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/microSALT/cli.py

"""This is the main entry point of microSALT.
By: Isak Sylvin, @sylvinite"""

#!/usr/bin/env python

import json
import logging
import os
import sys

import click

from microSALT import __version__, logging_levels, preset_config
from microSALT.utils.job_creator import Job_Creator
from microSALT.utils.referencer import Referencer
from microSALT.utils.reporter import Reporter
from microSALT.utils.scraper import Scraper

default_sampleinfo = {
    "CG_ID_project": "XXX0000",
    "CG_ID_sample": "XXX0000A1",
    "Customer_ID_project": "100100",
    "Customer_ID_sample": "10XY123456",
    "Customer_ID": "cust000",
    "application_tag": "SOMTIN100",
    "date_arrival": "0001-01-01 00:00:00",
    "date_libprep": "0001-01-01 00:00:00",
    "date_sequencing": "0001-01-01 00:00:00",
    "method_libprep": "Not in LIMS",
    "method_sequencing": "Not in LIMS",
    "organism": "Staphylococcus aureus",
    "priority": "standard",
    "reference": "None",
}

logger = logging.getLogger("main_logger")

if preset_config == "":
    click.echo(
        "ERROR - No properly set-up config under neither envvar MICROSALT_CONFIG nor ~/.microSALT/config.json. Exiting."
    )
    sys.exit(-1)


@click.pass_context
def set_cli_config(ctx, config):
    if config != "":
        if os.path.exists(config):
            try:
                t = ctx.obj["config"]
                with open(os.path.abspath(config), "r") as conf:
                    ctx.obj["config"] = json.load(conf)
                ctx.obj["config"]["folders"]["expec"] = t["folders"]["expec"]
                ctx.obj["config"]["folders"]["adapters"] = t["folders"]["adapters"]
                ctx.obj["config"]["config_path"] = os.path.abspath(config)
            except Exception:
                pass


def done():
    click.echo("INFO - Execution finished!")
    logger.debug("INFO - Execution finished!")


def review_sampleinfo(pfile):
    """Reviews sample info. Returns loaded json object"""

    try:
        with open(pfile) as json_file:
            data = json.load(json_file)
    except Exception:
        click.echo("Unable to read provided sample info file as json. Exiting..")
        sys.exit(-1)

    if isinstance(data, list):
        for entry in data:
            for k, v in default_sampleinfo.items():
                if k not in entry:
                    click.echo(
                        "WARNING - Parameter {} needs to be provided in sample json. Formatting example: ({})".format(
                            k, v
                        )
                    )
    else:
        for k, v in default_sampleinfo.items():
            if k not in data:
                click.echo(
                    "WARNING - Parameter {} needs to be provided in sample json. Formatting example: ({})".format(
                        k, v
                    )
                )
    return data


@click.group()
@click.version_option(__version__)
@click.option(
    "--logging-level",
    default="INFO",
    type=click.Choice(list(logging_levels.keys())),
    help="Set the logging level for the CLI",
)
@click.pass_context
def root(ctx, logging_level):
    """microbial Sequence Analysis and Loci-based Typing (microSALT) pipeline"""
    ctx.obj = {}
    ctx.obj["config"] = preset_config
    logger.setLevel(logging_levels[logging_level])
    for handler in logger.handlers:
        handler.setLevel(logging_levels[logging_level])
    logger.debug(f"Setting logging level to {logging_levels[logging_level]}")


@root.command()
@click.argument("sampleinfo_file")
@click.option("--input", help="Full path to input folder", default="")
@click.option("--config", help="microSALT config to override default", default="")
@click.option(
    "--dry",
    help="Builds instance without posting to SLURM",
    default=False,
    is_flag=True,
)
@click.option(
    "--email",
    default=preset_config["regex"]["mail_recipient"],
    help="Forced e-mail recipient",
)
@click.option("--skip_update", default=False, help="Skips downloading of references", is_flag=True)
@click.option(
    "--force_update",
    default=False,
    help="Forces downloading of pubMLST references",
    is_flag=True,
)
@click.option("--untrimmed", help="Use untrimmed input data", default=False, is_flag=True)
@click.pass_context
def analyse(
    ctx,
    sampleinfo_file,
    input,
    config,
    dry,
    email,
    skip_update,
    force_update,
    untrimmed,
):
    """Sequence analysis, typing and resistance identification"""
    # Run section
    pool = []
    trimmed = not untrimmed
    set_cli_config(config)
    ctx.obj["config"]["regex"]["mail_recipient"] = email
    ctx.obj["config"]["dry"] = dry
    if not os.path.isdir(input):
        click.echo("ERROR - Sequence data folder {} does not exist.".format(input))
        ctx.abort()
    for subfolder in os.listdir(input):
        if os.path.isdir("{}/{}".format(input, subfolder)):
            pool.append(subfolder)

    run_settings = {
        "input": input,
        "dry": dry,
        "email": email,
        "skip_update": skip_update,
        "trimmed": not untrimmed,
        "pool": pool,
    }

    # Samples section
    sampleinfo = review_sampleinfo(sampleinfo_file)
    run_creator = Job_Creator(
        config=ctx.obj["config"],
        log=logger,
        sampleinfo=sampleinfo,
        run_settings=run_settings,
    )

    ext_refs = Referencer(
        config=ctx.obj["config"],
        log=logger,
        sampleinfo=sampleinfo,
        force=force_update,
    )
    click.echo("INFO - Checking versions of references..")
    try:
        if not skip_update:
            ext_refs.identify_new(project=True)
            ext_refs.update_refs()
            click.echo("INFO - Version check done. Creating sbatch jobs")
        else:
            click.echo("INFO - Skipping version check.")
    except Exception as e:
        click.echo("{}".format(e))
    if len(sampleinfo) > 1:
        run_creator.project_job()
    elif len(sampleinfo) == 1:
        run_creator.project_job(single_sample=True)
    else:
        ctx.abort()

    done()


@root.group()
@click.pass_context
def utils(ctx):
    """Utilities for specific purposes"""
    pass


@utils.group()
@click.pass_context
def refer(ctx):
    """Manipulates MLST organisms"""
    pass


@utils.command()
@click.argument("sampleinfo_file")
@click.option("--input", help="Full path to project folder", default="")
@click.option(
    "--track",
    help="Run a specific analysis track",
    default="default",
    type=click.Choice(["default", "typing", "qc", "cgmlst"]),
)
@click.option("--config", help="microSALT config to override default", default="")
@click.option(
    "--dry",
    help="Builds instance without posting to SLURM",
    default=False,
    is_flag=True,
)
@click.option(
    "--email",
    default=preset_config["regex"]["mail_recipient"],
    help="Forced e-mail recipient",
)
@click.option("--skip_update", default=False, help="Skips downloading of references", is_flag=True)
@click.option(
    "--report",
    default="default",
    type=click.Choice(["default", "typing", "motif_overview", "qc", "json_dump", "st_update"]),
)
@click.option("--output", help="Report output folder", default="")
@click.pass_context
def finish(ctx, sampleinfo_file, input, track, config, dry, email, skip_update, report, output):
    """Sequence analysis, typing and resistance identification"""
    # Run section
    pool = []
    set_cli_config(config)
    ctx.obj["config"]["regex"]["mail_recipient"] = email
    ctx.obj["config"]["dry"] = dry
    if not os.path.isdir(input):
        click.echo("ERROR - Sequence data folder {} does not exist.".format(input))
        ctx.abort()
    if output == "":
        output = input
    for subfolder in os.listdir(input):
        if os.path.isdir("{}/{}".format(input, subfolder)):
            pool.append(subfolder)

    run_settings = {
        "input": input,
        "track": track,
        "dry": dry,
        "email": email,
        "skip_update": skip_update,
    }

    # Samples section
    sampleinfo = review_sampleinfo(sampleinfo_file)
    ext_refs = Referencer(config=ctx.obj["config"], log=logger, sampleinfo=sampleinfo)
    click.echo("INFO - Checking versions of references..")
    try:
        if not skip_update:
            ext_refs.identify_new(project=True)
            ext_refs.update_refs()
            click.echo("INFO - Version check done. Creating sbatch jobs")
        else:
            click.echo("INFO - Skipping version check.")
    except Exception as e:
        click.echo("{}".format(e))

    res_scraper = Scraper(config=ctx.obj["config"], log=logger, sampleinfo=sampleinfo, input=input)
    if isinstance(sampleinfo, list) and len(sampleinfo) > 1:
        res_scraper.scrape_project()
        # for subfolder in pool:
        #  res_scraper.scrape_sample()
    else:
        res_scraper.scrape_sample()

    codemonkey = Reporter(
        config=ctx.obj["config"],
        log=logger,
        sampleinfo=sampleinfo,
        output=output,
        collection=True,
    )
    codemonkey.report(report)
    done()


@refer.command()
@click.argument("organism")
@click.option("--force", help="Redownloads existing organism", default=False, is_flag=True)
@click.pass_context
def add(ctx, organism, force):
    """Adds a new internal organism from pubMLST"""
    referee = Referencer(config=ctx.obj["config"], log=logger, force=force)
    try:
        referee.add_pubmlst(organism)
    except Exception as e:
        click.echo(e.args[0])
        ctx.abort()
    click.echo("INFO - Checking versions of all references..")
    referee = Referencer(config=ctx.obj["config"], log=logger, force=force)
    referee.update_refs()


@refer.command()
@click.pass_context
def observe(ctx):
    """Lists all stored organisms"""
    refe = Referencer(config=ctx.obj["config"], log=logger)
    click.echo("INFO - Currently stored organisms:")
    for org in sorted(refe.existing_organisms()):
        click.echo(org.replace("_", " ").capitalize())


@utils.command()
@click.argument("sampleinfo_file")
@click.option(
    "--email",
    default=preset_config["regex"]["mail_recipient"],
    help="Forced e-mail recipient",
)
@click.option(
    "--type",
    default="default",
    type=click.Choice(["default", "typing", "motif_overview", "qc", "json_dump", "st_update"]),
)
@click.option("--output", help="Full path to output folder", default="")
@click.option("--collection", default=False, is_flag=True)
@click.pass_context
def report(ctx, sampleinfo_file, email, type, output, collection):
    """Re-generates report for a project"""
    ctx.obj["config"]["regex"]["mail_recipient"] = email
    sampleinfo = review_sampleinfo(sampleinfo_file)
    codemonkey = Reporter(
        config=ctx.obj["config"],
        log=logger,
        sampleinfo=sampleinfo,
        output=output,
        collection=collection,
    )
    codemonkey.report(type)
    done()


@utils.command()
@click.pass_context
def view(ctx):
    """Starts an interactive webserver for viewing"""
    codemonkey = Reporter(config=ctx.obj["config"], log=logger)
    codemonkey.start_web()


@utils.command()
@click.option("--input", help="Full path to project folder", default=os.getcwd())
@click.pass_context
def generate(ctx, input):
    """Creates a blank sample info json for the given input folder"""
    input = os.path.abspath(input)
    project_name = os.path.basename(input)

    defaults = default_sampleinfo.copy()

    pool = []
    if not os.path.isdir(input):
        click.echo("ERROR - Sequence data folder {} does not exist.".format(project_name))
        ctx.abort()
    elif input != os.getcwd():
        for subfolder in os.listdir(input):
            if os.path.isdir("{}/{}".format(input, subfolder)):
                pool.append(defaults.copy())
                pool[-1]["CG_ID_project"] = project_name
                pool[-1]["CG_ID_sample"] = subfolder
    else:
        project_name = "default_sample_info"
        pool.append(defaults.copy())

    with open("{}/{}.json".format(os.getcwd(), project_name), "w") as output:
        json.dump(pool, output, indent=2)
    click.echo("INFO - Created {}.json in current folder".format(project_name))
    done()


@utils.group()
@click.pass_context
def resync(ctx):
    """Updates internal ST with pubMLST equivalent"""


@resync.command()
@click.option(
    "--type",
    default="list",
    type=click.Choice(["report", "list"]),
    help="Output format",
)
@click.option("--customer", default="all", help="Customer id filter")
@click.option("--skip_update", default=False, help="Skips downloading of references", is_flag=True)
@click.option(
    "--email",
    default=preset_config["regex"]["mail_recipient"],
    help="Forced e-mail recipient",
)
@click.option("--output", help="Full path to output folder", default="")
@click.pass_context
def review(ctx, type, customer, skip_update, email, output):
    """Generates information about novel ST"""
    # Trace exists by some samples having pubMLST_ST filled in. Make trace function later
    ctx.obj["config"]["regex"]["mail_recipient"] = email
    ext_refs = Referencer(config=ctx.obj["config"], log=logger)
    if not skip_update:
        ext_refs.update_refs()
        ext_refs.resync()
    click.echo("INFO - Version check done. Generating output")
    if type == "report":
        codemonkey = Reporter(config=ctx.obj["config"], log=logger, output=output)
        codemonkey.report(type="st_update", customer=customer)
    elif type == "list":
        ext_refs.resync(type=type)
    done()


@resync.command()
@click.option("--force-update", default=False, is_flag=True, help="Forces update")
@click.pass_context
def update_refs(ctx, force_update: bool):
    """Updates all references"""
    ext_refs = Referencer(config=ctx.obj["config"], log=logger, force=force_update)
    ext_refs.update_refs()
    done()


@resync.command()
@click.option("--force-update", default=False, is_flag=True, help="Forces update")
@click.pass_context
def update_from_static(ctx, force_update: bool):
    """Updates a specific organism"""
    ext_refs = Referencer(config=ctx.obj["config"], force=force_update, log=logger)
    ext_refs.fetch_external()
    done()


@resync.command()
@click.argument("organism")
@click.option("--force-update", default=False, is_flag=True, help="Forces update")
@click.option("--external", is_flag=True, default=False, help="Updates from external sources")
@click.pass_context
def update_organism(ctx, external: bool, force_update: bool, organism: str):
    """Updates a specific organism"""
    ext_refs = Referencer(config=ctx.obj["config"], log=logger, force=force_update)
    ext_refs.update_organism(external=external, organism=organism)
    done()


@resync.command()
@click.argument("sample_name")
@click.option(
    "--force",
    default=False,
    is_flag=True,
    help="Resolves sample without checking for pubMLST match",
)
@click.pass_context
def overwrite(ctx, sample_name, force):
    """Flags sample as resolved"""
    ext_refs = Referencer(config=ctx.obj["config"], log=logger)
    ext_refs.resync(type="overwrite", sample=sample_name, ignore=force)
    done()

1	"""This is the main entry point of microSALT.
2	By: Isak Sylvin, @sylvinite"""
3
4	#!/usr/bin/env python
5
6	import json	1✔
7	import logging	1✔
8	import os	1✔
9	import sys	1✔
10		1✔
11	import click	1✔
12		1✔
13	from microSALT import __version__, logging_levels, preset_config
14	from microSALT.utils.job_creator import Job_Creator	1✔
15	from microSALT.utils.referencer import Referencer	1✔
16	from microSALT.utils.reporter import Reporter	1✔
17	from microSALT.utils.scraper import Scraper	1✔
18		1✔
19	default_sampleinfo = {	1✔
20	"CG_ID_project": "XXX0000",
21	"CG_ID_sample": "XXX0000A1",	1✔
22	"Customer_ID_project": "100100",
23	"Customer_ID_sample": "10XY123456",
24	"Customer_ID": "cust000",
25	"application_tag": "SOMTIN100",
26	"date_arrival": "0001-01-01 00:00:00",
27	"date_libprep": "0001-01-01 00:00:00",
28	"date_sequencing": "0001-01-01 00:00:00",
29	"method_libprep": "Not in LIMS",
30	"method_sequencing": "Not in LIMS",
31	"organism": "Staphylococcus aureus",
32	"priority": "standard",
33	"reference": "None",
34	}
35
36	logger = logging.getLogger("main_logger")
37
38	if preset_config == "":
39	click.echo(	1✔
40	"ERROR - No properly set-up config under neither envvar MICROSALT_CONFIG nor ~/.microSALT/config.json. Exiting."	×
41	)
42	sys.exit(-1)
43		×
44
45	@click.pass_context
46	def set_cli_config(ctx, config):	1✔
47	if config != "":
48	if os.path.exists(config):	×
49	try:	×
50	t = ctx.obj["config"]	×
51	with open(os.path.abspath(config), "r") as conf:	×
52	ctx.obj["config"] = json.load(conf)	×
53	ctx.obj["config"]["folders"]["expec"] = t["folders"]["expec"]	×
54	ctx.obj["config"]["folders"]["adapters"] = t["folders"]["adapters"]	×
55	ctx.obj["config"]["config_path"] = os.path.abspath(config)	×
56	except Exception:	×
57	pass	×
58		×
59
60	def done():
61	click.echo("INFO - Execution finished!")	1✔
62	logger.debug("INFO - Execution finished!")	×
63		×
64
65	def review_sampleinfo(pfile):
66	"""Reviews sample info. Returns loaded json object"""	1✔
67
68	try:
69	with open(pfile) as json_file:	×
70	data = json.load(json_file)	×
71	except Exception:	×
72	click.echo("Unable to read provided sample info file as json. Exiting..")	×
73	sys.exit(-1)	×
74		×
75	if isinstance(data, list):
76	for entry in data:	×
77	for k, v in default_sampleinfo.items():	×
78	if k not in entry:	×
79	click.echo(	×
80	"WARNING - Parameter {} needs to be provided in sample json. Formatting example: ({})".format(	×
81	k, v
82	)
83	)
84	else:
85	for k, v in default_sampleinfo.items():
86	if k not in data:	×
87	click.echo(	×
88	"WARNING - Parameter {} needs to be provided in sample json. Formatting example: ({})".format(	×
89	k, v
90	)
91	)
92	return data
93		×
94
95	@click.group()
96	@click.version_option(__version__)	1✔
97	@click.option(	1✔
98	"--logging-level",	1✔
99	default="INFO",
100	type=click.Choice(list(logging_levels.keys())),
101	help="Set the logging level for the CLI",
102	)
103	@click.pass_context
104	def root(ctx, logging_level):	1✔
105	"""microbial Sequence Analysis and Loci-based Typing (microSALT) pipeline"""
106	ctx.obj = {}
107	ctx.obj["config"] = preset_config	×
108	logger.setLevel(logging_levels[logging_level])	×
109	for handler in logger.handlers:	×
110	handler.setLevel(logging_levels[logging_level])	×
111	logger.debug(f"Setting logging level to {logging_levels[logging_level]}")	×
112
113
114	@root.command()	1✔
115	@click.argument("sampleinfo_file")	1✔
116	@click.option("--input", help="Full path to input folder", default="")	1✔
117	@click.option("--config", help="microSALT config to override default", default="")	1✔
118	@click.option(	1✔
119	"--dry",
120	help="Builds instance without posting to SLURM",
121	default=False,
122	is_flag=True,
123	)
124	@click.option(	1✔
125	"--email",
126	default=preset_config["regex"]["mail_recipient"],
127	help="Forced e-mail recipient",
128	)
129	@click.option("--skip_update", default=False, help="Skips downloading of references", is_flag=True)	1✔
130	@click.option(	1✔
131	"--force_update",
132	default=False,
133	help="Forces downloading of pubMLST references",
134	is_flag=True,
135	)
136	@click.option("--untrimmed", help="Use untrimmed input data", default=False, is_flag=True)	1✔
137	@click.pass_context	1✔
138	def analyse(
139	ctx,
140	sampleinfo_file,
141	input,
142	config,
143	dry,
144	email,
145	skip_update,
146	force_update,
147	untrimmed,
148	):
149	"""Sequence analysis, typing and resistance identification"""
150	# Run section
151	pool = []	×
152	trimmed = not untrimmed	×
153	set_cli_config(config)	×
154	ctx.obj["config"]["regex"]["mail_recipient"] = email	×
155	ctx.obj["config"]["dry"] = dry	×
156	if not os.path.isdir(input):	×
157	click.echo("ERROR - Sequence data folder {} does not exist.".format(input))	×
158	ctx.abort()	×
159	for subfolder in os.listdir(input):	×
160	if os.path.isdir("{}/{}".format(input, subfolder)):	×
161	pool.append(subfolder)	×
162
163	run_settings = {	×
164	"input": input,
165	"dry": dry,
166	"email": email,
167	"skip_update": skip_update,
168	"trimmed": not untrimmed,
169	"pool": pool,
170	}
171
172	# Samples section
173	sampleinfo = review_sampleinfo(sampleinfo_file)	×
174	run_creator = Job_Creator(	×
175	config=ctx.obj["config"],
176	log=logger,
177	sampleinfo=sampleinfo,
178	run_settings=run_settings,
179	)
180
181	ext_refs = Referencer(	×
182	config=ctx.obj["config"],
183	log=logger,
184	sampleinfo=sampleinfo,
185	force=force_update,
186	)
187	click.echo("INFO - Checking versions of references..")	×
188	try:	×
189	if not skip_update:	×
190	ext_refs.identify_new(project=True)	×
191	ext_refs.update_refs()	×
192	click.echo("INFO - Version check done. Creating sbatch jobs")	×
193	else:
194	click.echo("INFO - Skipping version check.")	×
195	except Exception as e:	×
196	click.echo("{}".format(e))	×
197	if len(sampleinfo) > 1:	×
198	run_creator.project_job()	×
199	elif len(sampleinfo) == 1:	×
200	run_creator.project_job(single_sample=True)	×
201	else:
202	ctx.abort()	×
203
204	done()	×
205
206
207	@root.group()	1✔
208	@click.pass_context	1✔
209	def utils(ctx):
210	"""Utilities for specific purposes"""
211	pass	×
212
213
214	@utils.group()	1✔
215	@click.pass_context	1✔
216	def refer(ctx):
217	"""Manipulates MLST organisms"""
218	pass	×
219
220
221	@utils.command()	1✔
222	@click.argument("sampleinfo_file")	1✔
223	@click.option("--input", help="Full path to project folder", default="")	1✔
224	@click.option(	1✔
225	"--track",
226	help="Run a specific analysis track",
227	default="default",
228	type=click.Choice(["default", "typing", "qc", "cgmlst"]),
229	)
230	@click.option("--config", help="microSALT config to override default", default="")	1✔
231	@click.option(	1✔
232	"--dry",
233	help="Builds instance without posting to SLURM",
234	default=False,
235	is_flag=True,
236	)
237	@click.option(	1✔
238	"--email",
239	default=preset_config["regex"]["mail_recipient"],
240	help="Forced e-mail recipient",
241	)
242	@click.option("--skip_update", default=False, help="Skips downloading of references", is_flag=True)	1✔
243	@click.option(	1✔
244	"--report",
245	default="default",
246	type=click.Choice(["default", "typing", "motif_overview", "qc", "json_dump", "st_update"]),
247	)
248	@click.option("--output", help="Report output folder", default="")	1✔
249	@click.pass_context	1✔
250	def finish(ctx, sampleinfo_file, input, track, config, dry, email, skip_update, report, output):
251	"""Sequence analysis, typing and resistance identification"""
252	# Run section
253	pool = []	×
254	set_cli_config(config)	×
255	ctx.obj["config"]["regex"]["mail_recipient"] = email	×
256	ctx.obj["config"]["dry"] = dry	×
257	if not os.path.isdir(input):	×
258	click.echo("ERROR - Sequence data folder {} does not exist.".format(input))	×
259	ctx.abort()	×
260	if output == "":	×
261	output = input	×
262	for subfolder in os.listdir(input):	×
263	if os.path.isdir("{}/{}".format(input, subfolder)):	×
264	pool.append(subfolder)	×
265
266	run_settings = {	×
267	"input": input,
268	"track": track,
269	"dry": dry,
270	"email": email,
271	"skip_update": skip_update,
272	}
273
274	# Samples section
275	sampleinfo = review_sampleinfo(sampleinfo_file)	×
276	ext_refs = Referencer(config=ctx.obj["config"], log=logger, sampleinfo=sampleinfo)	×
277	click.echo("INFO - Checking versions of references..")	×
278	try:	×
279	if not skip_update:	×
280	ext_refs.identify_new(project=True)	×
281	ext_refs.update_refs()	×
282	click.echo("INFO - Version check done. Creating sbatch jobs")	×
283	else:
284	click.echo("INFO - Skipping version check.")	×
285	except Exception as e:	×
286	click.echo("{}".format(e))	×
287
288	res_scraper = Scraper(config=ctx.obj["config"], log=logger, sampleinfo=sampleinfo, input=input)	×
289	if isinstance(sampleinfo, list) and len(sampleinfo) > 1:
290	res_scraper.scrape_project()
291	# for subfolder in pool:	×
292	# res_scraper.scrape_sample()	×
293	else:
294	res_scraper.scrape_sample()
295
296	codemonkey = Reporter(	×
297	config=ctx.obj["config"],
298	log=logger,	×
299	sampleinfo=sampleinfo,
300	output=output,
301	collection=True,
302	)
303	codemonkey.report(report)
304	done()
305		×
306		×
307	@refer.command()
308	@click.argument("organism")
309	@click.option("--force", help="Redownloads existing organism", default=False, is_flag=True)	1✔
310	@click.pass_context	1✔
311	def add(ctx, organism, force):	1✔
312	"""Adds a new internal organism from pubMLST"""	1✔
313	referee = Referencer(config=ctx.obj["config"], log=logger, force=force)
314	try:
315	referee.add_pubmlst(organism)	×
316	except Exception as e:	×
317	click.echo(e.args[0])	×
318	ctx.abort()	×
319	click.echo("INFO - Checking versions of all references..")	×
320	referee = Referencer(config=ctx.obj["config"], log=logger, force=force)	×
321	referee.update_refs()	×
322		×
323		×
324	@refer.command()
325	@click.pass_context
326	def observe(ctx):	1✔
327	"""Lists all stored organisms"""	1✔
328	refe = Referencer(config=ctx.obj["config"], log=logger)
329	click.echo("INFO - Currently stored organisms:")
330	for org in sorted(refe.existing_organisms()):	×
331	click.echo(org.replace("_", " ").capitalize())	×
332		×
333		×
334	@utils.command()
335	@click.argument("sampleinfo_file")
336	@click.option(	1✔
337	"--email",	1✔
338	default=preset_config["regex"]["mail_recipient"],	1✔
339	help="Forced e-mail recipient",
340	)
341	@click.option(
342	"--type",
343	default="default",	1✔
344	type=click.Choice(["default", "typing", "motif_overview", "qc", "json_dump", "st_update"]),
345	)
346	@click.option("--output", help="Full path to output folder", default="")
347	@click.option("--collection", default=False, is_flag=True)
348	@click.pass_context	1✔
349	def report(ctx, sampleinfo_file, email, type, output, collection):	1✔
350	"""Re-generates report for a project"""	1✔
351	ctx.obj["config"]["regex"]["mail_recipient"] = email
352	sampleinfo = review_sampleinfo(sampleinfo_file)
353	codemonkey = Reporter(	×
354	config=ctx.obj["config"],	×
355	log=logger,	×
356	sampleinfo=sampleinfo,
357	output=output,
358	collection=collection,
359	)
360	codemonkey.report(type)
361	done()
362		×
363		×
364	@utils.command()
365	@click.pass_context
366	def view(ctx):	1✔
367	"""Starts an interactive webserver for viewing"""	1✔
368	codemonkey = Reporter(config=ctx.obj["config"], log=logger)
369	codemonkey.start_web()
370		×
371		×
372	@utils.command()
373	@click.option("--input", help="Full path to project folder", default=os.getcwd())
374	@click.pass_context	1✔
375	def generate(ctx, input):	1✔
376	"""Creates a blank sample info json for the given input folder"""	1✔
377	input = os.path.abspath(input)
378	project_name = os.path.basename(input)
379		×
380	defaults = default_sampleinfo.copy()	×
381
382	pool = []	×
383	if not os.path.isdir(input):
384	click.echo("ERROR - Sequence data folder {} does not exist.".format(project_name))	×
385	ctx.abort()	×
386	elif input != os.getcwd():	×
387	for subfolder in os.listdir(input):	×
388	if os.path.isdir("{}/{}".format(input, subfolder)):	×
389	pool.append(defaults.copy())	×
390	pool[-1]["CG_ID_project"] = project_name	×
391	pool[-1]["CG_ID_sample"] = subfolder	×
392	else:	×
393	project_name = "default_sample_info"	×
394	pool.append(defaults.copy())
395		×
396	with open("{}/{}.json".format(os.getcwd(), project_name), "w") as output:	×
397	json.dump(pool, output, indent=2)
398	click.echo("INFO - Created {}.json in current folder".format(project_name))	×
399	done()	×
400		×
401		×
402	@utils.group()
403	@click.pass_context
404	def resync(ctx):	1✔
405	"""Updates internal ST with pubMLST equivalent"""	1✔
406
407
408	@resync.command()
409	@click.option(
410	"--type",	1✔
411	default="list",	1✔
412	type=click.Choice(["report", "list"]),
413	help="Output format",
414	)
415	@click.option("--customer", default="all", help="Customer id filter")
416	@click.option("--skip_update", default=False, help="Skips downloading of references", is_flag=True)
417	@click.option(	1✔
418	"--email",	1✔
419	default=preset_config["regex"]["mail_recipient"],	1✔
420	help="Forced e-mail recipient",
421	)
422	@click.option("--output", help="Full path to output folder", default="")
423	@click.pass_context
424	def review(ctx, type, customer, skip_update, email, output):	1✔
425	"""Generates information about novel ST"""	1✔
426	# Trace exists by some samples having pubMLST_ST filled in. Make trace function later
427	ctx.obj["config"]["regex"]["mail_recipient"] = email
428	ext_refs = Referencer(config=ctx.obj["config"], log=logger)
429	if not skip_update:	×
430	ext_refs.update_refs()	×
431	ext_refs.resync()	×
432	click.echo("INFO - Version check done. Generating output")	×
433	if type == "report":	×
434	codemonkey = Reporter(config=ctx.obj["config"], log=logger, output=output)	×
435	codemonkey.report(type="st_update", customer=customer)	×
436	elif type == "list":	×
437	ext_refs.resync(type=type)	×
438	done()	×
439		×
440		×
441	@resync.command()
442	@click.option("--force-update", default=False, is_flag=True, help="Forces update")
443	@click.pass_context	1✔
444	def update_refs(ctx, force_update: bool):	1✔
445	"""Updates all references"""	1✔
446	ext_refs = Referencer(config=ctx.obj["config"], log=logger, force=force_update)	1✔
447	ext_refs.update_refs()
448	done()	×
449		×
450		×
451	@resync.command()
452	@click.option("--force-update", default=False, is_flag=True, help="Forces update")
453	@click.pass_context	1✔
454	def update_from_static(ctx, force_update: bool):	1✔
455	"""Updates a specific organism"""	1✔
456	ext_refs = Referencer(config=ctx.obj["config"], force=force_update, log=logger)	1✔
457	ext_refs.fetch_external()
458	done()	×
459		×
460		×
461	@resync.command()
462	@click.argument("organism")
463	@click.option("--force-update", default=False, is_flag=True, help="Forces update")	1✔
464	@click.option("--external", is_flag=True, default=False, help="Updates from external sources")	1✔
465	@click.pass_context	1✔
466	def update_organism(ctx, external: bool, force_update: bool, organism: str):	1✔
467	"""Updates a specific organism"""	1✔
468	ext_refs = Referencer(config=ctx.obj["config"], log=logger, force=force_update)	1✔
469	ext_refs.update_organism(external=external, organism=organism)
470	done()	×
471		×
472		×
473	@resync.command()
474	@click.argument("sample_name")
475	@click.option(	1✔
476	"--force",	1✔
477	default=False,	1✔
478	is_flag=True,
479	help="Resolves sample without checking for pubMLST match",
480	)
481	@click.pass_context
482	def overwrite(ctx, sample_name, force):
483	"""Flags sample as resolved"""	1✔
484	ext_refs = Referencer(config=ctx.obj["config"], log=logger)
485	ext_refs.resync(type="overwrite", sample=sample_name, ignore=force)
486	done()	×

Clinical-Genomics / microSALT / #359

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