Mercurial > repos > geco-team > gmql_download
changeset 0:35d52820e7c7 draft default tip
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dynamic_utils.py Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,281 @@ +#!/usr/bin/env python +# -------------------------------------------------------------------------------- +# Class for the dynamic options in the GMQL tools +# -------------------------------------------------------------------------------- +# Luana Brancato, luana.brancato@mail.polimi.it +# -------------------------------------------------------------------------------- + +import sys, requests + + +def validate(request_context, error_map, params, inputs): + """Generic validate function, it checks if the user is valid.""" + + user = params.get('authToken', '') + + if user: + try: + validate_user(user.file_name) + except: + error_msg = 'User has expired' + error_map['authToken'] = error_msg + + +def validate_upload(request_context, error_map, params, inputs): + """Validate function for uploading tool. It also checks the chosen ds name does not exists already.""" + + validate(request_context, error_map, params, inputs) + + name = params.get('name') + + user = params.get('authToken') + + #This MUST be changed in the future to a parametric solution. Hopefully in the future Galaxy will allow + #validation without external scripts + + url = 'http://genomic.elet.polimi.it/gmql-rest/datasets' + + datasets = get(url, user=user.file_name) + list_datasets = [x['name'] for x in datasets['datasets']] + + if name in list_datasets: + error_msg = 'Dataset already exists. Choose another name.' + error_map['name'] = error_msg + + +def validate_variables(request_context, error_map, params, inputs): + """Validate function for gmql_compositor. It checks that all queries input variables + have been previously defined. """ + + validate(request_context, error_map, params, inputs) + + output_vars = set([]) + + # TODO: Include in the check output variables eventually defined previously in another query + + for op in params.get('operations'): + op_curr = op.get('operation') + if op_curr.get('input', ''): + input_var = op_curr.get('input').get('input_var', '') + if input_var: + if input_var not in output_vars: + error_msg = '%s has not been defined yet\n' % (input_var) + name = '|'.join(['operations_%d' % (op.get('__index__')), 'operation', 'input', 'input_var']) + error_map[name] = error_msg + else: + for key in op_curr.keys(): + if key.startswith('input_var'): + input_var = op_curr.get(key) + if input_var: + if input_var not in output_vars: + error_msg = '%s has not been defined yet\n' % (input_var) + name = '|'.join(['operations_%d' % (op.get('__index__')), 'operation', key]) + error_map[name] = error_msg + + # Update output_vars with the result of current operation + output_vars.add(op_curr.get('output_var')) + + +def validate_user(user): + """Check if the user is a valid one""" + + if user: + with open(user, 'r') as f: + valid = f.readline().rstrip('\n').split('\t')[2] + if valid == 'False': + raise Exception, "User has expired" + + +def get_metadata_attr(user, ds, ds_list): + options = [] + + try: + validate_user(user) + if ds_list: + + owner = '' + + with open(ds_list, 'r') as f: + for d in f.readlines(): + if d.split('\t')[0] == ds: + owner = d.split('\t')[1].rstrip('\n') + f.close() + + attr_list = get_metadata(user, ds, str(owner)) + + for i, att in enumerate(attr_list['attributes']): + options.append((att.get('key', ' '), att.get('key', ' '), i == 0)) + + return options + + else: + return options + except: + return options + + +def get_metadata_values(user, ds, ds_list, att): + options = [] + + try: + validate_user(user) + if ds_list: + + owner = '' + + with open(ds_list, 'r') as f: + for d in f.readlines(): + if d.split('\t')[0] == ds: + owner = d.split('\t')[1].rstrip('\n') + f.close() + + attr_list = get_metadata(user, ds, str(owner), att) + + # By default first option is '*' i.e. any value + options.append(('any value', '*', 0)) + + for i, att in enumerate(attr_list['values']): + options.append(('%s (%d)' % (att.get('text', ' '), att.get('count', 0)), att.get('text', ' '), i == 0)) + + return options + + else: + return options + except: + return options + + +def get_metadata(user, ds, owner='', att_name=''): + """Return the metadata attributes names for the given dataset""" + + url = 'http://genomic.elet.polimi.it/gmql-rest/metadata/{datasetName}/filter' + + # Format url + if (owner == 'public'): + url = url.format(datasetName='public.' + ds) + else: + url = url.format(datasetName=ds) + + if att_name: + url = '{url}/{att}'.format(url=url, att=att_name) + + content = dict() + content.update(attributes=[]) + + metadata = post(url, content, user=user) + + return metadata + + +def read_token(input): + """It takes the tabular file with the information over the user + name authToken valid_flag + It checks if the user is still valid and extract the authToken for the REST calls""" + + with open(input, 'r') as f_in: + user = f_in.readline().rstrip('\n').split('\t') + + if user[2]: + token = user[1] + else: + stop_err("This session is no longer valid") + + return token + + +def get(url, user=None, response_type='json'): + """GET Request + :param url: url where to fetch the requested resource + :param user: for authenticated requests; if not provided make an unauthenticated request (es. for login) + :param response_type: type of the fetched response. + JSON ( Default ) + TEXT + ZIP + FILE + """ + + # Set request headers + headers = dict() + + if user: + headers.update({'X-AUTH-TOKEN': read_token(user)}) + + if response_type == 'text': + headers.update({'Accept': 'text/plain'}) + elif response_type == 'zip': + pass + elif response_type == 'file': + headers.update({'Accept': 'file'}) + else: + headers.update({'Accept': 'application/json'}) + + # Make the request + response = requests.get(url, headers=headers) + + # Check returned server status + status_code = response.status_code + + # Read result. If Server OK, read according to response_type. Raise an error otherwise. + if status_code == requests.codes.ok: + if response_type == 'json': + return response.json() + elif response_type == 'text': + return response.text + else: + return response + elif status_code == requests.codes.unauthorized: + #expire_user(user) + stop_err("You are not authorized to do this. \nPlease login first.") + elif status_code == requests.codes.not_found: + stop_err("Resource not found for this user.") + else: + stop_err("Error {code}: {reason}\n{message}".format(code=status_code, + reason=response.reason, + message=response.content)) + +def post(url, payload, user=None, params=None, content_type='json', response_type='json') : + """ POST Request + :param url: url where to post data + :param payload: payload for the post request. Type is specified by content_type. + :param user: for authenticated requests; if not provided make an unauthenticated request (es. for registration) + :param params: optional query parameters + :param content_type + :param response_type: Default is json + """ + + + # Set request headers + headers = dict() + + if user: + headers.update({'X-AUTH-TOKEN': read_token(user)}) + + headers.update({'Accept': 'application/json'}) + + if content_type == 'text' : + headers.update({'Content-Type' : 'text/plain'}) + response = requests.post(url, params=params, headers=headers, data=payload) + elif content_type == 'multiform' : + response = requests.post(url, params=params, headers=headers, files=payload) + else : + headers.update({'Content-Type': 'application/json'}) + response = requests.post(url, params=params, headers=headers, json=payload) + + # Check returned server status + status_code = response.status_code + + + if status_code == requests.codes.ok : + return response.json() + elif status_code == requests.codes.unauthorized : + #expire_user(user) + stop_err("You are not authorized to do this. \nPlease login first.") + else : + stop_err("Error {code}: {reason}\n{message}".format(code=status_code, + reason=response.reason, + message=response.content)) + + +def stop_err(msg): + sys.stderr.write("%s\n" % msg) + sys.exit() \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gmql_rest.yaml Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,43 @@ +--- +GMQL_URL : + http://genomic.elet.polimi.it/gmql-rest #server to use +access: + prefix: '' + operations: + user: [user] + guest: [guest] + register: [register] + login: [login] + logout: [logout] +metadata: + prefix: 'metadata' + operations: + list: ['{datasetName}', filter] +repository: + prefix: datasets + operations: + list_datasets : [] + list_samples : ['{datasetName}'] + delete_dataset : ['{datasetName}'] + rename_dataset : ['{datasetName}', rename, '{newDatasetName}'] + download_zip : ['{datasetName}', zip] + download_sample : ['{datasetName}','{sample}',region] + download_meta : ['{datasetName}','{sample}',metadata] + upload_url : ['{datasetName}',uploadSampleUrls] + upload_data : ['{datasetName}',uploadSample] + schema : ['{datasetName}',schema] + params: + upload_url: schemaName + upload_data: schemaName +query_exec: + prefix: queries + operations: + compile: [compile] + run: [run,'{name}','{output}'] +query_monitor : + prefix: jobs + operations: + jobs: [] + log: ['{jobid}',log] + stop: ['{jobid}',stop] + status: ['{jobid}',trace]
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gmql_rest_datasets.py Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,411 @@ +# Galaxy plugin to REST access to the GMQL services +# (Datasets) +# ---------------------------------------------------------------------------- +# Luana Brancato, luana.brancato@mail.polimi.it +# ---------------------------------------------------------------------------- + +import argparse + +import tempfile +import json +from utilities import * + +module = 'repository' + + +def list_datasets(user, output, saveResult=True): + """Retrieve the list of available datasets""" + + call = 'list_datasets' + url = compose_url(module,call) + + datasets = get(url, user=user) + list_datasets = datasets['datasets'] + + if saveResult: + with open(output,'w') as f: + for ds in list_datasets: + f.write("{name}\t{owner}\n".format(name=ds['name'],owner=ds['owner'])) + f.close() + else: + return list_datasets + + +def list_samples(user, output, ds): + """List the samples of a given dataset""" + + call = 'list_samples' + url = compose_url(module,call) + + # Specify for which dataset. + # If it's a public dataset, the 'public.' prefix must be added to the dataset name + + # Check if the ds is public or not + owner = '' + for d in list_datasets(user, '', False): + if d['name'] == ds : + owner = d['owner'] + + if (owner=='public'): + url = url.format(datasetName='public.'+ ds) + else : + url = url.format(datasetName=ds) + + samples = get(url, user=user) + list_s = samples['samples'] + + with open(output, 'w') as f_out: + for s in list_s: + f_out.write("{id}\t{name}\t{ext}\n".format(id=s['id'], name=s['name'],ext=s['path'].rsplit('.',1)[1])) + + +def rename_dataset(user, output, ds, new): + """Rename a dataset from the user's private space""" + + call = 'rename_dataset' + url = compose_url(module,call) + url = url.format(datasetName=ds, newDatasetName=new) + + outcome = get(url, user=user) + + # Return the updated list of user's datasets + list_datasets(user, output) + + # Write on stdout the operation outcome + sys.stdout.write("Rename: {result}".format(result=outcome['result'])) + + +def delete_dataset(user, output, ds): + """Delete a dataset from the user's private space""" + + call = 'delete_dataset' + url = compose_url(module,call) + url = url.format(datasetName=ds) + + outcome = delete(url, user=user) + + #Return the updated list of user's datasets + list_datasets(user, output) + + #Write on stdout the operation outcome + sys.stdout.write("Delete: {result}".format(result=outcome['result'])) + + +def upload_samples_url(user, output, dataset, schema, samples, updatedDsList): + """Upload a dataset given the urls of the samples and their schema""" + + #Compose the url for the REST call + call = 'upload_url' + url = compose_url(module,call) + url = url.format(datasetName=dataset) + + content = dict() + + # Put back escaped '&' + samples = samples.replace('__amp__', '&') + schema = schema.replace('__amp__', '&') + + # If schema type is given, add the option to the url. Otherwise, it check if the provided schema is a valid url. + + params = dict () + + if schema in ['bed','bedGraph','NarrowPeak','BroadPeak','vcf'] : + params = add_url_param(params, module, call, schema) + else: + #check_schema = validators.url(schema) + #if isinstance(check_schema, validators.utils.ValidationFailure): stop_err("Schema URL not valid") + content.update(schema_file=schema) + + + # Samples are listed one per line. It lists them looking for the new line marker ('__cn__') + samples_list = samples.split('__cn__') + + # The regexp in input can allow a final empty string. The following removes it if present. + if not samples_list[-1]: + samples_list.remove("") + + # # For each sample url, check if it is valid. If at least ones is not, upload fails + # # and which one is saved in the outcome. + # for s in samples_list: + # check_url = validators.url(s) + # if isinstance(check_url, validators.utils.ValidationFailure): + # with open(output, 'w') as f_out: + # f_out.write("This resource couldn't be loaded (invalid url)\n") + # f_out.write("Line %d: %s" % (samples_list.index(s) + 1, s)) + # stop_err("Some URLs are not valid.\nCheck the output file for details.") + + content.update(data_files=samples_list) + + result = post(url, content, user=user, params=params) + + #Return the list of updated samples + list_imported(result, output) + + #Return the updated list of samples + list_datasets(user, updatedDsList) + + +def upload_samples(user, output, dataset, schema, samples, updatedDsList): + """Upload a dataset from the local instance""" + + + #Compose the url for the REST call + call = 'upload_data' + url = compose_url(module, call) + url = url.format(datasetName=dataset) + + #Files dict for payload + files = dict () + + # If the schema type is give, add the option to the url. + params = dict () + + + if schema in ['bed','bedGraph','NarrowPeak','BroadPeak','vcf'] : + params = add_url_param(params, module, call, schema) + else : + # Add the schema given to the payload dictionary + files.update({'schema' : ('{ds}.xml'.format(ds=dataset), open(schema, 'rb'))}) + + # Read samples file path and add them to the form object + # The structure is + # FILENAME PATH + + with open(samples, "r") as file: + s = map(lambda x: x.rstrip('\n').split('\t'), file) + s = [x for x in s if len(x)>1] + #s = [x for x in s if x[0].__contains__('.dat')] + map(lambda x: files.update({'file%d' % (s.index(x) + 1) : (x[0], open(x[1], 'rb'))}), s) + + # Post call + + result = post(url, files, user=user, params=params, content_type='multiform') + + #Return the list of updated samples + list_imported(result, output) + + + #Return the updated list of samples + list_datasets(user, updatedDsList) + + + +def list_imported(result, output) : + """When uploading a ds, the server returns a json object describing what has been imported + INPUT JSON FIELDS - + imported: samples imported with their metadata + autoMetadata: samples imported without metadata (those have been auto generated) """ + + samples = list () + + if 'imported' in result : + imported = result.get('imported') + if imported: + samples.append(result.get('imported')) + if 'autoMetadata' in result : + am = result.get('autoMetadata') + if am : + samples.append(result.get('autoMetadata')) + + + with open(output, 'w') as f_out: + for l in samples: + for s in l : + if 'id' in s and s['id']: + id = s['id'] + else : + id = l.index(s) + 1 + if 'path' in s : + ext = s['path'].rsplit('.')[1] + else : + n = s['name'].rsplit('.') + if n.__len__()>1 : + ext = n[1] + else : + ext = '' + + name = s['name'] + + f_out.write("{id}\t{name}\t{ext}\n".format(id=id, name=name,ext=ext)) + + +def download_samples(user, output, dataset): + """ Download the samples of the given dataset in form of a compressed zip archive.""" + + call = 'download_zip' + + url = compose_url(module, call) + url = url.format(datasetName=dataset) + + # Fetch the archive. + + data = get(url, user=user, response_type='zip') + + with open(output, 'wb') as fd: + for chunk in data.iter_content(chunk_size=128): + fd.write(chunk) + +def get_sample(user, output, dataset, name): + """Retrieve a sample given its name and the dataset it belongs to""" + + call = 'download_sample' + + url = compose_url(module,call) + url = url.format(datasetName=dataset,sample=name) + + data = get(url, user=user, response_type='file') + + with open(output, 'wb') as fd: + for chunk in data.iter_content(chunk_size=128): + fd.write(chunk) + + +def get_sample_meta(user, output, dataset, name): + """Retrieve a sample metadata given its name and the dataset it belongs to""" + + call = 'download_meta' + + url = compose_url(module, call) + url = url.format(datasetName=dataset, sample=name) + + data = get(url, user=user, response_type='file') + + with open(output, 'wb') as fd: + for chunk in data.iter_content(chunk_size=128): + fd.write(chunk) + +def import_samples(user, ds) : + + + # Retrieve the list of the samples in the resulting dataset + # The list is stored in a temporary file + temp = tempfile.NamedTemporaryFile(delete=False) + list_samples(user, temp.name, ds) + + # Retrieve names and extensions of the samples + with open(temp.name, "r") as t: + samples = map(lambda x: helper_samples(x), t) + t.close() + + os.makedirs('samples') + os.makedirs('metadata') + + # Create a new dict containing names and actual path to files + + for s in samples: + + # Get the sample + get_sample(user, "samples/{name}.{ext}".format(name=s['name'].replace('_',''), ext=s['ext']), ds, s['name']) + + # Get its metadata + get_sample_meta(user,"metadata/{name}.meta".format(name=s['name'].replace('_','')),ds,s['name']) + +def helper_samples(s): + """From a list of samples retrieve name and extension""" + split = s.split('\t') + sample = dict() + sample.update(name=split[1]) + sample.update(ext=split[2].rstrip('\n')) + + return sample + + +def get_schema(user, ds, file) : + """Get the schema field of the input dataset and save it in file""" + + call = "schema" + + url = compose_url(module, call) + + # Check if the ds is public or not + owner = '' + for d in list_datasets(user, '', False): + if d['name'] == ds : + owner = d['owner'] + + if (owner=='public'): + url = url.format(datasetName='public.'+ ds) + else : + url = url.format(datasetName=ds) + + schema = get(url, user=user) + + + with open(file,'w') as f_out: + for f in schema['fields'] : + f_out.write('{field}\t{type}\n'.format(field=f['name'],type=f['type'])) + + + +def set_columns_names(user, ds_name, samples_file, schema_file): + + get_schema(user,ds_name, schema_file) + + cwd = os.getcwd().rsplit('/',1)[0] + file = '/'.join([cwd, 'galaxy.json']) + + with open(schema_file, 'r') as f_in: + columns = [x.split('\t') for x in f_in] + column_names = [x[0] for x in columns] + column_types = [x[1].rstrip('\n') for x in columns] + + metadata = dict() + metadata.update(column_names=column_names, + column_types=column_types) + + + with open(file, 'w') as f_out: + with open(samples_file, 'r') as f_in: + samples_list = map(lambda x: x, f_in) + samples_list.pop() + for s in samples_list: + config = dict() + config.update(type='new_primary_dataset', + filename=s, + metadata=metadata) + f_out.write(json.dumps(config) + '\n') + + + +def stop_err(msg): + sys.stderr.write("%s\n" % msg) + sys.exit() + + +def __main__(): + + parser = argparse.ArgumentParser() + parser.add_argument("output") + parser.add_argument("-opt_out1") + parser.add_argument("-user") + parser.add_argument("-cmd") + parser.add_argument("-samples") + parser.add_argument("-dataset") + parser.add_argument("-new_name") + parser.add_argument("-schema") + parser.add_argument("-add_output") + + args = parser.parse_args() + + if args.cmd == 'list': + list_datasets(args.user, args.output) + if args.cmd == 'samples': + list_samples(args.user, args.output, args.dataset) + if args.cmd == 'rename' : + rename_dataset(args.user, args.output, args.dataset, args.new_name) + if args.cmd == 'delete': + delete_dataset(args.user, args.output, args.dataset) + if args.cmd == 'upload_url': + upload_samples_url(args.user, args.output, args.dataset, args.schema, args.samples, args.add_output) + if args.cmd == 'upload' : + upload_samples(args.user, args.output, args.dataset, args.schema, args.samples, args.add_output) + if args.cmd == 'import': + import_samples(args.user, args.dataset) + if args.cmd == 'download' : + download_samples(args.user,args.output,args.dataset) + if args.cmd == 'schema' : + set_columns_names(args.user, args.dataset, args.samples, args.output) + + +if __name__ == "__main__": + __main__()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gmql_rest_datasets_download.xml Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,90 @@ +<tool id="gmql_download" name="GMLQ Import Dataset" version="0.1.1"> + <macros> + <import>gmql_rest_macros.xml</import> + </macros> + <command><![CDATA[ + #if $operation == 'import' : + python $__tool_directory__/gmql_rest_datasets.py '' -user=$authToken -cmd=import -dataset=${dataset} + #else : + python $__tool_directory__/gmql_rest_datasets.py $ds_archive -user=$authToken -cmd=download -dataset=${dataset} + #end if + ]]></command> + <code file="dynamic_utils.py"> + <hook validate_input="validate" /> + </code> + <inputs> + <param format="gmql_user" name="authToken" type="data" label="Select user" /> + <param name="gmql_datasets" type="data" format="gmql_repository" label="Working Datasets"/> + <param name="dataset" type="select" label="Select Dataset"> + <options from_dataset="gmql_datasets"> + <column name="value" index="0"/> + <filter column="1" type="static_value" value="public" keep="false"/> + </options> + </param> + <param name="operation" type="select" display="radio" multiple="false" label="Select the desired action"> + <option value="import">Import data as a collection</option> + <option value="zip">Download zip archive</option> + </param> + </inputs> + <outputs> + <data format="zip" name="ds_archive" label="${dataset} Compressed Archive"> + <filter>operation == 'zip'</filter> + </data> + <collection name="query_results_m" type="list" label="${dataset} metadata"> + <discover_datasets pattern="(?P<identifier_0>[\w]+)\.(?P<ext>[^\._]+)?" + directory="metadata"/> + <filter>operation == 'import'</filter> + </collection> + <collection name="query_results_s" type="list" label="${dataset}"> + <discover_datasets pattern="(?P<identifier_0>[\w]+)\.(?P<ext>[^\._]+)?" + directory="samples"/> + <filter>operation == 'import'</filter> + </collection> + </outputs> + <tests> + <test> + <param name="authToken" value="guest.gmql_user" /> + <param name="gmql_datasets" value="rep.gmql_repository" /> + <param name="dataset" value="Example1" /> + <param name="operation" value="zip" /> + <output name="ds_archive" file="Example1_Archive.zip" compare="sim_size" delta="0"/> + </test> + <test> + <param name="authToken" value="guest.gmql_user" /> + <param name="gmql_datasets" value="rep.gmql_repository" /> + <param name="dataset" value="Example1" /> + <param name="operation" value="import" /> + <collection name="query_results_s" type="list"> + <metadata name="name" value="Example1" /> + <discovered_dataset designation="sample1" file="sample1.bed"/> + <discovered_dataset designation="sample2" file="sample2.bed"/> + <discovered_dataset designation="sample3" file="sample3.bed"/> + </collection> + <collection name="query_results_m" type="list"> + <metadata name="name" value="Example1 metadata" /> + <discovered_dataset designation="sample1" file="sample1.bed.meta"/> + <discovered_dataset designation="sample2" file="sample2.bed.meta"/> + <discovered_dataset designation="sample3" file="sample3.bed.meta"/> + </collection> + </test> + </tests> + <help> +It allows importing in the current Galaxy history the selected dataset. + +---- + +**What it does** + +- **Import as Collection**: returning data consist of two collections, one for samples and one for their metadata +- **Download ZIP Archive**: returns the dataset as a zip archive + + +The user provides a list of datasets (gmql_repository file) and selects from there the dataset he wants to import. + +.. class:: warningmark + +A gmql_user authentication token is required for every action. + + </help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gmql_rest_macros.xml Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,28 @@ +<macros> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @article{Masseroli2015, + author = {{Marco Masseroli, Pietro Pinoli, Francesco Venco, Abdulrahman Kaitoua, Vahid Jalili, Fernando Palluzzi, Heiko Muller, Stefano Ceri}}, + doi = {10.1093/bioinformatics/btv048}, + isbn = {13674811 (Electronic)}, + issn = {14602059}, + journal = {Bioinformatics}, + number = {12}, + pages = {1881-1888}, + pmid = {25649616}, + title = {{GenoMetric Query Language: A novel approach to large-scale genomic data management}}, + volume = {31}, + year = {2015} + } + </citation> + <citation type="bibtex"> + @misc{BionformaticsGroup, + author = {{Bionformatics Group}, Politecnico di Milano}, + title = {{GMQL Documentation}}, + url = {http://www.bioinformatics.deib.polimi.it/genomic{\_}computing/GMQLsystem/documentation.html}, + } + </citation> + </citations> + </xml> +</macros> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TG/S_00000.gdm Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,3 @@ +chr1 99 150 * GMQL Region 4 . . 10 7.0638 -1 -1 +chr1 119 180 * GMQL Region 3 . . 24 19.7648 -1 -1 +chr1 219 240 * GMQL Region 8 . . 13 11.2001 -1 -1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TG/S_00000.gdm.meta Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,71 @@ +ID 1460 +avg_score 6 +cell AG04450 +cell_description fetal lung fibroblast +cell_karyotype normal +cell_lineage endoderm +cell_orderUrl http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=AG04450 +cell_organism human +cell_protocol Stam:AG04450_Stam_protocol.pdf +cell_sex Female +cell_tag AG04450 +cell_termId BTO:0000763 +cell_termUrl http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BTO&termId=BTO%3A0000763 +cell_tier 3 +cell_tissue lung +cell_type Cell Line +cell_vendorId AG04450 +cell_vendorName Coriell +composite wgEncodeUwDnase +dataType DnaseSeq +dataType_dataGroup Open Chromatin +dataType_description DNaseI HS Sequencing +dataType_label DNase-seq +dataType_tag DNASESEQ +dataType_type dataType +dataVersion ENCODE June 2010 Freeze +dateResubmitted 2010-06-17 +dateSubmitted 2010-01-07 +dateUnrestricted 2010-10-07 +dccAccession wgEncodeEH000506 +geoSampleAccession GSM736563 +grant Stam +grant_description Stamatoyannopoulous +grant_grantInst University of Washington +grant_label Stamatoyannopoulous +grant_projectName UW +grant_tag STAM +grant_type grant +lab UW +labExpId DS12255 +labVersion lmax-v1.0 +lab_description Stamatoyannopoulous - University of Washington +lab_grantPi Stam +lab_labInst University of Washington +lab_labPi Stam +lab_labPiFull John Stamatoyannopoulous +lab_label Stamatoyannopoulous - UW +lab_organism human +lab_tag UW +lab_type lab +md5sum 1250e67a89764a7e877bca3bbee70f62 +origAssembly hg18 +patient_age 75 +project wgEncode +replicate 2 +sex Female +size 1.8M +subId 1549 +tableName wgEncodeUwDnaseAg04450PkRep2 +treatment None +treatment_description No special treatment or protocol applies +treatment_label No treatment or prot +treatment_tag NONE +treatment_type control +type narrowPeak +url http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseAg04450PkRep2.narrowPeak.gz +view Peaks +view_description Regions of enriched signal in experiment +view_label Peaks +view_tag PKS +view_type view
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TG/S_00001.gdm Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,2 @@ +chr1 149 180 * GMQL Region 6 . . 35 30.2764 -1 -1 +chr1 229 235 * GMQL Region 9 . . 17 11.1675 -1 -1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TG/S_00001.gdm.meta Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,93 @@ +ID 1891 +antibody CTCF +antibody_antibodyDescription Rabbit polyclonal. Antibody Target: CTCF +antibody_lab Myers, Hardison, Snyder +antibody_label CTCF (07-729) +antibody_lots 1350637 DAM1472197 +antibody_orderUrl http://www.millipore.com/catalogue/item/07-729 +antibody_tag CTCF +antibody_target CTCF +antibody_targetClass TFSS +antibody_targetDescription CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. +antibody_targetId GeneCard:CTCF +antibody_targetUrl http://www.genecards.org/cgi-bin/carddisp.pl?gene=CTCF +antibody_type Antibody +antibody_validation Human_-_CTCF_(07-729)(Western_blot,Motif_Enrichment):human_CTCF_validation_Myers.pdf Human_-_CTCF_(07-729)(Western_blot):human_CTCF_07-729_validation_Snyder.pdf Mouse_-_CTCF(Western_blot):mouse_CTCF_validation_Hardison.pdf +antibody_vendorId 07-729 +antibody_vendorName Millipore +avg_score 7.5 +cell AG04450 +cell_description fetal lung fibroblast +cell_karyotype normal +cell_lineage endoderm +cell_orderUrl http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=AG04450 +cell_organism human +cell_protocol Stam:AG04450_Stam_protocol.pdf +cell_sex Male +cell_tag AG04450 +cell_termId BTO:0000763 +cell_termUrl http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BTO&termId=BTO%3A0000763 +cell_tier 2 +cell_tissue lung +cell_type Cell Line +cell_vendorId AG04450 +cell_vendorName Coriell +composite wgEncodeUwTfbs +control std +controlId wgEncodeEH000930 +control_description Standard input signal for most experiments. +control_label Standard Control +control_tag STD +control_type control +dataType ChipSeq +dataType_dataGroup TFBS & Histones +dataType_description Chromatin IP Sequencing +dataType_label ChIP-seq +dataType_tag CHIPSEQ +dataType_type dataType +dataVersion ENCODE Jan 2011 Freeze +dateSubmitted 2010-10-23 +dateUnrestricted 2011-07-23 +dccAccession wgEncodeEH000976 +geoSampleAccession GSM749769 +grant Stam +grant_description Stamatoyannopoulous +grant_grantInst University of Washington +grant_label Stamatoyannopoulous +grant_projectName UW +grant_tag STAM +grant_type grant +lab UW +labExpId DS16029 +labVersion lmax-v1.0 +lab_description Stamatoyannopoulous - University of Washington +lab_grantPi Stam +lab_labInst University of Washington +lab_labPi Stam +lab_labPiFull John Stamatoyannopoulous +lab_label Stamatoyannopoulous - UW +lab_organism human +lab_tag UW +lab_type lab +md5sum 3c6b5bf3eefc28b6bab4ef37916011a1 +origAssembly hg19 +patient_age 63 +project wgEncode +replicate 1 +setType exp +sex Male +size 776K +subId 2663 +tableName wgEncodeUwTfbsAg04450CtcfStdPkRep1 +treatment None +treatment_description No special treatment or protocol applies +treatment_label No treatment or prot +treatment_tag NONE +treatment_type control +type narrowPeak +url http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsAg04450CtcfStdPkRep1.narrowPeak.gz +view Peaks +view_description Regions of enriched signal in experiment +view_label Peaks +view_tag PKS +view_type view
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TG/S_00002.gdm Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,11 @@ +chr2 99 150 * GMQL Region 10 . . 9 5.27936 -1 -1 +chr2 199 240 * GMQL Region 9 . . 22 19.6922 -1 -1 +chr2 399 440 * GMQL Region 0.9 . . 15 15.1452 -1 -1 +chr2 539 570 * GMQL Region 0.9 . . 15 15.1452 -1 -1 +chr4 49 100 + GMQL Region 0.9 . . 15 15.1452 -1 -1 +chr4 149 179 - GMQL Region 0.9 . . 15 15.1452 -1 -1 +chr4 199 249 - GMQL Region 0.9 . . 15 15.1452 -1 -1 +chr5 99 200 * GMQL Region 4 . . 15 17.1452 -1 -1 +chr5 299 340 + GMQL Region 4 . . 15 15.1452 -1 -1 +chr5 319 340 - GMQL Region 3 . . 15 17.1452 -1 -1 +chr5 379 420 - GMQL Region 3 . . 15 17.1452 -1 -1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TG/S_00002.gdm.meta Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,71 @@ +ID 1459 +Info example text +avg_score 5 +cell AG04450 +cell_description fetal lung fibroblast +cell_karyotype normal +cell_lineage endoderm +cell_orderUrl http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=AG04450 +cell_organism human +cell_protocol Stam:AG04450_Stam_protocol.pdf +cell_sex Male +cell_tag AG04450 +cell_termId BTO:0000763 +cell_termUrl http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BTO&termId=BTO%3A0000763 +cell_tier 2 +cell_tissue lung +cell_type Cell Line +cell_vendorId AG04450 +cell_vendorName Coriell +composite wgEncodeUwDnase +dataType DnaseSeq +dataType_dataGroup Open Chromatin +dataType_description DNaseI HS Sequencing +dataType_label DNase-seq +dataType_tag DNASESEQ +dataType_type dataType +dataVersion ENCODE June 2010 Freeze +dateResubmitted 2010-06-17 +dateSubmitted 2010-01-07 +dateUnrestricted 2010-10-07 +dccAccession wgEncodeEH000506 +geoSampleAccession GSM736514 +grant Stam +grant_description Stamatoyannopoulous +grant_grantInst University of Washington +grant_label Stamatoyannopoulous +grant_projectName UW +grant_tag STAM +grant_type grant +lab UW +labExpId DS12270 +labVersion lmax-v1.0 +lab_description Stamatoyannopoulous - University of Washington +lab_grantPi Stam +lab_labInst University of Washington +lab_labPi Stam +lab_labPiFull John Stamatoyannopoulous +lab_label Stamatoyannopoulous - UW +lab_organism human +lab_tag UW +lab_type lab +md5sum 8f7c4f145d130385f9b5e732961b3c42 +origAssembly hg18 +project wgEncode +replicate 1 +sex Male +size 1.7M +subId 1550 +tableName wgEncodeUwDnaseAg04450PkRep1 +treatment None +treatment_description No special treatment or protocol applies +treatment_label No treatment or prot +treatment_tag NONE +treatment_type control +type narrowPeak +url http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseAg04450PkRep1.narrowPeak.gz +view Peaks +view_description Regions of enriched signal in experiment +view_label Peaks +view_tag PKS +view_type view
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TG/schema.xml Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,18 @@ +<?xml version='1.0' encoding='UTF-8'?> +<gmqlSchemaCollection name="queryname_20180417_000927_TG" xmlns="http://genomic.elet.polimi.it/entities"> + <gmqlSchema type="Peak" coordinate_system="default"> + <field type="STRING">chr</field> + <field type="LONG">left</field> + <field type="LONG">right</field> + <field type="CHAR">strand</field> + <field type="STRING">source</field> + <field type="STRING">feature</field> + <field type="DOUBLE">score</field> + <field type="STRING">frame</field> + <field type="STRING">name</field> + <field type="DOUBLE">signal</field> + <field type="DOUBLE">pvalue</field> + <field type="DOUBLE">qvalue</field> + <field type="DOUBLE">peak</field> + </gmqlSchema> +</gmqlSchemaCollection> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cover1.gmql_query Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,2 @@ +IN = SELECT () Example_Dataset_1 ; +OUT = COVER (1, ANY; groupby: cell, antibody_target; aggregate: min_pvalue AS MIN(pvalue)) IN ;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cover2.gmql_query Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,4 @@ +IN = SELECT () Example_Dataset_1 ; +OUT1 = FLAT (2, 4; groupby: cell) IN ; +OUT2 = SUMMIT (2, 4; groupby: cell) IN ; +OUT3 = HISTOGRAM (ALL / 2, (ALL + 1) / 2; groupby: antibody_target) IN ;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/difference1.gmql_query Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,3 @@ +IN = SELECT () Example_Dataset_1 ; +IN2 = SELECT () Example_Dataset_2 ; +OUT = DIFFERENCE (exact: true; joinby: cell) IN IN2;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/extend1.gmql_query Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,2 @@ +OUT = SELECT () Example_Dataset_1 ; +OUT2 = EXTEND (avg_score AS AVG(score), max_p AS MAX(pvalue)) OUT ;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/group1.gmql_query Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,2 @@ +OUT = SELECT () Example_Dataset_1 ; +OUT2 = GROUP (cell_tissue; meta_aggregates: min_tier AS MIN(cell_tier); region_keys: score; region_aggregates: min_signal AS MIN(signal)) OUT ;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/guest.gmql_user Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,1 @@ +Guest 833ed58f-d1d3-4963-8bf3-46e0562beac2 True
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/guest2.gmql_user Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,1 @@ +Guest 3134ead6-4661-4994-a7c6-2fc2ae0a56da True
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/join1.gmql_query Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,3 @@ +IN = SELECT () Example_Dataset_1 ; +IN2 = SELECT () Example_Dataset_2 ; +OUT = JOIN (MD(1), UP; output: RIGHT; joinby: cell) IN IN2;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/join2.gmql_query Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,3 @@ +IN = SELECT () Example_Dataset_1 ; +IN2 = SELECT () Example_Dataset_2 ; +OUT = JOIN (DL(0); on_attributes: score, chr; output: INT; joinby: cell, provider) IN IN2;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/map1.gmql_query Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,3 @@ +IN = SELECT () Example_Dataset_1 ; +IN2 = SELECT () Example_Dataset_2 ; +OUT = MAP (avg_score AS AVG(score), min_score AS MIN(score), chr_list AS BAG(chr); count_name: mapped_n; joinby: cell_tissue) IN IN2;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/merge1.gmql_query Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,2 @@ +OUT = SELECT () Example_Dataset_1 ; +OUT2 = MERGE (groupby: EXACT(antibody_target)) OUT ;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/order1.gmql_query Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,2 @@ +OUT = SELECT () Example_Dataset_1 ; +OUT2 = ORDER (ID; meta_top: 5; region_order: score DESC, start) OUT ;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/project1.gmql_query Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,2 @@ +OUT = SELECT () Example_Dataset_1 ; +OUT2 = PROJECT (ALLBUT name; frame; metadata: cell; region_update: lengh AS stop - start) OUT ;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/query.gmql_query Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,2 @@ +VAR = SELECT (grant == 'Stam') Example_Dataset_1 ; +MATERIALIZE VAR INTO TG;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rep.gmql_repository Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,42 @@ +Example1 guest_new880 +ChIA_PET public +Example_Dataset_1 public +Example_Dataset_2 public +GRCh38_ANNOTATION_GENCODE public +GRCh38_ANNOTATION_REFSEQ public +GRCh38_ENCODE_BROAD_AUG_2017 public +GRCh38_ENCODE_BROAD_NOV_2017 public +GRCh38_ENCODE_NARROW_AUG_2017 public +GRCh38_ENCODE_NARROW_NOV_2017 public +GRCh38_TCGA_copy_number public +GRCh38_TCGA_copy_number_masked public +GRCh38_TCGA_gene_expression public +GRCh38_TCGA_methylation public +GRCh38_TCGA_miRNA_expression public +GRCh38_TCGA_miRNA_isoform_expression public +GRCh38_TCGA_somatic_mutation_masked public +HG19_ANNOTATION_GENCODE public +HG19_ANNOTATION_REFSEQ public +HG19_BED_ANNOTATION public +HG19_ENCODE_BROAD_AUG_2017 public +HG19_ENCODE_BROAD_NOV_2016 public +HG19_ENCODE_BROAD_NOV_2017 public +HG19_ENCODE_NARROW_AUG_2017 public +HG19_ENCODE_NARROW_NOV_2016 public +HG19_ENCODE_NARROW_NOV_2017 public +HG19_ROADMAP_EPIGENOMICS_BED public +HG19_ROADMAP_EPIGENOMICS_BROADPEAK public +HG19_TCGA_cnv public +HG19_TCGA_dnamethylation public +HG19_TCGA_dnaseq public +HG19_TCGA_mirnaseq_isoform public +HG19_TCGA_mirnaseq_mirna public +HG19_TCGA_rnaseq_exon public +HG19_TCGA_rnaseq_gene public +HG19_TCGA_rnaseq_spljxn public +HG19_TCGA_rnaseqv2_exon public +HG19_TCGA_rnaseqv2_gene public +HG19_TCGA_rnaseqv2_isoform public +HG19_TCGA_rnaseqv2_spljxn public +TADs_Aiden public +TADs_Dixon public
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample1.bed Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,12475 @@ +chr1 10464 10465 CHR1_P0001_R1 1000 + +chr1 11873 11874 CHR1_P0001_R2 1000 + +chr1 13420 13421 CHR1_P0001_R3 1000 + +chr1 15945 15946 CHR1_M0001_R10 1000 - +chr1 17480 17481 CHR1_M0001_R2 1000 - +chr1 18003 18004 CHR1_M0001_R9 1000 - +chr1 18733 18734 CHR1_M0001_R8 1000 - +chr1 19172 19173 CHR1_M0001_R6 1000 - +chr1 19735 19736 CHR1_M0001_R5 1000 - +chr1 20510 20511 CHR1_M0001_R7 1000 - +chr1 24892 24893 CHR1_M0001_R4 1000 - +chr1 26794 26795 CHR1_P0002_R1 1000 + +chr1 29348 29349 CHR1_M0001_R1 1000 - +chr1 29554 29555 CHR1_P0003_R1 1000 + +chr1 29889 29890 CHR1_M0001_R3 1000 - +chr1 36073 36074 CHR1_M0002_R1 1000 - +chr1 65561 65562 CHR1_P0004_R1 1000 + +chr1 69085 69086 CHR1_P0004_R2 1000 + +chr1 105534 105535 CHR1_M0004_R1 1000 - +chr1 137188 137189 CHR1_M0005_R2 1000 - +chr1 139459 139460 CHR1_M0005_R1 1000 - +chr1 251849 251850 CHR1_M0006_R1 1000 - +chr1 261364 261365 CHR1_P0005_R1 1000 + +chr1 324713 324714 CHR1_P0006_R1 1000 + +chr1 348281 348282 CHR1_M0007_R1 1000 - +chr1 367658 367659 CHR1_P0007_R1 1000 + +chr1 420205 420206 CHR1_P0008_R1 1000 + +chr1 455711 455712 CHR1_M0008_R1 1000 - +chr1 462271 462272 CHR1_P0009_R1 1000 + +chr1 528069 528070 CHR1_P0010_R1 1000 + +chr1 564682 564683 CHR1_M0009_R1 1000 - +chr1 565034 565035 CHR1_P0011_R1 1000 + +chr1 565946 565947 CHR1_M0009_P1557 1000 - +chr1 566776 566777 CHR1_P0012_R1 1000 + +chr1 567249 567250 CHR1_M0009_P2860 1000 - +chr1 568037 568038 CHR1_M0009_P3648 1000 - +chr1 568209 568210 CHR1_P0013_R1 1000 + +chr1 569580 569581 CHR1_P0014_R1 1000 + +chr1 569810 569811 CHR1_M0009_P5421 1000 - +chr1 622034 622035 CHR1_M0010_R1 1000 - +chr1 664909 664910 CHR1_M0011_R1 1000 - +chr1 688889 688890 CHR1_M0012_R1 1000 - +chr1 714020 714021 CHR1_M0013_R1 1000 - +chr1 714287 714288 CHR1_P0015_P38463 1000 + +chr1 731090 731091 CHR1_M0014_R1 1000 - +chr1 752750 752751 CHR1_P0015_R1 1000 + +chr1 762883 762884 CHR1_M0015_R1 1000 - +chr1 763067 763068 CHR1_P0016_R1 1000 + +chr1 766984 766985 CHR1_P0017_R1 1000 + +chr1 791390 791391 CHR1_P0018_R2 1000 + +chr1 791897 791898 CHR1_P0018_R3 1000 + +chr1 792894 792895 CHR1_P0018_R1 1000 + +chr1 812283 812284 CHR1_M0016_R1 1000 - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample1.bed.meta Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,3 @@ +ann_type TSS +provider UCSC +assembly hg19
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample2.bed Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,111 @@ +chr1 3190581 3191428 element_705 900 +chr1 8130439 8131887 element_1833 900 +chr1 10593123 10594209 element_677 200 +chr1 10732070 10733118 element_289 900 +chr1 10757664 10758631 element_361 200 +chr1 10781239 10781744 element_389 900 +chr1 10851570 10852173 element_408 900 +chr1 10925202 10925728 element_417 200 +chr1 10965129 10966144 element_241 900 +chr1 27049620 27050905 element_569 900 +chr1 32510030 32510913 element_645 900 +chr1 33722494 33723960 element_917 200 +chr1 33828789 33830947 element_1388 900 +chr1 38494689 38495688 element_1105 200 +chr1 38560194 38561606 element_238 900 +chr1 38627529 38629265 element_1124 200 +chr1 38656780 38657626 element_1179 200 +chr1 38662809 38664040 element_790 200 +chr1 38735942 38737376 element_1008 200 +chr1 38791998 38793333 element_1098 200 +chr1 38801888 38802630 element_270 200 +chr1 38819171 38820577 element_1045 200 +chr1 39192609 39194134 element_1031 900 +chr1 39248757 39250129 element_1139 900 +chr1 39291500 39292441 element_850 200 +chr1 41710596 41712937 element_1674 200 +chr1 44500383 44503337 element_1857 900 +chr1 44715420 44716129 element_277 900 +chr1 44989824 44991149 element_280 900 +chr1 49112757 49113363 element_295 200 +chr1 51006090 51007314 element_247 200 +chr1 51034546 51036289 element_194 900 +chr1 51098841 51099913 element_197 200 +chr1 51165195 51166786 element_200 900 +chr1 54925046 54928826 element_1487 900 +chr1 59522325 59524092 element_1485 900 +chr1 60102624 60105491 element_1609 200 +chr1 61086857 61087871 element_683 200 +chr1 61917795 61920190 element_1309 900 +chr1 62045460 62048159 element_1484 900 +chr1 62053433 62055908 element_1450 900 +chr1 63369349 63370894 element_311 900 +chr1 63443534 63444884 element_168 900 +chr1 63464282 63465717 element_169 900 +chr1 63665219 63666122 element_764 900 +chr1 82557436 82558140 element_436 200 +chr1 82663553 82664196 element_437 200 +chr1 82664608 82665419 element_438 200 +chr1 83220709 83221363 element_439 200 +chr1 83252219 83253218 element_440 200 +chr1 83310680 83311769 element_441 200 +chr1 83345366 83346271 element_442 900 +chr1 83360512 83361298 element_443 200 +chr1 83411289 83412040 element_444 200 +chr1 83878319 83879217 element_445 200 +chr1 87795192 87796737 element_809 900 +chr1 87803415 87805212 element_1134 200 +chr1 87821621 87823082 element_174 900 +chr1 87821793 87822910 element_322 900 +chr1 88028658 88029378 element_323 200 +chr1 88065041 88066530 element_1217 900 +chr1 88108084 88109396 element_1002 900 +chr1 88183654 88184961 element_1058 200 +chr1 88402821 88404888 element_1055 200 +chr1 88535719 88538390 element_1198 900 +chr1 88577535 88578821 element_1200 200 +chr1 88595049 88596320 element_1135 200 +chr1 88615687 88616927 element_878 900 +chr1 88646698 88648145 element_1216 200 +chr1 88686076 88687740 element_1107 900 +chr1 88841735 88843091 element_1068 200 +chr1 88875731 88877192 element_988 200 +chr1 88926796 88928508 element_327 900 +chr1 91305562 91307215 element_612 900 +chr1 92271540 92273987 element_1499 200 +chr1 97610491 97611741 element_671 900 +chr1 113540056 113542020 element_1672 900 +chr1 119028026 119029955 element_1428 900 +chr1 119452558 119453594 element_499 200 +chr1 163359231 163360494 element_1156 200 +chr1 163441941 163442842 element_762 900 +chr1 163507965 163509139 element_1185 900 +chr1 163939700 163940637 element_201 200 +chr1 164023244 164024214 element_202 200 +chr1 164197827 164199172 element_1230 200 +chr1 164620038 164621164 element_1235 900 +chr1 164637575 164639037 element_203 200 +chr1 164668592 164669823 element_1144 900 +chr1 164672787 164674206 element_970 200 +chr1 164700259 164701522 element_1136 200 +chr1 167296954 167299046 element_1331 900 +chr1 169910396 169913079 element_1442 900 +chr1 181121049 181123654 element_1862 900 +chr1 198263562 198265742 element_1322 900 +chr1 198339402 198341607 element_1443 200 +chr1 204423958 204424935 element_1368 900 +chr1 209064233 209067059 element_1694 200 +chr1 209989050 209989824 element_932 900 +chr1 210433698 210437258 element_1617 200 +chr1 213498112 213501134 element_1324 900 +chr1 213597964 213599524 element_204 900 +chr1 215888921 215890374 element_366 200 +chr1 216772416 216773458 element_175 200 +chr1 217766122 217767351 element_734 200 +chr1 218207432 218208498 element_1257 900 +chr1 218222277 218224086 element_1255 200 +chr1 221906778 221908480 element_1663 200 +chr1 232753930 232757436 element_1714 200 +chr1 243876467 243877893 element_545 900 +chr1 243895796 243896468 element_214 200 +chr1 244217325 244218426 element_476 200
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample2.bed.meta Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,4 @@ +ann_type enhancer +provider UCSC +name VistaEnhancers +assembly hg19
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample3.bed Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,1096 @@ +chr1 324287 324345 NR_028327 0 + +chr1 567704 567793 NR_106781 0 - +chr1 764382 764484 NR_047522 0 + +chr1 901876 901994 NM_032129 0 + +chr1 1021257 1021392 NM_017891 0 - +chr1 1139778 1139866 NM_148901 0 - +chr1 1163847 1164326 NM_016547 0 - +chr1 1178441 1178532 NM_001014980 0 - +chr1 1230097 1230196 NM_030649 0 - +chr1 1231489 1231550 NR_106784 0 - +chr1 1248414 1248504 NM_017871 0 - +chr1 1394540 1394611 NM_001039211 0 + +chr1 1447522 1447853 NM_001170535 0 + +chr1 1461840 1461911 NM_001170536 0 + +chr1 1480242 1480382 NM_014188 0 - +chr1 1551887 1551994 NM_001170686 0 + +chr1 1563652 1563779 NM_001170688 0 + +chr1 1573123 1573245 NM_033490 0 - +chr1 1576408 1576474 NM_033490 0 - +chr1 1637080 1637171 NM_033529 0 - +chr1 1647784 1647917 NM_033489 0 - +chr1 1670674 1671143 NM_182838 0 - +chr1 1670674 1671143 NM_001199787 0 - +chr1 1682670 1684499 NM_023018 0 - 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+chr1 231902885 231903015 NM_001164556 0 + +chr1 231906580 231906816 NM_001012957 0 + +chr1 231906580 231907408 NM_001164549 0 + +chr1 232144530 232144795 NM_001164537 0 + +chr1 232162180 232162298 NM_001164537 0 + +chr1 232172437 232177019 NM_001164537 0 + +chr1 232551239 232551371 NM_020808 0 - +chr1 232940637 232946092 NM_019090 0 + +chr1 233388386 233388534 NM_014801 0 - +chr1 234509975 234510135 NM_001206641 0 + +chr1 234546190 234546277 NM_005646 0 - +chr1 235277082 235277225 NM_014765 0 - +chr1 235318195 235318427 NM_001161533 0 - +chr1 235330209 235331967 NM_001206794 0 - +chr1 235335932 235336079 NM_031371 0 - +chr1 235377083 235377341 NM_016374 0 - +chr1 235383616 235383860 NM_001206794 0 - +chr1 235386480 235386575 NM_016374 0 - +chr1 235403627 235403766 NM_001206794 0 - +chr1 235599858 235599923 NM_001079515 0 + +chr1 236016299 236016360 NR_031718 0 - +chr1 236388369 236388439 NM_019891 0 - +chr1 236719399 236719558 NM_018072 0 - +chr1 236767721 236767841 NM_018072 0 - +chr1 236988637 236988699 NM_000254 0 + +chr1 236990128 236990196 NM_001291940 0 + +chr1 237001713 237001899 NM_001291939 0 + +chr1 237057656 237057857 NM_000254 0 + +chr1 237586391 237586548 NM_001035 0 + +chr1 237755038 237755153 NM_001035 0 + +chr1 237850754 237850804 NM_001035 0 + +chr1 237862264 237862325 NM_001035 0 + +chr1 240975217 240975343 NM_001282773 0 - +chr1 241033354 241033419 NM_002924 0 - +chr1 241146378 241146429 NM_001282775 0 - +chr1 241676902 241677013 NM_000143 0 - +chr1 242020646 242020784 NM_003686 0 + +chr1 242024707 242024804 NM_006027 0 + +chr1 242030131 242030357 NM_003686 0 + +chr1 243332929 243333056 NM_001042404 0 - +chr1 243716030 243716245 NM_005465 0 - +chr1 243776972 243777041 NM_005465 0 - +chr1 243776972 243777041 NM_001206729 0 - +chr1 244541864 244541941 NM_001276348 0 + +chr1 245025762 245025836 NM_031844 0 - +chr1 245912641 245912966 NM_022743 0 - +chr1 246805050 246805072 NM_152609 0 + +chr1 247020992 247021116 NM_015446 0 - +chr1 247108848 247109129 NR_037894 0 - +chr1 247108848 247109129 NR_037892 0 - +chr1 247473000 247473108 NM_032752 0 - +chr1 247586531 247586651 NM_001243133 0 + +chr1 247670359 247670535 NM_001281838 0 + +chr1 247693433 247695842 NM_198074 0 - +chr1 247701977 247702093 NM_001281834 0 + +chr1 247712346 247712522 NM_145278 0 + +chr1 249120033 249120154 NM_030645 0 - +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample3.bed.meta Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,4 @@ +ann_type exons +provider RefSeq +name RefSeqGeneExons +assembly hg19
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/select1.gmql_query Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,1 @@ +OUT = SELECT (grant == 'Stam') Example_Dataset_1 ;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/select2.gmql_query Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,1 @@ +OUT = SELECT (patient_age == '64' AND cell == '8988T'; region: score > 3) Example_Dataset_1 ;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/select3.gmql_query Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,2 @@ +OUT = SELECT (patient_age == '64' AND cell == '8988T'; region: score > 3) Example_Dataset_1 ; +OUT2 = SELECT (semijoin: cell IN OUT) Example_Dataset_2 ;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/union1.gmql_query Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,3 @@ +IN = SELECT () Example_Dataset_1 ; +IN2 = SELECT () Example_Dataset_2 ; +OUT = UNION () IN IN2;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/utilities.py Tue Jun 26 09:01:39 2018 -0400 @@ -0,0 +1,226 @@ +# Helper functions to perform REST calls on the GMQL server. +# ---------------------------------------------------------------------------- +# Luana Brancato, luana.brancato@mail.polimi.it +# ---------------------------------------------------------------------------- + +import sys +import os +import yaml +import requests + + +def load_parts(module, call) : + """Given the module and the single operation, returns the fragments for the url to call""" + + y_path = os.path.join(os.path.dirname(os.path.abspath(__file__)),'gmql_rest.yaml') + + with open(y_path,'r') as yamlf : + cfg = yaml.load(yamlf) + + parts = list () + + gmql = cfg['GMQL_URL'] + prefix = cfg[module]['prefix'] + op = cfg[module]['operations'][call] + + parts.append(gmql) + if prefix : + parts.append(prefix) + + for p in op : + parts.append(p) + + return parts + +def compose_url(module, call) : + """Given the fragments of a url, return the composite one""" + + parts = load_parts(module,call) + url = '/'.join(parts) + + return url + +def add_url_param(params, module, op, value,) : + """Given the params dict, add a new pair of key:value with the given value and the key set for given module and operation""" + + y_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'gmql_rest.yaml') + + with open(y_path, 'r') as yamlf: + cfg = yaml.load(yamlf) + yamlf.close() + + key = cfg[module]['params'][op] + + params.update({key : value}) + + return params + + +def read_token(input): + """It takes the tabular file with the information over the user + name authToken valid_flag + It checks if the user is still valid and extract the authToken for the REST calls""" + + with open(input,'r') as f_in : + user = f_in.readline().rstrip('\n').split('\t') + + if user[2] : + token = user[1] + else : + stop_err("This session is no longer valid") + + + return token + +def expire_user(input): + """Set the validity flag of a user token to false""" + + with open(input,'r') as f: + user = f.readline().rstrip('\n').split('\t') + + user[2] = False + + with open(input,'w') as f : + f.write('{fullName}\t{token}\t{valid}\n'.format(fullName=user[0], token=user[1], + valid=user[2])) + + +def get(url, user=None, response_type='json') : + """GET Request + :param url: url where to fetch the requested resource + :param user: for authenticated requests; if not provided make an unauthenticated request (es. for login) + :param response_type: type of the fetched response. + JSON ( Default ) + TEXT + ZIP + FILE + """ + + #Set request headers + headers = dict () + + if user : + headers.update({'X-AUTH-TOKEN' : read_token(user)}) + + if response_type == 'text' : + headers.update({'Accept' : 'text/plain'}) + elif response_type == 'zip' : + pass + elif response_type == 'file' : + headers.update({'Accept' : 'file'}) + else : + headers.update({'Accept' : 'application/json'}) + + + #Make the request + response = requests.get(url, headers=headers) + + #Check returned server status + status_code = response.status_code + + #Read result. If Server OK, read according to response_type. Raise an error otherwise. + if status_code == requests.codes.ok : + if response_type == 'json' : + return response.json() + elif response_type == 'text' : + return response.text + else : + return response + elif status_code == requests.codes.unauthorized : + expire_user(user) + stop_err("You are not authorized to do this. \nPlease login first.") + elif status_code == requests.codes.not_found : + stop_err("Resource not found for this user.") + else : + stop_err("Error {code}: {reason}\n{message}".format(code=status_code, + reason=response.reason, + message=response.content)) + + +def post(url, payload, user=None, params=None, content_type='json', response_type='json') : + """ POST Request + :param url: url where to post data + :param payload: payload for the post request. Type is specified by content_type. + :param user: for authenticated requests; if not provided make an unauthenticated request (es. for registration) + :param params: optional query parameters + :param content_type + :param response_type: Default is json + """ + + + # Set request headers + headers = dict() + + if user: + headers.update({'X-AUTH-TOKEN': read_token(user)}) + + headers.update({'Accept': 'application/json'}) + + if content_type == 'text' : + headers.update({'Content-Type' : 'text/plain'}) + response = requests.post(url, params=params, headers=headers, data=payload) + elif content_type == 'multiform' : + response = requests.post(url, params=params, headers=headers, files=payload) + else : + headers.update({'Content-Type': 'application/json'}) + response = requests.post(url, params=params, headers=headers, json=payload) + + # Check returned server status + status_code = response.status_code + + + if status_code == requests.codes.ok : + return response.json() + elif status_code == requests.codes.unauthorized : + content = response.content + if content.__contains__("The username or password you entered don't match") : + stop_err("The username or password you entered don't match") + else: + expire_user(user) + stop_err("You are not authorized to do this. \nPlease login first.") + else : + stop_err("Error {code}: {reason}\n{message}".format(code=status_code, + reason=response.reason, + message=response.content)) + + + +def delete(url, user=None, response_type='json') : + """DELETE request + :param url: url where to post data + :param user: for authenticated requests; if not provided make an unauthenticated request (es. for registration) + :param response_type: Default is json + """ + + # Set request headers + headers = dict() + + if user: + headers.update({'X-AUTH-TOKEN': read_token(user)}) + + headers.update({'Accept': 'application/json'}) + + #Make the request + response = requests.delete(url, headers=headers) + + #Check returned server status + status_code = response.status_code + + + #If Server OK, read result. Raise an error otherwise. + if status_code == requests.codes.ok : + return response.json() + elif status_code == requests.codes.unauthorized : + expire_user(user) + stop_err("You are not authorized to do this. \nPlease login first.") + elif status_code == requests.codes.not_found : + stop_err("Resource not found for this user.") + else : + stop_err("Error {code}: {reason}".format(code=status_code, + reason=response.reason)) + + + +def stop_err(msg): + sys.stderr.write("%s\n" % msg) + sys.exit()