def test_valid_args(tmp_environ):
if os.path.isdir("pairef_valid_args"):
# Preparation - clean rests from previously examined test that
# has been interrupted
shutil.rmtree("pairef_valid_args")
arguments = "--HKLIN " + str(config("mdm2_merged.mtz")) + \
" --XYZIN " + str(config("mdm2_1-60A.pdb")) + \
" -i 1.6" + \
" -r " + RES_SHELLS_GOOD + \
" -p valid_args" + \
" -t"
cp = run(arguments)
expected_stdout_1 = """
__ _ ___ __ ___ ___
)_) /_) ) )_) )_ )_
/ / / _(_ / \ (__ (
automatic PAIRed REFinement protocol
"""
# run date and time: ...
expected_stdout_2 = """
Please cite: "Paired refinement under the control of PAIREF"
M. Maly, K. Diederichs, J. Dohnalek, P. Kolenko (2020) IUCrJ 7
Command line arguments: """ + arguments + """
Program has been executed with following input parameters:
"""
expected_stdout_2 += " * XYZIN: " + str(config("mdm2_1-60A.pdb")) + "\n"
expected_stdout_2 += " * HKLIN: " + str(config("mdm2_merged.mtz")) + "\n"
expected_stdout_2 += """ * Project name: valid_args
* Resolution shells: 1.55,1.50,1.45,1.40,1.35,1.30
* Light-testing mode (REFMAC5 will not be executed).
"""
expected_stdout_2 += "Resolution of the merged diffraction data " + \
str(config("mdm2_merged.mtz")) + ": 61.93-1.25 A"
expected_stdout_2 += """
Manual setting of initial high resolution limit will be used: 1.60 A.
High resolution diffraction limits: 1.55 A, 1.50 A, 1.45 A, 1.40 A, 1.35 A, 1.30 A
"""
expected_stdout_2 += \
" * Data with FreeRflag set 0 will be excluded during refinement.\n"
# expected_stdout_2 += "\n"
# expected_stdout_2 += "Current working directory: " \
# "" + tempfile.gettempdir() + "/pairef_valid_args\n"
# expected_stdout_2 += \
# "------> RESULTS AND THE CURRENT STATUS OF CALCULATIONS ARE LISTED" \
# " IN A HTML LOG FILE " + tempfile.gettempdir() + \
# "/pairef_valid_args/PAIREF_valid_args.html\n\n"
stdout_all = cp.stdout.splitlines(True)
stdout_1 = "".join(stdout_all[:6])
stdout_2 = "".join(stdout_all[9:-4])
# stdout_2 = "".join(stdout_all[9:])
assert stdout_1 == expected_stdout_1
assert stdout_2 == expected_stdout_2
assert os.path.isdir("pairef_valid_args")
shutil.rmtree("pairef_valid_args")
assert cp.returncode == 0
assert not cp.stderr
def __init__(self, config_file, kafka_config_file, verbose):
self.logger = helper.setup_logging(self.__class__.__name__, verbose)
self.db_connection = DBConnection(verbose)
self.kafka_consumer = None
self.kafka_params = helper.config(kafka_config_file)
self.db_params = helper.config(config_file, "db")
self.params = helper.config(config_file)
def test_file_not_exists(tmp_environ):
cp = run("--HKLIN " + str(config("foo.mtz")) + ""
" --XYZIN " + str(config("mdm2_1-60A.pdb")) + ""
" -i 2" + ""
" -r " + RES_SHELLS_GOOD + ""
" -p file_not_exists")
assert cp.returncode != 0
# assert not cp.stdout
# assert cp.stderr == help + "\ncctbx.python -m pairef: error: " \
# "The file " + str(config("foo.mtz")) + " does not exist!\n"
assert cp.stderr == "error: " \
"The file " + str(config("foo.mtz")) + " does not exist!\n"
def test_invalid_res_shells_setting(tmp_environ,
res_init, res_shells, error_message):
if os.path.isdir("pairef_bad_res_shells_setting"):
# Preparation - clean rests from previously examined test that
# has been interrupted
shutil.rmtree("pairef_bad_res_shells_setting")
cp = run("--HKLIN " + str(config("mdm2_merged.mtz")) + ""
" --XYZIN " + str(config("mdm2_1-60A.pdb")) + ""
" -i " + res_init + ""
" -r " + res_shells + ""
" -p bad_res_shells_setting" + ""
" -t")
assert cp.returncode != 0
# assert not cp.stdout
assert cp.stderr == error_message
def test_matplotlib_bar(tmp_environ):
shutil.copy2(config("A_R-values.csv"), tempfile.gettempdir())
args = AttrDict()
args.project = "A"
args.complete_cross_validation = False
matplotlib_bar(args, values="R-values")
assert os.path.isfile("A_R-values.png")
os.remove("A_R-values.csv")
os.remove("A_R-values.png")
def test_write_log_html(tmp_environ):
versions_dict = {"refmac_version": "N/A", "pairef_version": "N/A"}
args = AttrDict()
args.xyzin = "fake.pdb"
args.hklin = "fake.mtz"
args.hklin_unmerged = "fake.HKL"
args.libin = "fake.mtz"
args.comin = "fake.com"
args.tlsin = "fake.tls"
args.defin = None
args.phenix = None
args.project = "A"
args.ncyc = 11
args.weight = None
args.tlsin_keep = None
args.tls_ncyc = None
args.flag = 0
args.add_to_bfactor = None
args.complete_cross_validation = False
args.no_modification = None
args.prerefinement_ncyc = None
args.reset_bfactor = None
args.add_to_bfactor = None
args.set_bfactor = None
args.shake_sites = None
args.constant_grid = None
shutil.copy2(config("A_R-values.csv"), tempfile.gettempdir())
shells_ready_with_res_init = (1.8, 1.7, 1.6)
shells = (1.8, 1.7, 1.6, 1.5)
flag_sets = range(20)
htmlfilename_in_progress = write_log_html(shells,
shells_ready_with_res_init, args,
versions_dict, flag_sets)
assert os.path.isfile(htmlfilename_in_progress)
with open(htmlfilename_in_progress, "r") as htmlfile_in_progress:
htmlfile_in_progress_content = htmlfile_in_progress.read()
assert "Calculations are still in progress" in htmlfile_in_progress_content
assert "</html>" in htmlfile_in_progress_content
os.remove(htmlfilename_in_progress)
htmlfilename_done = write_log_html(shells,
shells,
args,
versions_dict,
flag_sets,
done=True)
assert os.path.isfile(htmlfilename_done)
with open(htmlfilename_done, "r") as htmlfile_done:
htmlfile_done_content = htmlfile_done.read()
assert "Calculations are still in progress" not in htmlfile_done_content
assert "</html>" in htmlfile_done_content
os.remove(htmlfilename_done)
os.remove("A_R-values.csv")
def handle_expired_error(e):
try:
identify = e.get(helper.config('JWT_IDENTITY_CLAIM', 'identify'), None)
claims = e.get(helper.config('JWT_USER_CLAIMS', {}))
response = TokenExpired('Access token expired.').to_response()
response.headers['Authorization'] = create_access_token(identify, user_claims=claims)
query = g.get('query', None)
if query is not None:
expired_data = json.loads(response.get_data())
pre_script = expired_data.get('script', '')
sub_script = '$scope.term.retry(\'%s\', \'%s\', %s)' \
% (query.app, query.command, '[\'' + '\',\''.join(query.arguments) + '\']')
expired_data['script'] = pre_script + sub_script
response.set_data(json.dumps(expired_data))
return response
except Exception as be:
return TokenDiscarded(str(be)).to_response()
def test_matplotlib_line_Rgap(tmp_environ):
shutil.copy2(config("NK_Rgap.csv"), tempfile.gettempdir())
matplotlib_line(
shells=(1.8),
project="NK",
statistics="Rgap",
n_bins_low=10,
title="$\it{R}_{\mathrm{free}}-"
"\it{R}_{\mathrm{work}}$",
multiscale=False,
# title=r"$\it{R}_{\mathrm{free}}-"
# r"\it{R}_{\mathrm{work}}$", multiscale=False,
filename_suffix="Rgap")
assert os.path.isfile("NK_Rgap.png")
os.remove("NK_Rgap.csv")
os.remove("NK_Rgap.png")
def test_matplotlib_line_Rvalues(tmp_environ, statistics, title,
filename_suffix, pngfile):
files_in = [
"NK_R00_1-80A.csv", "NK_R00_1-70A.csv", "NK_R00_1-60A.csv",
"NK_R00_1-50A.csv"
]
for f in files_in:
shutil.copy2(config(f), tempfile.gettempdir())
matplotlib_line(shells=(1.8, 1.7, 1.6, 1.5),
project="NK",
statistics=statistics,
n_bins_low=10,
title=title,
multiscale=False,
filename_suffix=filename_suffix)
assert os.path.isfile(pngfile)
files = files_in + [pngfile]
for f in files:
os.remove(f)
'--rouge_only',
help='Only compute ROUGE scores, without writing summaries',
action='store_true')
parser.add_argument(
'--ind_rouge_scores',
help='Compute individual ROUGE scores for significance testing',
action='store_true')
args = parser.parse_args()
# Load vocab file
logging.info("Opening vocab file: {}".format(args.vocab_file))
with open(args.vocab_file, 'rb') as f:
vocab = pickle.load(f, encoding='latin1')
# Set up configs
config(args, vocab)
# Create directories if needed
args.ref_dir = os.path.join(args.data_dir, 'ref')
args.hyp_dir = os.path.join(args.data_dir, 'model')
args.article_dir = os.path.join(args.data_dir, 'articles')
if not os.path.exists(args.ref_dir):
raise ValueError(
"Please create reference summary directory, named 'ref'.")
if not os.path.exists(args.article_dir):
raise ValueError("Please create article directory, named 'articles'.")
if not os.path.exists(args.hyp_dir): os.mkdir(args.hyp_dir)
if args.rouge_only: compute_rouge(args)
elif args.ind_rouge_scores: write_rouge_scores(args)
else: make_summaries(args)
from helper import run_ok, config, user, pr_labels
RADIOACTIVE_WASE = '\n'.join([
f' PR https://github.com/{user}/filabel-testrepo2/pull/{num} - OK'
for num in reversed(range(1, 111 + 1))
]) + '\n'
RADIOACTIVE_WASE_ADD = RADIOACTIVE_WASE.replace('\n', '\n + danger\n')
RADIOACTIVE_WASE_DEL = RADIOACTIVE_WASE.replace('\n', '\n - danger\n')
auth = config("auth.real.cfg")
def test_radioactive_waste_empty():
cp = run_ok(f'--config-labels "{config("labels.empty.cfg")}" '
f'--config-auth "{auth}" '
f'{user}/filabel-testrepo2')
assert '\n' + cp.stdout == f'''
REPO {user}/filabel-testrepo2 - OK
{RADIOACTIVE_WASE}'''
assert pr_labels('filabel-testrepo2', 1) == []
assert pr_labels('filabel-testrepo2', 42) == []
assert pr_labels('filabel-testrepo2', 110) == []
def test_radioactive_waste_add():
cp = run_ok(f'--config-labels "{config("labels.radiation.cfg")}" '
f'--config-auth "{auth}" '
f'{user}/filabel-testrepo2')
assert '\n' + cp.stdout == f'''
import shutil
from pairef.commons import twodec, twodecname, fourdec, extract_from_file
from helper import run, config
@pytest.mark.parametrize(
["value_in", "value_twodec", "value_twodecname", "value_fourdec"],
[(2, "2.00", "2-00", "2.0000"), (0.617, "0.62", "0-62", "0.6170")])
def test_twodec_twodecname_fourdec(value_in, value_twodec, value_twodecname,
value_fourdec):
assert twodec(value_in) == value_twodec
assert twodecname(value_in) == value_twodecname
assert fourdec(value_in) == value_fourdec
filename = config("lysozyme_1-40A.log")
filename_fake = config("foo")
searched_stats = "Resolution limits"
searched_Rfree = "Free R factor"
table_stats_i = """Resolution limits = 39.355 1.402
Number of used reflections = 21761
Percentage observed = 97.1541
Percentage of free reflections = 5.0028
Overall R factor = 0.2103
Free R factor = 0.2236
Average Fourier shell correlation = 0.9155
AverageFree Fourier shell correlation= 0.9072
Overall weighted R factor = 0.2013
Free weighted R factor = 0.2116
Overall weighted R2 factor = 0.2598
Free weighted R2 factor = 0.2707
class MWindow(QWidget, Ui_MWindow):
# MDMailer Class handles everything except graphics
mdm = None
# recipientsWindow
recWin = recipientsWindow()
Mail_Thread = QThread()
config = helper.config()
send_signal = pyqtSignal()
export_pdf_act = None
def __init__(self, parent=None):
super().__init__(parent)
# construct MDMailer with server Info
self.mdm = MDMailer_(self.config.get_email(),
self.config.get_smtp(),
self.config.get_port(),
self.config.get_username(),
self.config.get_password())
# Connect Stuff here ...
self.mdtext.textedit.textChanged.connect(self.compile)
self.send_btn.pressed.connect(self.send)
self.add_att_btn.pressed.connect(self.add_att)
self.send_signal.connect(self.mdm.send)
self.mdm.finished_sending.connect(self.reenable_send)
self.mdm.progress2.connect(self.progress_bar.setMaximum)
self.mdm.progress1.connect(self.progress_bar.setValue)
self.multi_rec_btn.pressed.connect(self.open_recipientsWindow)
self.recWin.ready.connect(self.get_recipients)
del_att_short = QShortcut(QKeySequence(Qt.Key_Delete), self.attachments)
del_att_short.activated.connect(self.del_att)
self.export_pdf_act = QShortcut(QKeySequence("Ctrl+E"), self)
self.export_pdf_act.activated.connect(self.export_pdf)
self.stylesheet = """
.QPushButton {
background-color: #4CAF50;
border: none;
color: white;
padding: 5px 11px;
text-align: center;
text-decoration: none;
font-size: 16px;
}
.QPushButton:hover {
background-color: #555;
border: none;
color: white;
padding: 5px 11px;
text-align: center;
text-decoration: none;
font-size: 16px;
}
.QLineEdit {
background-color: #ddd;
font-size: 16px;
border-radius: 0px;
}
.QPlainTextEdit {
background-color: #fff;
font-size: 16px;
border-radius: 0px;
}
.QFileDialog:QPushButton {
background-color: #4CAF50;
border: none;
color: white;
padding: 5px 11px;
text-align: center;
text-decoration: none;
font-size: 16px;
}
.QListWidget {
background-color: #fff;
font-size: 16px;
}
.QProgressBar {
color: #FFFFFF;
border: none;
padding: 0px 0px;
margin: -3px;
border-radius: 0px;
}
.QProgressBar:chunk {
background-color: #4CAF50;
border: none;
padding: 0px 0px;
margin: 0px;
border-radius: 0px;
}
"""
self.setStyleSheet(self.stylesheet)
self.Mail_Thread.start()
self.mdm.moveToThread(self.Mail_Thread)
# Show html from plain text
def compile(self):
cursor = self.mdtext.textedit.textCursor()
cursor.movePosition(9, 1)
md_text_plain = self.mdtext.textedit.toPlainText()
md_text_plain = self.show_code_inline(md_text_plain)
html_c = self.mdm.get_html(md_text_plain, self.subject_edit.text())
scroll = self.html_view.page().mainFrame().scrollPosition()
max_y = self.html_view.page().mainFrame().scrollBarMaximum(2)
end = False
if scroll.y() == max_y:
end = True
self.html_view.setHtml(html_c)
if end:
scroll.setY(self.html_view.page().mainFrame().scrollBarMaximum(2))
self.html_view.page().mainFrame().setScrollPosition(scroll)
# Send Mail
def send(self):
self.mdm.mail_text = self.show_code_inline(self.mdtext.textedit.toPlainText())
self.mdm.subject = self.subject_edit.text()
to = self.to_edit.text()
if to != "":
rec = [to]
self.mdm.rec = rec
else:
if self.mdm.rec == [""]:
msg_box = QMessageBox()
msg_box.setIcon(QMessageBox.Information)
msg_box.setWindowTitle("No valid E-Mail address found")
msg_box.setInformativeText("No valid E-Mail address found")
files = []
for i in range(self.attachments.count()):
files.append(str(self.attachments.item(i).data(3)))
for i in re.findall(r"<att>?\(([^\)]*)\)", self.mdm.mail_text):
files.append(str(i))
re.sub(r"<att>?\(([^\)]*)\)", "", self.mdm.mail_text)
self.mdm.files = files
#self.mdm.send_mail(mail_text, subject, rec, files=files)
self.send_signal.emit()
self.send_signal.disconnect()
def add_att(self):
fd = QFileDialog()
files = fd.getOpenFileNames()
for f in files[0]:
item = QListWidgetItem()
item.setData(3, f)
item.setText(os.path.basename(f))
self.attachments.addItem(item)
def del_att(self):
for item in self.attachments.selectedItems():
tmp = self.attachments.takeItem(self.attachments.row(item))
del tmp
def open_recipientsWindow(self):
self.recWin.show()
def get_recipients(self):
self.mdm.rec = self.recWin.get_recipients()
self.recWin.close()
@pyqtSlot()
def reenable_send(self):
self.send_signal.connect(self.mdm.send)
def show_code_inline(self, text):
incs = re.findall(r"(<inc>?\[([^\]]*)\]\(([^\)]*)\))", text)
for inc in incs:
filename = None
for i in range(self.attachments.count()):
if str(self.attachments.item(i).data(2)) == inc[1]:
filename = self.attachments.item(i).data(3)
break
if not filename:
if os.path.isfile(inc[1]):
filename = inc[1]
else:
continue
lines = re.search(r'\blines="([ ]*[\d]+[ ]*-[ ]*[\d]+[ ]*)"', inc[2])
with open(filename, 'r') as file:
code = file.read()
if lines:
opts = inc[2].replace(lines[0], "")
lines = lines[1].split("-")
code = "\n".join(code.splitlines()[int(lines[0]) - 1:int(lines[1])])
else:
opts = inc[2]
if ("no_code" not in opts):
code = "~~~ " + opts + "\n" + code + "\n~~~"
text = text.replace(inc[0], code)
return text
def export_pdf(self):
filename, t = QFileDialog.getSaveFileName(None, "Export to PDF", ".pdf", "pdf (*.pdf)")
if filename == "":
return
html = self.html_view.page().mainFrame().toHtml()
pdfkit.from_string(html, filename)
import flask
import importlib
from helper import env, config, user
config_env = config('web_secret.cfg')
config_env_nosecret = config('web_nosecret.cfg')
def _import_app():
import committee
importlib.reload(committee) # force reload (config could change)
if hasattr(committee, 'app'):
return committee.app
elif hasattr(committee, 'create_app'):
return committee.create_app(None)
else:
raise RuntimeError(
"Can't find a Flask app. "
"Either instantiate `committee.app` variable "
"or implement `committee.create_app(dummy)` function. "
"See https://flask.palletsprojects.com/en/1.1.x/patterns/appfactories/"
"for additional information."
)
def _test_app():
app = _import_app()
app.config['TESTING'] = True
return app.test_client()
def test_integration_quick_mdm2(tmp_environ):
print("\nPerforming a quick integration test using mdm2 demo data"
", please wait...\n")
if os.path.isdir(dir_project):
# Preparation - clean rests from previously examined test that
# has been interrupted
shutil.rmtree(dir_project)
arguments = "--HKLIN " + str(config("mdm2_merged.mtz")) + \
" --XYZIN " + str(config("mdm2_1-60A.pdb")) + \
" -u " + hklin_unmerged + " -i 1.6 -r 1.55,1.5 -p test_quick_mdm2"
cp = run(arguments)
assert cp.returncode == 0
# assert not cp.stderr
expected_stdout_1 = """
__ _ ___ __ ___ ___
)_) /_) ) )_) )_ )_
/ / / _(_ / \ (__ (
automatic PAIRed REFinement protocol
version: """ + str(__version__) + "\n"
# run date and time: ...
expected_stdout_2 = """
Please cite: "Paired refinement under the control of PAIREF"
M. Maly, K. Diederichs, J. Dohnalek, P. Kolenko (2020) IUCrJ 7
Command line arguments: """ + arguments + """
Program has been executed with following input parameters:
"""
expected_stdout_2 += " * XYZIN: " + str(config("mdm2_1-60A.pdb")) + "\n"
expected_stdout_2 += " * HKLIN: " + str(config("mdm2_merged.mtz")) + "\n"
expected_stdout_2 += " * HKLIN unmerged: " + hklin_unmerged + "\n"
expected_stdout_2 += """ * Project name: test_quick_mdm2
* Resolution shells: 1.55,1.5
"""
expected_stdout_2 += "Resolution of the merged diffraction data " + \
str(config("mdm2_merged.mtz")) + ": 61.93-1.25 A\n"
expected_stdout_2 += "Resolution of the unmerged diffraction data " + \
hklin_unmerged + ": 61.90-1.24 A"
expected_stdout_2 += """
Manual setting of initial high resolution limit will be used: 1.60 A.
High resolution diffraction limits: 1.55 A, 1.50 A
"""
expected_stdout_2 += \
" * Data with FreeRflag set 0 will be excluded during refinement.\n"
expected_stdout_3 = """Refinement using REFMAC5:
* Calculating initial statistics at 1.60 A resolution...
Collecting statistics from logfiles...
* Refining using data up to 1.55 A resolution...
Running command:
refmac5 HKLIN mdm2_merged.mtz XYZIN test_quick_mdm2_R00_1-60A.pdb HKLOUT test_quick_mdm2_R00_1-55A.mtz XYZOUT test_quick_mdm2_R00_1-55A.pdb LIBOUT test_quick_mdm2_R00_1-55A.cif
Calculating statistics of the refined structure model... . . .
Collecting statistics from logfiles...
Updating graphs...
Preliminary suggested cutoff: 1.XX A
* Refining using data up to 1.50 A resolution...
Running command:
refmac5 HKLIN mdm2_merged.mtz XYZIN test_quick_mdm2_R00_1-55A.pdb HKLOUT test_quick_mdm2_R00_1-50A.mtz XYZOUT test_quick_mdm2_R00_1-50A.pdb LIBOUT test_quick_mdm2_R00_1-50A.cif
Calculating statistics of the refined structure model... . . . .
Collecting statistics from logfiles...
Updating graphs...
Preliminary suggested cutoff: 1.XX A
* Calculating merging statistics... . . . . . . . .
Using labels=I,SIGI
Suggested cutoff:
"""
stdout_all = cp.stdout.splitlines(True)
assert "Preliminary suggested cutoff:" in stdout_all[43]
stdout_all[43] = " Preliminary suggested cutoff: 1.XX A\n"
assert "Preliminary suggested cutoff:" in stdout_all[51]
stdout_all[51] = " Preliminary suggested cutoff: 1.XX A\n"
stdout_1 = "".join(stdout_all[:7])
stdout_2 = "".join(stdout_all[9:27])
stdout_3 = "".join(stdout_all[32:57])
assert stdout_1 == expected_stdout_1
assert stdout_2 == expected_stdout_2
assert stdout_3 == expected_stdout_3
assert "1.60 A" in stdout_all[57]
assert os.path.isdir(dir_project)
os.chdir(dir_project)
with open("PAIREF_out.log", "r") as stdout_logfile:
stdout_log = stdout_logfile.readlines()
assert "Preliminary suggested cutoff:" in stdout_log[43]
stdout_log[43] = " Preliminary suggested cutoff: 1.XX A\n"
assert "Preliminary suggested cutoff:" in stdout_log[51]
stdout_log[51] = " Preliminary suggested cutoff: 1.XX A\n"
print("STDOUT:\n" + cp.stdout)
stdout_log_1 = "".join(stdout_log[:7])
stdout_log_2 = "".join(stdout_log[9:27])
stdout_log_3 = "".join(stdout_log[32:57])
assert stdout_log_1 == expected_stdout_1
assert stdout_log_2 == expected_stdout_2
assert stdout_log_3 == expected_stdout_3
assert "1.60 A" in stdout_log[57]
files_out = \
["mdm2_1-60A.pdb",
"mdm2_merged.mtz",
"mdm2_unmerged.mtz",
"PAIREF_cutoff.txt",
"PAIREF_out.log",
"PAIREF_test_quick_mdm2.html",
"styles.css",
"test_quick_mdm2_1-60A.pdb",
"test_quick_mdm2_CCfree.png",
"test_quick_mdm2_CC.png",
"test_quick_mdm2_CCwork.png",
"test_quick_mdm2_Comp_Mult.png",
"test_quick_mdm2_Intensities.png",
"test_quick_mdm2_merging_stats.csv",
"test_quick_mdm2_No_reflections.png",
"test_quick_mdm2_No_work_free_reflections.png",
"test_quick_mdm2_Optical_resolution.csv",
"test_quick_mdm2_Optical_resolution.png",
"test_quick_mdm2_R00_1-50A_comparison_at_1-50A.log",
"test_quick_mdm2_R00_1-50A_comparison_at_1-50A.mtz",
"test_quick_mdm2_R00_1-50A_comparison_at_1-55A.log",
"test_quick_mdm2_R00_1-50A_comparison_at_1-55A.mtz",
"test_quick_mdm2_R00_1-50A_comparison_at_1-55A_prev_pair.log",
"test_quick_mdm2_R00_1-50A_comparison_at_1-55A_prev_pair.mtz",
"test_quick_mdm2_R00_1-50A_comparison_at_1-60A.log",
"test_quick_mdm2_R00_1-50A_comparison_at_1-60A.mtz",
"test_quick_mdm2_R00_1-50A.csv",
"test_quick_mdm2_R00_1-50A.log",
"test_quick_mdm2_R00_1-50A.mmcif",
"test_quick_mdm2_R00_1-50A.mtz",
"test_quick_mdm2_R00_1-50A.pdb",
# "test_quick_mdm2_R00_1-50A_sfcheck.log",
# "test_quick_mdm2_R00_1-50A_sfcheck.out",
# "test_quick_mdm2_R00_1-50A_sfcheck.ps",
# "test_quick_mdm2_R00_1-50A_sfcheck.xml",
"test_quick_mdm2_R00_1-50A_stats_vs_cycle.png",
"test_quick_mdm2_R00_1-55A_comparison_at_1-55A.log",
"test_quick_mdm2_R00_1-55A_comparison_at_1-55A.mtz",
"test_quick_mdm2_R00_1-55A_comparison_at_1-60A.log",
"test_quick_mdm2_R00_1-55A_comparison_at_1-60A.mtz",
"test_quick_mdm2_R00_1-55A_comparison_at_1-60A_prev_pair.log",
"test_quick_mdm2_R00_1-55A_comparison_at_1-60A_prev_pair.mtz",
"test_quick_mdm2_R00_1-55A.csv",
"test_quick_mdm2_R00_1-55A.log",
"test_quick_mdm2_R00_1-55A.mmcif",
"test_quick_mdm2_R00_1-55A.mtz",
"test_quick_mdm2_R00_1-55A.pdb",
# "test_quick_mdm2_R00_1-55A_sfcheck.log",
# "test_quick_mdm2_R00_1-55A_sfcheck.out",
# "test_quick_mdm2_R00_1-55A_sfcheck.ps",
# "test_quick_mdm2_R00_1-55A_sfcheck.xml",
"test_quick_mdm2_R00_1-55A_stats_vs_cycle.png",
"test_quick_mdm2_R00_1-60A_comparison_at_1-60A.log",
"test_quick_mdm2_R00_1-60A_comparison_at_1-60A.mtz",
"test_quick_mdm2_R00_1-60A.csv",
"test_quick_mdm2_R00_1-60A.log",
"test_quick_mdm2_R00_1-60A.mmcif",
"test_quick_mdm2_R00_1-60A.mtz",
"test_quick_mdm2_R00_1-60A.pdb",
# "test_quick_mdm2_R00_1-60A_sfcheck.log",
# "test_quick_mdm2_R00_1-60A_sfcheck.out",
# "test_quick_mdm2_R00_1-60A_sfcheck.ps",
# "test_quick_mdm2_R00_1-60A_sfcheck.xml",
"test_quick_mdm2_R00_Rgap.csv",
"test_quick_mdm2_R00_R-values.csv",
"test_quick_mdm2_Rfree.png",
"test_quick_mdm2_Rgap.csv",
"test_quick_mdm2_Rgap.png",
"test_quick_mdm2_Rmerge_Rmeas_Rpim.png",
"test_quick_mdm2_R-values.csv",
"test_quick_mdm2_R-values.png",
"test_quick_mdm2_Rwork.png"]
for f in files_out:
assert os.path.isfile(f)
# Rfree decrease?
# with open("test_quick_mdm2_R-values.csv", "r") as csvfile:
# csvfile_lines = csvfile.readlines()
# lines = [1, 2]
# for line in lines:
# assert float(csvfile_lines[line].split()[6]) < 0
# But CC* is lower than CCwork so suggested cutoff should be 1.60 A
with open("PAIREF_cutoff.txt", "r") as result:
assert result.read() == "1.60"
assert filecmp.cmp("test_quick_mdm2_R-values.csv",
"test_quick_mdm2_R00_R-values.csv")
assert filecmp.cmp("test_quick_mdm2_Rgap.csv",
"test_quick_mdm2_R00_Rgap.csv")
assert filecmp.cmp("test_quick_mdm2_R00_1-60A.log",
"test_quick_mdm2_R00_1-60A_comparison_at_1-60A.log")
assert filecmp.cmp("test_quick_mdm2_R00_1-60A.mtz",
"test_quick_mdm2_R00_1-60A_comparison_at_1-60A.mtz")
with open("PAIREF_test_quick_mdm2.html", "r") as htmlfile:
htmlfile_content = htmlfile.read()
assert "Calculations are still in progress" not in htmlfile_content
assert "</html>" in htmlfile_content
# Clean up
os.chdir("..")
shutil.rmtree(dir_project)
