#240

Committed 31 Jul 2024 01:38PM UTC coverage: 75.808% (-6.0%) from 81.849%

Build # #240

Build Type

Pull #165

travis-ci

Committed by

karlnyr

Commit Message

remove bad tests

Pull Request Pull Request #165: Use of --isolate flag, and update of SPAdes assembler

Run Details

5 of 11 new or added lines in 3 files covered. (45.45%)

155 existing lines in 3 files now uncovered.

1993 of 2629 relevant lines covered (75.81%)

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Source File
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72.53

/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 validate_assembly_mode(ctx, param, value):
    allowed_values = ["careful", "isolate"]
    if value not in allowed_values:
        raise click.BadParameter(
            f"Invalid value: {value}. Allowed values are {', '.join(allowed_values)}"
        )
    return value


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

Clinical-Genomics / microSALT / #240

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