def export_gene_items(file_path) :
genes = Gene.objects.all() # get all lab objects
if genes: # check if empty
outfile = open(file_path+'/gene-items.xml', 'w') # open and write to lab-items.xml
for gene in genes:
toxoplasma_mutant_list = ToxoplasmaMutant.objects.all().filter(target_gene=gene)
antibody_list = Antibody.objects.all().filter(target_gene=gene)
# Only export if there is a related toxoplasma mutant or antibody
if toxoplasma_mutant_list or antibody_list:
outfile.write('<item id="Gene_' + str(gene.id) + '" class="Gene">\n')
outfile.write('\t<attribute name="primaryIdentifier" value="' + str(gene.gene_id) + '" />\n')
outfile.write('\t<attribute name="symbol" value="' + str(gene.gene_id) + '" />\n')
outfile.write('\t<attribute name="name" value="' + str(gene.description) + '" />\n')
if toxoplasma_mutant_list:
exporter_utility.write_collection_items(outfile, toxoplasma_mutant_list, 'ToxoplasmaMutant', 'toxoplasmaMutants')
if antibody_list:
exporter_utility.write_collection_items(outfile, antibody_list, 'Antibody', 'antibodies')
outfile.write('</item>\n')
outfile.close() # close file
def export_protocol_items(file_path) :
protocols = Protocol.objects.all().filter(current=True) # get all objects
if protocols: # check if empty
outfile = open(file_path+'/protocol-items.xml', 'w') # open and write to *-items.xml
for protocol in protocols:
submission_list = [] # submissions
applied_protocol_list = AppliedProtocol.objects.all().filter(protocol=protocol)
for applied_protocol in applied_protocol_list:
if applied_protocol.submission.publishable == True:
submission_list.append(applied_protocol.submission)
submission_list = list(set(submission_list)) # Get rid of duplicates
# Only export if there is a related objects
if submission_list:
outfile.write('<item id="Protocol_' + str(protocol.id) + '" class="Protocol">\n')
outfile.write('\t<attribute name="name" value="' + protocol.name + '" />\n')
outfile.write('\t<attribute name="description" value="' + protocol.description + '" />\n')
outfile.write('\t<attribute name="type" value="' + protocol.protocol_type.name + '" />\n')
outfile.write('\t<attribute name="version" value="' + str(protocol.version) + '" />\n')
exporter_utility.write_collection_items(outfile, submission_list, 'Submission', 'submissions')
outfile.write('</item>\n')
outfile.close() # close file
def export_persistent_datafile_items(file_path, url) :
persistent_datafiles = PersistentDataFile.objects.all() # get all objects
if persistent_datafiles: # check if empty
outfile = open(file_path+'/persistent-datafile-items.xml', 'w') # open and write to *-items.xml
for persistent_datafile in persistent_datafiles:
submission_data_list = SubmissionData.objects.all().filter(object_id=persistent_datafile.id)
submission_list = [] # submissions
for submission_data in submission_data_list:
applied_protocol_list = []
if submission_data.applied_protocol_input:
applied_protocol_list.append(submission_data.applied_protocol_input)
if submission_data.applied_protocol_output:
applied_protocol_list.append(submission_data.applied_protocol_output)
for applied_protocol in applied_protocol_list:
if applied_protocol.submission.publishable == True:
submission_list.append(applied_protocol.submission)
submission_list = list(set(submission_list)) # Get rid of duplicates
# Only export if there is a related objects
if submission_list:
outfile.write('<item id="PersistentDataFile_' + str(persistent_datafile.id) + '" class="PersistentDataFile">\n')
outfile.write('\t<attribute name="name" value="' + persistent_datafile.name + '" />\n')
outfile.write('\t<attribute name="type" value="' + persistent_datafile.file_type.name + '" />\n')
outfile.write('\t<attribute name="url" value="' + url + '/persistent/' + persistent_datafile.name + '" />\n')
exporter_utility.write_collection_items(outfile, submission_list, 'Submission', 'submissions')
outfile.write('</item>\n')
outfile.close() # close file
def export_experimental_factor_items(file_path) :
experimental_factors = ExperimentalFactor.objects.all() # get all objects
if experimental_factors: # check if empty
outfile = open(file_path+'/experimental-factor-items.xml', 'w') # open and write to *-items.xml
for experimental_factor in experimental_factors:
submission_data_list = SubmissionData.objects.all().filter(object_id=experimental_factor.id)
submission_list = [] # submissions
for submission_data in submission_data_list:
applied_protocol_list = []
if submission_data.applied_protocol_input:
applied_protocol_list.append(submission_data.applied_protocol_input)
if submission_data.applied_protocol_output:
applied_protocol_list.append(submission_data.applied_protocol_output)
for applied_protocol in applied_protocol_list:
if applied_protocol.submission.publishable == True:
submission_list.append(applied_protocol.submission)
submission_list = list(set(submission_list)) # Get rid of duplicates
# Only export if there is a related objects
if submission_list:
outfile.write('<item id="ExperimentalFactor_' + str(experimental_factor.id) + '" class="ExperimentalFactor">\n')
outfile.write('\t<attribute name="type" value="' + experimental_factor.name.name + '" />\n')
outfile.write('\t<attribute name="value" value="' + experimental_factor.value + '" />\n')
exporter_utility.write_collection_items(outfile, submission_list, 'Submission', 'submissions')
outfile.write('</item>\n')
outfile.close() # close file
def export_submission_datafile_items(file_path, url) :
# create directories if it doesn't exists
if not os.path.exists(file_path+'/peaks/chromosome'):
os.makedirs(file_path+'/peaks/chromosome')
if not os.path.exists(file_path+'/peaks/contig'):
os.makedirs(file_path+'/peaks/contig')
if not os.path.exists(file_path+'/peaks/supercontig'):
os.makedirs(file_path+'/peaks/supercontig')
if not os.path.exists(file_path+'/gene_list'):
os.makedirs(file_path+'/gene_list')
submission_datafiles = SubmissionDataFile.objects.all() # get all objects
gene_list_list = [] # for submission data gene list
if submission_datafiles: # check if empty
outfile = open(file_path+'/submission-datafile-items.xml', 'w') # open and write to *-items.xml
for submission_datafile in submission_datafiles:
submission_data_list = SubmissionData.objects.all().filter(object_id=submission_datafile.id)
submission_list = [] # submissions
for submission_data in submission_data_list:
applied_protocol_list = []
if submission_data.applied_protocol_input:
applied_protocol_list.append(submission_data.applied_protocol_input)
if submission_data.applied_protocol_output:
applied_protocol_list.append(submission_data.applied_protocol_output)
for applied_protocol in applied_protocol_list:
if applied_protocol.submission.publishable == True:
submission_list.append(applied_protocol.submission)
submission_list = list(set(submission_list)) # Get rid of duplicates
# Only export if there is a related objects
if submission_list:
outfile.write('<item id="SubmissionDataFile_' + str(submission_datafile.id) + '" class="SubmissionDataFile">\n')
outfile.write('\t<attribute name="name" value="' + submission_datafile.name + '" />\n')
outfile.write('\t<attribute name="type" value="' + submission_datafile.file_type.name + '" />\n')
submission_id_list = submission_datafile.name.split('_')
outfile.write('\t<attribute name="url" value="' + url + '/' + submission_id_list[0] + '/' + submission_datafile.name + '" />\n')
exporter_utility.write_collection_items(outfile, submission_list, 'Submission', 'submissions')
outfile.write('</item>\n')
if 'peaks' in submission_datafile.name:
export_peaks_submission_datafile(submission_datafile.data_file.path, file_path+'/peaks/', submission_datafile.name) # export peaks.gff into one folder
if 'gene_list' in submission_datafile.name:
export_gene_list_submission_datafile(submission_datafile.data_file.path, file_path+'/gene_list/'+submission_datafile.name) # export of gene_list.txt
gene_list_list.append(file_path+'/gene_list/'+submission_datafile.name) # append to gene list list
outfile.close() # close file
if gene_list_list: # consolidate gene list into one list
consolidate_gene_list_submission_datafile(file_path, gene_list_list)
def export_organism_items(file_path):
organisms = Organism.objects.all() # get all lab objects
if organisms: # check if empty
outfile = open(file_path + "/organism-items.xml", "w") # open and write to lab-items.xml
for organism in organisms:
toxoplasma_mutant_list = ToxoplasmaMutant.objects.all().filter(organism=organism)
# Only export if there is a related toxoplasma mutant
if toxoplasma_mutant_list:
outfile.write('<item id="Organism_' + str(organism.id) + '" class="Organism">\n')
outfile.write('\t<attribute name="taxonId" value="' + str(organism.taxon_id) + '" />\n')
exporter_utility.write_collection_items(
outfile, toxoplasma_mutant_list, "ToxoplasmaMutant", "toxoplasmaMutants"
)
outfile.write("</item>\n")
outfile.close() # close file
def export_publication_items(file_path) :
publications = Publication.objects.all() # get all objects
if publications: # check if empty
outfile = open(file_path+'/publication-items.xml', 'w') # open and write to *-items.xml
for publication in publications:
dbxrefs_list = publication.dbxrefs.all() # dbxrefs
for dbxref in dbxrefs_list:
if dbxref.db.name == 'Pubmed':
pubmed_id = dbxref.accession
project_list = Project.objects.all().filter(publications=publication).filter(publishable=True)
experiment_list = Experiment.objects.all().filter(publications=publication).filter(publishable=True)
submission_list = Submission.objects.all().filter(publications=publication).filter(publishable=True)
# Only export if there is a related objects
if pubmed_id and (project_list or experiment_list or submission_list):
outfile.write('<item id="Publication_' + str(publication.id) + '" class="Publication">\n')
outfile.write('\t<attribute name="pubMedId" value="' + str(pubmed_id) + '" />\n')
outfile.write('\t<attribute name="title" value="' + str(publication.unique_name) + '" />\n')
if project_list:
exporter_utility.write_collection_items(outfile, project_list, 'Project', 'projects')
if experiment_list:
exporter_utility.write_collection_items(outfile, experiment_list, 'Experiment', 'experiments')
if submission_list:
exporter_utility.write_collection_items(outfile, submission_list, 'Submission', 'submissions')
outfile.write('</item>\n')
outfile.close() # close file
def export_microarray_items(file_path):
microarrays = MicroArray.objects.all() # get all objects
if microarrays: # check if empty
outfile = open(file_path + "/microarray-items.xml", "w") # open and write to *-items.xml
for microarray in microarrays:
submission_data_list = SubmissionData.objects.all().filter(object_id=microarray.id)
submission_list = [] # submissions
for submission_data in submission_data_list:
applied_protocol_list = []
if submission_data.applied_protocol_input:
applied_protocol_list.append(submission_data.applied_protocol_input)
if submission_data.applied_protocol_output:
applied_protocol_list.append(submission_data.applied_protocol_output)
for applied_protocol in applied_protocol_list:
if applied_protocol.submission.publishable == True:
submission_list.append(applied_protocol.submission)
submission_list = list(set(submission_list)) # Get rid of duplicates
# Only export if there is a related objects
if submission_list:
outfile.write('<item id="MicroArray_' + str(microarray.id) + '" class="MicroArray">\n')
outfile.write('\t<attribute name="name" value="' + microarray.name + '" />\n')
outfile.write('\t<attribute name="platform" value="' + microarray.platform.name + '" />\n')
outfile.write('\t<attribute name="format" value="' + microarray.microarray_format.name + '" />\n')
outfile.write('\t<attribute name="version" value="' + microarray.version + '" />\n')
outfile.write('\t<attribute name="genomeName" value="' + microarray.genome_name.name + '" />\n')
outfile.write('\t<attribute name="genomeVersion" value="' + microarray.genome_version + '" />\n')
exporter_utility.write_collection_items(outfile, submission_list, "Submission", "submissions")
outfile.write("</item>\n")
outfile.close() # close file
def export_data_analysis_items(file_path):
data_analyses = DataAnalysis.objects.all() # get all objects
if data_analyses: # check if empty
outfile = open(file_path + "/data-analysis-items.xml", "w") # open and write to *-items.xml
for data_analysis in data_analyses:
submission_data_list = SubmissionData.objects.all().filter(object_id=data_analysis.id)
submission_list = [] # submissions
for submission_data in submission_data_list:
applied_protocol_list = []
if submission_data.applied_protocol_input:
applied_protocol_list.append(submission_data.applied_protocol_input)
if submission_data.applied_protocol_output:
applied_protocol_list.append(submission_data.applied_protocol_output)
for applied_protocol in applied_protocol_list:
if applied_protocol.submission.publishable == True:
submission_list.append(applied_protocol.submission)
submission_list = list(set(submission_list)) # Get rid of duplicates
# Only export if there is a related objects
if submission_data_list or submission_list:
outfile.write('<item id="DataAnalysis_' + str(data_analysis.id) + '" class="DataAnalysis">\n')
outfile.write('\t<attribute name="name" value="' + data_analysis.name + '" />\n')
outfile.write('\t<attribute name="platform" value="' + data_analysis.platform + '" />\n')
outfile.write('\t<attribute name="version" value="' + data_analysis.version + '" />\n')
outfile.write('\t<attribute name="module" value="' + data_analysis.module + '" />\n')
outfile.write('\t<attribute name="parameter" value="' + data_analysis.parameter + '" />\n')
if data_analysis.data_analysis_type:
outfile.write('\t<attribute name="type" value="' + data_analysis.data_analysis_type.name + '" />\n')
exporter_utility.write_collection_items(outfile, submission_list, "Submission", "submissions")
outfile.write("</item>\n")
outfile.close() # close file
def export_applied_protocol_items(file_path) :
applied_protocols = AppliedProtocol.objects.all() # get all objects
if applied_protocols: # check if empty
outfile = open(file_path+'/applied-protocol-items.xml', 'w') # open and write to *-items.xml
for applied_protocol in applied_protocols:
input_list = SubmissionData.objects.all().filter(applied_protocol_input=applied_protocol) # submission data
output_list = SubmissionData.objects.all().filter(applied_protocol_output=applied_protocol) # submission data
input_list = list(set(input_list)) # Get rid of duplicates
output_list = list(set(output_list)) # Get rid of duplicates
outfile.write('<item id="AppliedProtocol_' + str(applied_protocol.id) + '" class="AppliedProtocol">\n')
outfile.write('\t<attribute name="step" value="' + str(applied_protocol.step) + '" />\n')
exporter_utility.write_reference_item(outfile, applied_protocol.protocol, 'Protocol', 'protocol')
exporter_utility.write_reference_item(outfile, applied_protocol.submission, 'Submission', 'submission')
if input_list:
exporter_utility.write_collection_items(outfile, input_list, 'SubmissionData', 'inputs')
if output_list:
exporter_utility.write_collection_items(outfile, output_list, 'SubmissionData', 'outputs')
outfile.write('</item>\n')
outfile.close() # close file
def export_antibody_items(file_path) :
antibodies = Antibody.objects.all() # get all objects
if antibodies: # check if empty
outfile = open(file_path+'/antibody-items.xml', 'w') # open and write to *-items.xml
for antibody in antibodies:
submission_data_list = SubmissionData.objects.all().filter(object_id=antibody.id)
submission_list = [] # submissions
for submission_data in submission_data_list:
applied_protocol_list = []
if submission_data.applied_protocol_input:
applied_protocol_list.append(submission_data.applied_protocol_input)
if submission_data.applied_protocol_output:
applied_protocol_list.append(submission_data.applied_protocol_output)
for applied_protocol in applied_protocol_list:
if applied_protocol.submission.publishable == True:
submission_list.append(applied_protocol.submission)
submission_list = list(set(submission_list)) # Get rid of duplicates
experiment_list = [] # experiment
for submission in submission_list:
experiment_list.extend(submission.experiments.all().filter(publishable=True)) # experiments
experiment_list = list(set(experiment_list)) # Get rid of duplicates
project_list = [] # projects
for experiment in experiment_list:
project_list.extend(experiment.projects.all().filter(publishable=True))
project_list = list(set(project_list)) # Get rid of duplicates
# Only export if there is a related objects
if submission_data_list or project_list or experiment_list or submission_list:
outfile.write('<item id="Antibody_' + str(antibody.id) + '" class="Antibody">\n')
outfile.write('\t<attribute name="name" value="' + antibody.name + '" />\n')
outfile.write('\t<attribute name="targetName" value="' + antibody.target_name + '" />\n')
outfile.write('\t<attribute name="source" value="' + antibody.source + '" />\n')
outfile.write('\t<attribute name="epitope" value="' + antibody.epitope + '" />\n')
if antibody.animal_host:
outfile.write('\t<attribute name="hostOrganism" value="' + antibody.animal_host.name + '" />\n')
else:
outfile.write('\t<attribute name="hostOrganism" value="" />\n')
if antibody.target_gene:
exporter_utility.write_reference_item(outfile, antibody.target_gene, 'Gene', 'targetGene')
if project_list:
exporter_utility.write_collection_items(outfile, project_list, 'Project', 'projects')
if experiment_list:
exporter_utility.write_collection_items(outfile, experiment_list, 'Experiment', 'experiments')
if submission_list:
exporter_utility.write_collection_items(outfile, submission_list, 'Submission', 'submissions')
outfile.write('</item>\n')
outfile.close() # close file
def export_lab_items(file_path) :
labs = Lab.objects.all() # get all lab objects
if labs: # check if empty
outfile = open(file_path+'/lab-items.xml', 'w') # open and write to *-items.xml
for lab in labs:
lab_members = lab.lab_members.all() # Grab all lab members
project_list = [] # projects
experiment_list = [] # experiments
submission_list = [] # submissions
# For each member of the lab
for lab_member in lab_members:
tmp_project_list = Project.objects.all().filter(contributors=lab_member).filter(publishable=True)
if tmp_project_list:
project_list.extend(tmp_project_list)
tmp_experiment_list = Experiment.objects.all().filter(contributors=lab_member).filter(publishable=True)
if tmp_experiment_list:
experiment_list.extend(tmp_experiment_list)
tmp_submission_list = Submission.objects.all().filter(contributors=lab_member).filter(publishable=True)
if tmp_submission_list:
submission_list.extend(tmp_submission_list)
project_list = list(set(project_list)) # Get rid of duplicates
experiment_list = list(set(experiment_list)) # Get rid of duplicates
submission_list = list(set(submission_list)) # Get rid of duplicates
# Only export if there is a related objects
if project_list or experiment_list or submission_list:
outfile.write('<item id="Lab_' + str(lab.id) + '" class="Lab">\n')
outfile.write('\t<attribute name="name" value="' + lab.name + '" />\n')
outfile.write('\t<attribute name="piFirstName" value="' + lab.pi_first_name + '" />\n')
outfile.write('\t<attribute name="piLastName" value="' + lab.pi_last_name + '" />\n')
outfile.write('\t<attribute name="affiliation" value="' + lab.affiliation + '" />\n')
if project_list:
exporter_utility.write_collection_items(outfile, project_list, 'Project', 'projects')
if experiment_list:
exporter_utility.write_collection_items(outfile, experiment_list, 'Experiment', 'experiments')
if submission_list:
exporter_utility.write_collection_items(outfile, submission_list, 'Submission', 'submissions')
outfile.write('</item>\n')
outfile.close() # close file
def export_toxoplasma_mutant_items(file_path) :
toxoplasma_mutants = ToxoplasmaMutant.objects.all() # get all objects
if toxoplasma_mutants: # check if empty
outfile = open(file_path+'/toxoplasma-mutant-items.xml', 'w') # open and write to *-items.xml
for toxoplasma_mutant in toxoplasma_mutants:
submission_data_list = SubmissionData.objects.all().filter(object_id=toxoplasma_mutant.id)
submission_list = [] # submissions
for submission_data in submission_data_list:
applied_protocol_list = []
if submission_data.applied_protocol_input:
applied_protocol_list.append(submission_data.applied_protocol_input)
if submission_data.applied_protocol_output:
applied_protocol_list.append(submission_data.applied_protocol_output)
for applied_protocol in applied_protocol_list:
if applied_protocol.submission.publishable == True:
submission_list.append(applied_protocol.submission)
submission_list = list(set(submission_list)) # Get rid of duplicates
experiment_list = [] # experiment
for submission in submission_list:
experiment_list.extend(submission.experiments.all().filter(publishable=True)) # experiments
experiment_list = list(set(experiment_list)) # Get rid of duplicates
project_list = [] # projects
for experiment in experiment_list:
project_list.extend(experiment.projects.all().filter(publishable=True))
project_list = list(set(project_list)) # Get rid of duplicates
# Only export if there is a related objects
if submission_data_list or project_list or experiment_list or submission_list:
outfile.write('<item id="ToxoplasmaMutant_' + str(toxoplasma_mutant.id) + '" class="ToxoplasmaMutant">\n')
outfile.write('\t<attribute name="name" value="' + toxoplasma_mutant.name + '" />\n')
outfile.write('\t<attribute name="targetName" value="' + toxoplasma_mutant.target_name + '" />\n')
outfile.write('\t<attribute name="mutantSelection" value="' + toxoplasma_mutant.selection.name + '" />\n')
outfile.write('\t<attribute name="mutantType" value="' + toxoplasma_mutant.mutation_type.name + '" />\n')
outfile.write('\t<attribute name="mutantBackground" value="' + toxoplasma_mutant.background.name + '" />\n')
strain = ''
background = ''
organism_property_list = OrganismProperty.objects.all().filter(organism=toxoplasma_mutant.organism) # organism property
for organism_property in organism_property_list:
if organism_property.organism_property_type.name == 'organism strain':
strain = organism_property.organism_property_value.name
if organism_property.organism_property_type.name == 'organism type':
background = organism_property.organism_property_value.name
outfile.write('\t<attribute name="strain" value="' + strain + '" />\n')
outfile.write('\t<attribute name="background" value="' + background + '" />\n')
if toxoplasma_mutant.target_gene:
exporter_utility.write_reference_item(outfile, toxoplasma_mutant.target_gene, 'Gene', 'targetGene')
if toxoplasma_mutant.organism:
exporter_utility.write_reference_item(outfile, toxoplasma_mutant.organism, 'Organism', 'organism')
if project_list:
exporter_utility.write_collection_items(outfile, project_list, 'Project', 'projects')
if experiment_list:
exporter_utility.write_collection_items(outfile, experiment_list, 'Experiment', 'experiments')
if submission_list:
exporter_utility.write_collection_items(outfile, submission_list, 'Submission', 'submissions')
outfile.write('</item>\n')
outfile.close() # close file
def export_project_items(file_path) :
projects = Project.objects.all().filter(publishable=True) # get all objects
if projects: # check if empty
outfile = open(file_path+'/project-items.xml', 'w') # open and write to *-items.xml
for project in projects:
publication_list = project.publications.all() # publications
lab_list = [] # labs
contributors = project.contributors.all() # Grab all project contributors
# Grab all the projects by each member of the lab
for contributor in contributors:
tmp_list = Lab.objects.all().filter(lab_members=contributor)
if tmp_list:
lab_list.extend(tmp_list)
lab_list = list(set(lab_list)) # Get rid of duplicates
experiment_list = Experiment.objects.all().filter(projects=project).filter(publishable=True) # experiments
submission_list = [] # submissions
# Grab all the submissions
for experiment in experiment_list:
tmp_list = Submission.objects.all().filter(experiments=experiment).filter(publishable=True)
if tmp_list:
submission_list.extend(tmp_list)
submission_list = list(set(submission_list)) # Get rid of duplicates
organism_list = [] # organisms
toxoplasma_mutant_list = [] # toxoplasma mutants
antibody_list = [] # antibody
# Grab all the submission data
for submission in submission_list:
applied_protocol_list = AppliedProtocol.objects.all().filter(submission=submission)
for applied_protocol in applied_protocol_list:
submission_data_list = SubmissionData.objects.all().filter(Q(applied_protocol_input=applied_protocol) | Q(applied_protocol_output=applied_protocol))
for submission_data in submission_data_list:
if submission_data.content_type==ContentType.objects.get_for_model(ToxoplasmaMutant):
toxoplasma_mutant_list.append(submission_data.content_object)
organism_list.append(submission_data.content_object.organism)
if submission_data.content_type==ContentType.objects.get_for_model(Antibody):
antibody_list.append(submission_data.content_object)
organism_list = list(set(organism_list)) # Get rid of duplicates
toxoplasma_mutant_list = list(set(toxoplasma_mutant_list)) # Get rid of duplicates
antibody_list = list(set(antibody_list)) # Get rid of duplicates
# Only export if there is a related objects
if publication_list or lab_list or experiment_list or submission_list or organism_list or toxoplasma_mutant_list or antibody_list:
outfile.write('<item id="Project_' + str(project.id) + '" class="Project">\n')
outfile.write('\t<attribute name="name" value="' + project.name + '" />\n')
outfile.write('\t<attribute name="description" value="' + project.description + '" />\n')
if publication_list:
exporter_utility.write_collection_items(outfile, publication_list, 'Publication', 'publications')
if lab_list:
exporter_utility.write_collection_items(outfile, lab_list, 'Lab', 'labs')
if experiment_list:
exporter_utility.write_collection_items(outfile, experiment_list, 'Experiment', 'experiments')
if submission_list:
exporter_utility.write_collection_items(outfile, submission_list, 'Submission', 'submissions')
if organism_list:
exporter_utility.write_collection_items(outfile, organism_list, 'Organism', 'organisms')
if toxoplasma_mutant_list:
exporter_utility.write_collection_items(outfile, toxoplasma_mutant_list, 'ToxoplasmaMutant', 'toxoplasmaMutants')
if antibody_list:
exporter_utility.write_collection_items(outfile, antibody_list, 'Antibody', 'antibodies')
outfile.write('</item>\n')
outfile.close() # close file
def export_submission_items(file_path) :
submissions = Submission.objects.all().filter(publishable=True) # get all objects
if submissions: # check if empty
outfile = open(file_path+'/submission-items.xml', 'w') # open and write to *-items.xml
for submission in submissions:
publication_list = submission.publications.all() # publications
lab_list = [] # labs
contributors = submission.contributors.all() # Grab all submission contributors
# Grab all the submission by each member of the lab
for contributor in contributors:
tmp_list = Lab.objects.all().filter(lab_members=contributor)
if tmp_list:
lab_list.extend(tmp_list)
lab_list = list(set(lab_list)) # Get rid of duplicates
experiment_list = submission.experiments.all().filter(publishable=True) # experiments
project_list = [] # projects
for experiment in experiment_list:
tmp_list = experiment.projects.all().filter(publishable=True)
project_list.extend(tmp_list)
project_list = list(set(project_list)) # Get rid of duplicates
applied_protocol_list = [] # applied protocols
protocol_list = [] # protocols
organism_list = [] # organisms
toxoplasma_mutant_list = [] # toxoplasma mutants
antibody_list = [] # antibodies
experimental_factor_list = [] # experimental factor
microarray_list = [] # microarray
sequencing_list = [] # sequencing
data_analysis_list = [] # data analysis
persistent_datafile_list = [] # persistent datafile
submission_datafile_list = [] # submission datafile
# Grab all the organisms and toxoplasma mutants
applied_protocol_list = AppliedProtocol.objects.all().filter(submission=submission)
for applied_protocol in applied_protocol_list:
protocol_list.append(applied_protocol.protocol) # protocols
submission_data_list = SubmissionData.objects.all().filter(Q(applied_protocol_input=applied_protocol) | Q(applied_protocol_output=applied_protocol))
for submission_data in submission_data_list:
if submission_data.content_type==ContentType.objects.get_for_model(ToxoplasmaMutant):
toxoplasma_mutant_list.append(submission_data.content_object)
organism_list.append(submission_data.content_object.organism)
if submission_data.content_type==ContentType.objects.get_for_model(Antibody):
antibody_list.append(submission_data.content_object)
if submission_data.content_type==ContentType.objects.get_for_model(ExperimentalFactor):
experimental_factor_list.append(submission_data.content_object)
if submission_data.content_type==ContentType.objects.get_for_model(MicroArray):
microarray_list.append(submission_data.content_object)
if submission_data.content_type==ContentType.objects.get_for_model(Sequencing):
sequencing_list.append(submission_data.content_object)
if submission_data.content_type==ContentType.objects.get_for_model(DataAnalysis):
data_analysis_list.append(submission_data.content_object)
if submission_data.content_type==ContentType.objects.get_for_model(PersistentDataFile):
persistent_datafile_list.append(submission_data.content_object)
if submission_data.content_type==ContentType.objects.get_for_model(SubmissionDataFile):
submission_datafile_list.append(submission_data.content_object)
protocol_list = list(set(protocol_list)) # Get rid of duplicates
organism_list = list(set(organism_list)) # Get rid of duplicates
toxoplasma_mutant_list = list(set(toxoplasma_mutant_list)) # Get rid of duplicates
antibody_list = list(set(antibody_list)) # Get rid of duplicates
experimental_factor_list = list(set(experimental_factor_list)) # Get rid of duplicates
microarray_list = list(set(microarray_list)) # Get rid of duplicates
sequencing_list = list(set(sequencing_list)) # Get rid of duplicates
data_analysis_list = list(set(data_analysis_list)) # Get rid of duplicates
persistent_datafile_list = list(set(persistent_datafile_list)) # Get rid of duplicates
submission_datafile_list = list(set(submission_datafile_list)) # Get rid of duplicates
# Only export if there is a related labs
if publication_list or lab_list or project_list or experiment_list or applied_protocol_list or protocol_list:
outfile.write('<item id="Submission_' + str(submission.id) + '" class="Submission">\n')
outfile.write('\t<attribute name="TCid" value="' + submission.generated_id + '" />\n')
outfile.write('\t<attribute name="name" value="' + submission.name + '" />\n')
outfile.write('\t<attribute name="description" value="' + submission.description + '" />\n')
outfile.write('\t<attribute name="technique" value="' + submission.technique.name + '" />\n')
outfile.write('\t<attribute name="qualityControl" value="' + submission.quality_control.name + '" />\n')
outfile.write('\t<attribute name="embargoDate" value="' + str(submission.date_embargo) + '" />\n')
outfile.write('\t<attribute name="publicReleaseDate" value="' + str(submission.date_created) + '" />\n')
outfile.write('\t<attribute name="replicateDate" value="' + str(submission.date_replicate) + '" />\n')
if publication_list:
exporter_utility.write_collection_items(outfile, publication_list, 'Publication', 'publications')
if lab_list:
exporter_utility.write_collection_items(outfile, lab_list, 'Lab', 'labs')
if project_list:
exporter_utility.write_collection_items(outfile, project_list, 'Project', 'projects')
if experiment_list:
exporter_utility.write_collection_items(outfile, experiment_list, 'Experiment', 'experiments')
if applied_protocol_list:
exporter_utility.write_collection_items(outfile, applied_protocol_list, 'AppliedProtocol', 'appliedProtocols')
if protocol_list:
exporter_utility.write_collection_items(outfile, protocol_list, 'Protocol', 'protocols')
if organism_list:
exporter_utility.write_collection_items(outfile, organism_list, 'Organism', 'organisms')
if toxoplasma_mutant_list:
exporter_utility.write_collection_items(outfile, toxoplasma_mutant_list, 'ToxoplasmaMutant', 'toxoplasmaMutants')
if antibody_list:
exporter_utility.write_collection_items(outfile, antibody_list, 'Antibody', 'antibodies')
if experimental_factor_list:
exporter_utility.write_collection_items(outfile, experimental_factor_list, 'ExperimentalFactor', 'experimentalFactors')
if microarray_list:
exporter_utility.write_collection_items(outfile, microarray_list, 'MicroArray', 'microArrays')
if sequencing_list:
exporter_utility.write_collection_items(outfile, sequencing_list, 'Sequencing', 'sequencings')
if data_analysis_list:
exporter_utility.write_collection_items(outfile, data_analysis_list, 'DataAnalysis', 'dataAnalyses')
if persistent_datafile_list:
exporter_utility.write_collection_items(outfile, persistent_datafile_list, 'PersistentDataFile', 'persistentDataFiles')
if submission_datafile_list:
exporter_utility.write_collection_items(outfile, submission_datafile_list, 'SubmissionDataFile', 'submissionDataFiles')
outfile.write('</item>\n')
outfile.close() # close file
