_dst))
cmds.append('cp %s %s' % (fig2_src, fig2_dst))
cmds.append('cp %s %s' % (fig3_src, fig3_dst))
cmds.append('cp %s %s' % (fig4_src, fig4_dst))
cmds.append('cp %s %s' % (fig6_src, fig6_dst))
cmds.append('cp %s %s' % (macros_src, macros_dst))
cmds.append('cp %s %s' % (static_paths['template'], template_dst))
cmds.append('cp %s %s' % (static_paths['aglogo'], pdf_dir))
cmds.append('cp %s %s' % (static_paths['fig1_legend'], pdf_dir))
cmds.append('cp %s %s' % (static_paths['fig2_legend'], pdf_dir))
cmds.append('cp %s %s' % (static_paths['fig2_2ndlegend'], pdf_dir))
cmds.append('cp %s %s' % (static_paths['fig3_legend'], pdf_dir))
cmds.append('cp %s %s' % (static_paths['fig4_overlay'], pdf_dir))
cmds.append('cp %s %s' % (static_paths['fig1_ovals'], pdf_dir))
cmds.append('cp %s %s' % (static_paths['fig2_ovals'], pdf_dir))
cmds.append('cp %s %s' % (static_paths['ball_legend'], pdf_dir))
cmds.append('cp %s %s' % (static_paths['title'], pdf_dir))
name_fmt = "echo '\n\def\yourname{%s}\n' >> %s"
if name is None:
cmds.append(name_fmt % ("unidentified", macros_dst))
else:
cmds.append(name_fmt % (name, macros_dst))
indiv_cmd = base_cmd_fmt % (static_paths['working_dir'], '; '.join(cmds))
latex_cmd = to_pdf_fmt % {'path': indiv_dir, 'input': template_dst}
return (indiv_cmd, latex_cmd)
def get_path(d, f):
"""Check and get a path, or throw IOError"""
path = os.path.join(d, f)
check_file(path)
return path