#265

Committed 30 Oct 2024 01:20PM UTC coverage: 76.105% (-6.0%) from 82.069%

Build # #265

Build Type

push

travis-ci

Committed by

web-flow

Commit Message

Merge pull request #178 from Clinical-Genomics/rc400 (major)

### Added 

- Release candidate microSALT 4.0.0

Run Details

8 of 16 new or added lines in 4 files covered. (50.0%)

260 existing lines in 5 files now uncovered.

1997 of 2624 relevant lines covered (76.11%)

0.76 hits per line

Source File
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73.57

/microSALT/cli.py

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

#!/usr/bin/env python

import click
import json
import os
import re
import subprocess
import sys
import yaml

from pkg_resources import iter_entry_points
from microSALT import __version__, preset_config, logger, wd
from microSALT.utils.scraper import Scraper
from microSALT.utils.job_creator import Job_Creator
from microSALT.utils.reporter import Reporter
from microSALT.utils.referencer import Referencer

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",
}


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 as e:
                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 as e:
        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 not k 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 not k 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.pass_context
def root(ctx):
    """microbial Sequence Analysis and Loci-based Typing (microSALT) pipeline"""
    ctx.obj = {}
    ctx.obj["config"] = preset_config
    ctx.obj["log"] = logger


@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=ctx.obj["log"],
        sampleinfo=sampleinfo,
        run_settings=run_settings,
    )

    ext_refs = Referencer(
        config=ctx.obj["config"],
        log=ctx.obj["log"],
        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=ctx.obj["log"], 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=ctx.obj["log"], 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=ctx.obj["log"],
        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=ctx.obj["log"], 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=ctx.obj["log"], force=force)
    referee.update_refs()


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

Clinical-Genomics / microSALT / #265

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