psdi-data-conversion 0.0.38__py3-none-any.whl → 0.0.39__py3-none-any.whl

psdi_data_conversion/static/javascript/convert.js

@@ -7,7 +7,9 @@
 
 
 import { getInputFlags, getOutputFlags, getInputArgFlags, getOutputArgFlags } from "./data.js";
-import { commonConvertReady, convertFile, getExtCheck, splitArchiveExt, isArchiveExt } from "./convert_common.js"
+import {
+    SAFE_CHAR_REGEX, commonConvertReady, convertFile, getExtCheck, splitArchiveExt, isArchiveExt
+} from "./convert_common.js"
 
 var token = "",
     in_ext = "",
@@ -51,8 +53,24 @@ function enterArgument(event) {
     }
 }
 
+
+/**
+ * Validate the input for a format option - if invalid, display the error message, if valid, hide it
+ *
+ * @param {*} event 
+ */
+function validateInput(event) {
+    var err_id = this.id.replace('text', 'err')
+    if (this.validity.patternMismatch) {
+        $('#' + err_id).css({ display: "block" })
+    } else {
+        $('#' + err_id).css({ display: "none" })
+    }
+}
+
 // Uploads a user-supplied file
 function submitFile() {
+
     const file = $("#fileToUpload")[0].files[0],
         [fname, ext] = splitArchiveExt(file.name);
 
@@ -78,9 +96,16 @@ function submitFile() {
     const checked_in = $('input[name=in_arg_check]:checked'),
         checked_out = $('input[name=out_arg_check]:checked');
 
+    let security_passed = true;
+
     checked_in.each(function () {
         read_arg_flags += $("#" + this.id).val()[0];
-        const arg = $("#in_arg_text" + this.id.substring(this.id.length - 1, this.id.length)).val();
+        const e = $("#in_arg_text" + this.id.substring(this.id.length - 1, this.id.length));
+        const arg = e.val();
+
+        if (e[0].validity.patternMismatch) {
+            security_passed = false;
+        }
 
         if (/\S/.test(arg)) {
             read_args += arg.trim() + '£';
@@ -92,7 +117,12 @@ function submitFile() {
 
     checked_out.each(function () {
         write_arg_flags += $("#" + this.id).val()[0];
-        const arg = $("#out_arg_text" + this.id.substring(this.id.length - 1, this.id.length)).val();
+        const e = $("#out_arg_text" + this.id.substring(this.id.length - 1, this.id.length));
+        const arg = e.val();
+
+        if (e[0].validity.patternMismatch) {
+            security_passed = false;
+        }
 
         if (/\S/.test(arg)) {
             write_args += arg.trim() + '£';
@@ -102,9 +132,21 @@ function submitFile() {
         }
     })
 
+    let alert_msg = '';
+
+    if (!security_passed) {
+        alert_msg += 'ERROR: One or more ticked options contains invalid characters. They must match the regex /' +
+            SAFE_CHAR_REGEX + '/ .\n';
+    }
+
     if (!all_args_entered) {
-        alert('All ticked option flags need additional information to be entered into the associated text box.');
-        return;
+        alert_msg += 'ERROR: All ticked options need additional information to be entered into the associated ' +
+            'text box.\n';
+    }
+
+    if (alert_msg) {
+        alert(alert_msg);
+        return
     }
 
     const coordinates = $('input[name="coordinates"]:checked').val(),
@@ -216,11 +258,17 @@ function addCheckboxes(argFlags, type) {
                 <tr>
                     <td><input type='checkbox' id="${type}_check${flagCount}" name=${type}_check value="${flag}"></input></td>
                     <td><label for="${type}_check${flagCount}">${flag} [${brief}]: ${description}<label></td>
-                    <td><input type='text' id=${type}_text${flagCount} placeholder='-- type info. here --'></input></td>
+                    <td><input type='text' id="${type}_text${flagCount}" placeholder='-- type info. here --'
+                         pattern='` + SAFE_CHAR_REGEX + `'></input>
+                         <p class="init-hidden" id="${type}_err${flagCount}"><strong>ERROR:</strong> Input contains
+                         invalid characters; it must match the regex 
+                         <code class="secondary">/` + SAFE_CHAR_REGEX + `/</code></p>
+                    </td>
                     <td><span id= ${type}_label${flagCount}>${furtherInfo}</span></td>
                 </tr>`);
 
             $(`#${type}_text${flagCount}`).hide();
+            $(`#${type}_text${flagCount}`).on('input', validateInput);
             $(`#${type}_label${flagCount}`).hide();
             $(`#${type}_check${flagCount}`).change(enterArgument);
 

psdi_data_conversion/static/javascript/convert_common.js

@@ -18,6 +18,20 @@ const TARGZ_EXT = "tar.gz"
 const TARBZ_EXT = "tar.bz"
 const TARXZ_EXT = "tar.xz"
 
+// Short list of safe allowed characters:
+// \w: All letters and digits
+// \s: All whitespace characters
+// .: Period
+// \-: Hyphen
+// :: Colon
+// +: Plus symbol
+// *: Asterisk
+// =: Equals sign
+// $: Dollar sign
+// /: Forward-slash
+// \\: Backslash
+export const SAFE_CHAR_REGEX = "[\\w\\s.\\-:+*=$\\/\\\\]*"
+
 // Whether or not file extensions will be checked
 let extCheck = true;
 
@@ -271,10 +285,10 @@ function checkFile(event) {
 }
 
 /**
- * Allow the file upload to only accept the expected type of file
+ * Allow the file upload to only accept the expected type of file, plus archives
  */
 function limitFileType() {
-    $("#fileToUpload")[0].accept = "." + in_ext;
+    $("#fileToUpload")[0].accept = "." + in_ext + ", .zip, .tar, .tar.gz, .tar.xz, .tar.bz";
 }
 
 /**

psdi_data_conversion/static/javascript/data.js

@@ -63,6 +63,24 @@ export async function getOutputFormats() {
     return outFormats.sort((a, b) => compare([a.extension, b.extension], [a.note, b.note]))
 }
 
+/**
+ * Gets the ID for a format, given its extension and note
+ * 
+ * @param {string} extension - The extension of the format, e.g. 'pdb'
+ * @param {string} note - The note of the format, e.g. 'Protein Databank'
+ * @returns {(int|null)} - The ID of the format if found, or else null
+ */
+export async function getFormatId(extension, note) {
+
+    var format = (data.formats.filter(format => (format.extension === extension) && (format.note === note)));
+
+    if (format === undefined) {
+        return null;
+    }
+
+    return format[0].id;
+}
+
 export async function getOutputFormatsForInputFormat(inExtension, inNote) {
 
     const inputFormat = (data.formats.filter(format => (format.extension === inExtension) && (format.note === inNote)))[0];

psdi_data_conversion/static/styles/format.css

@@ -44,6 +44,13 @@ form {
   }
 }
 
+/* Invalid input fields switch to alternate background */
+
+input:invalid {
+  background-color: var(--ifm-color-primary);
+  color           : var(--ifm-hero-text-color);
+}
+
 /* Converter details, user input and file conversion initially not displayed. */
 .init-hidden {
   display: none

psdi_data_conversion/testing/conversion_callbacks.py

@@ -6,10 +6,10 @@ conversion test, run with the functions and classes defined in the `utils.py` mo
 """
 
 import abc
-from collections.abc import Callable, Iterable
-from dataclasses import dataclass, field
 import os
 import re
+from collections.abc import Callable, Iterable
+from dataclasses import dataclass, field
 from tempfile import TemporaryDirectory
 
 from psdi_data_conversion.constants import DATETIME_RE_RAW

psdi_data_conversion/testing/conversion_test_specs.py

@@ -13,10 +13,11 @@ from psdi_data_conversion.converters.base import (FileConverterAbortException, F
 from psdi_data_conversion.converters.c2x import CONVERTER_C2X
 from psdi_data_conversion.converters.openbabel import CONVERTER_OB, COORD_GEN_KEY, COORD_GEN_QUAL_KEY
 from psdi_data_conversion.database import FileConverterDatabaseException
-from psdi_data_conversion.testing.conversion_callbacks import (CheckArchiveContents, CheckException, CheckLogContents,
-                                                               CheckLogContentsSuccess, CheckFileStatus,
+from psdi_data_conversion.testing.conversion_callbacks import (CheckArchiveContents, CheckException, CheckFileStatus,
+                                                               CheckLogContents, CheckLogContentsSuccess,
                                                                CheckStderrContents, CheckStdoutContents,
-                                                               MatchOutputFile, MultiCallback as MCB)
+                                                               MatchOutputFile)
+from psdi_data_conversion.testing.conversion_callbacks import MultiCallback as MCB
 from psdi_data_conversion.testing.utils import ConversionTestSpec as Spec
 
 l_all_test_specs: list[Spec] = []
@@ -39,7 +40,7 @@ l_all_test_specs.append(Spec(name="Standard Multiple Tests",
                              to_format=["pdb-0",
                                         "cif", "mol2", "xyz",
                                         "cif", "xyz", "xyz",
-                                        "cif", "xyz", "xyz",
+                                        "cif", "xyz-0", "xyz-0",
                                         "cml"],
                              from_format=[None,
                                           None, None, None,
@@ -57,6 +58,17 @@ l_all_test_specs.append(Spec(name="Standard Multiple Tests",
 """A basic set of test conversions which we expect to succeed without issue, running conversions with each of the
 Open Babel, Atomsk, and c2x converters"""
 
+l_all_test_specs.append(Spec(name="c2x Formats Tests",
+                             to_format=["res", "abi", "POSCAR", "cml"],
+                             converter_name=CONVERTER_C2X,
+                             callback=MCB(CheckFileStatus(),
+                                          CheckLogContentsSuccess()),
+                             compatible_with_gui=False,
+                             ))
+"""Test converting with c2x to a few different formats which require special input. This test isn't run in the GUI
+solely to save on resources, since there are unlikely to be an GUI-specific issues raised by this test that aren't
+caught in others."""
+
 archive_callback = MCB(CheckFileStatus(),
                        CheckArchiveContents(l_filename_bases=["caffeine-no-flags",
                                                               "caffeine-ia",
@@ -209,7 +221,7 @@ Not compatible with the GUI, since the GUI can't forcibly delete files uploaded
 
 l_all_test_specs.append(Spec(name="Failed conversion - bad input file",
                              filename=["quartz_err.xyz", "cyclopropane_err.mol"],
-                             to_format=["inchi", "xyz"],
+                             to_format=["inchi", "xyz-0"],
                              from_format=[None, "mol-0"],
                              expect_success=False,
                              converter_name=[CONVERTER_OB, CONVERTER_C2X],

psdi_data_conversion/testing/gui.py

@@ -6,10 +6,10 @@ Utilities to aid in testing of the GUI
 
 import os
 import shutil
-from tempfile import TemporaryDirectory
-
 import time
 from dataclasses import dataclass
+from tempfile import TemporaryDirectory
+
 import pytest
 from selenium.common.exceptions import TimeoutException
 from selenium.webdriver.common.alert import Alert
@@ -45,6 +45,11 @@ def wait_and_find_element(root: WebDriver | EC.WebElement, xpath: str, by=By.XPA
     return root.find_element(by, xpath)
 
 
+def wait_for_cover_hidden(root: WebDriver):
+    """Wait until the page cover is removed"""
+    WebDriverWait(root, TIMEOUT).until(EC.invisibility_of_element((By.XPATH, "//div[@id='cover']")))
+
+
 @dataclass
 class GuiTestSpecRunner():
     """Class which provides an interface to run test conversions through the GUI
@@ -253,25 +258,30 @@ class GuiSingleTestSpecRunner:
         4. Click the "Yes" button to confirm and go to the convert page
         """
 
-        # Get the homepage
+        # Get the homepage and wait for the cover to be removed
         self.driver.get(f"{self.origin}/")
+        wait_for_cover_hidden(self.driver)
 
         wait_for_element(self.driver, "//select[@id='fromList']/option")
 
         # Select from_format from the 'from' list.
+        full_from_format = f"{self._from_format_info.name}: {self._from_format_info.note}"
         self.driver.find_element(
-            By.XPATH, f"//select[@id='fromList']/option[starts-with(.,'{self._from_format_info.name}:')]").click()
+            By.XPATH, f"//select[@id='fromList']/option[starts-with(.,'{full_from_format}')]").click()
 
         # Select to_format from the 'to' list.
+        full_to_format = f"{self._to_format_info.name}: {self._to_format_info.note}"
         self.driver.find_element(
-            By.XPATH, f"//select[@id='toList']/option[starts-with(.,'{self._to_format_info.name}:')]").click()
+            By.XPATH, f"//select[@id='toList']/option[starts-with(.,'{full_to_format}')]").click()
 
         # Select converter from the available conversion options list.
         self.driver.find_element(
             By.XPATH, f"//select[@id='success']/option[contains(.,'{self.single_test_spec.converter_name}')]").click()
 
-        # Click on the "Yes" button to accept the converter and go to the conversion page
+        # Click on the "Yes" button to accept the converter and go to the conversion page, and wait for the cover to be
+        # removed there
         self.driver.find_element(By.XPATH, "//input[@id='yesButton']").click()
+        wait_for_cover_hidden(self.driver)
 
     def _set_conversion_settings(self):
         """Set settings on the convert page appropriately for the desired conversion
@@ -315,13 +325,11 @@ class GuiSingleTestSpecRunner:
                 continue
             flags_select = Select(wait_and_find_element(self.driver, f"//select[@id='{select_id}']"))
             for flag in l_flags:
-                found = False
                 for option in flags_select.options:
                     if option.text.startswith(f"{flag}:"):
                         flags_select.select_by_visible_text(option.text)
-                        found = True
                         break
-                if not found:
+                else:
                     raise ValueError(f"Flag {flag} was not found in {select_id} selection box for conversion from "
                                      f"{self._from_format_info.name} to {self._to_format_info.name} with "
                                      f"converter {self.single_test_spec.converter_name}")
@@ -343,7 +351,6 @@ class GuiSingleTestSpecRunner:
 
             # Look for and set each option
             for option in l_options:
-                found = False
                 for row in l_rows:
                     l_items = row.find_elements(By.XPATH, "./td")
                     label = l_items[1]
@@ -357,10 +364,9 @@ class GuiSingleTestSpecRunner:
                     input_box = wait_and_find_element(l_items[2], "./input")
                     input_box.send_keys(option[1:])
 
-                    found = True
                     break
 
-                if not found:
+                else:
                     raise ValueError(f"Option {option} was not found in {table_id} options table for conversion from "
                                      f"{self._from_format_info.name} to {self._to_format_info.name} with "
                                      f"converter {self.single_test_spec.converter_name}")

psdi_data_conversion/testing/utils.py

@@ -6,12 +6,12 @@ This module defines general classes and methods used for unit tests.
 
 from __future__ import annotations
 
-from dataclasses import dataclass, field
-from collections.abc import Callable, Iterable
-from math import isclose
 import os
 import shlex
 import sys
+from collections.abc import Callable, Iterable
+from dataclasses import dataclass, field
+from math import isclose
 from tempfile import TemporaryDirectory
 from typing import Any
 from unittest.mock import patch

{psdi_data_conversion-0.0.38.dist-info → psdi_data_conversion-0.0.39.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: psdi_data_conversion
-Version: 0.0.38
+Version: 0.0.39
 Summary: Chemistry file format conversion service, provided by PSDI
 Project-URL: Homepage, https://data-conversion.psdi.ac.uk/
 Project-URL: Documentation, https://psdi-uk.github.io/psdi-data-conversion/

{psdi_data_conversion-0.0.38.dist-info → psdi_data_conversion-0.0.39.dist-info}/RECORD

@@ -1,12 +1,12 @@
 psdi_data_conversion/__init__.py,sha256=urMsTqsTHTch1q4rMT9dgGnrvdPFMP9B8r-6Kr8H5sE,404
-psdi_data_conversion/app.py,sha256=Ef8gXALojMrHaEWp1VJqEJ9CqYPWnXKFyObzlorNy9A,13253
+psdi_data_conversion/app.py,sha256=A1TUVYuHUJKbtBXC0MbCDwyNcZgCYLDWyt_2lPLETK0,14212
 psdi_data_conversion/constants.py,sha256=JWYC2gXsEi6bBl_NdEBh5nLZ7qX2LZZV_DutfEHJ8qo,7390
-psdi_data_conversion/converter.py,sha256=wgh13gzkzouEyEg1cXZ8KfIUXerXFF8VU-a4WgSO9ZE,23185
-psdi_data_conversion/database.py,sha256=CmV-yPBMa1Y9Uq_6h_C_dgIq9yi-qRvZCXlnLHNfxd4,55170
-psdi_data_conversion/dist.py,sha256=Ju6BcEuLrB738diTbK6HX6ZBiZ40Ctq1exj44nSCMlE,2292
-psdi_data_conversion/file_io.py,sha256=UXxNxTl_EabQ96UrLp4b38ctkYhXV_KIHJeTuyRBVpM,8857
-psdi_data_conversion/log_utility.py,sha256=WIgQp0pMsFtJJZKgIhStBNnjLzC6gEIodQAoXji5ht0,8789
-psdi_data_conversion/main.py,sha256=LBGTj2K_tx_YSPe-9I2biN0XEUpEiCnqhHa0kox0kHU,41791
+psdi_data_conversion/converter.py,sha256=A9u_xnzQ_OFp_rttttBNwZNA4d56Fdbm9FpjgyCroUA,23211
+psdi_data_conversion/database.py,sha256=tgqUxW75eaWiEsiHNI7pUfMTIKmB23zrprSZ3ZDpO3Y,55967
+psdi_data_conversion/dist.py,sha256=LOcKEP7H7JA9teX1m-5awuBi69gmdhtUit7yxtCTOZ8,2293
+psdi_data_conversion/file_io.py,sha256=LvdPmnYL_7Xlcr-7LJjUbbky4gKiqTTvPRzdbtvQaJo,8794
+psdi_data_conversion/log_utility.py,sha256=CHAq-JvBnTKaE0SHK5hM5j2dTbfSli4iUc3hsf6dBhc,8789
+psdi_data_conversion/main.py,sha256=NaV5Pqe-8qYn7ybgok3t6RuRK1H_9ip68UWpV7DRgO0,41773
 psdi_data_conversion/security.py,sha256=wjdrMre29TpkF2NqrsXJ5sschSAnDzqLYTLUcNR21Qw,902
 psdi_data_conversion/bin/LICENSE_ATOMSK,sha256=-Ay6SFTAf9x-OaRAiOgMNoutfUMLHx5jQQA1HqZ6p7I,34886
 psdi_data_conversion/bin/LICENSE_C2X,sha256=-Ay6SFTAf9x-OaRAiOgMNoutfUMLHx5jQQA1HqZ6p7I,34886
@@ -16,9 +16,9 @@ psdi_data_conversion/bin/mac/atomsk,sha256=pqExRdkR8NSqSasHZjE74R_CiM6Dkr_yvfyak
 psdi_data_conversion/bin/mac/c2x,sha256=dI-bBoQ6uqc6KMYKJaq0x7ejJgOf_wysTxQA5BrF8AY,2581960
 psdi_data_conversion/converters/__init__.py,sha256=15Ldt06eyZ0bgNPB4qg419U0Zcjt6TUCTzjCBo8EIzM,210
 psdi_data_conversion/converters/atomsk.py,sha256=_V33me1e4HW0-YXvdE-z6PdwtSK2gYV6QZf5d8aPqH4,1523
-psdi_data_conversion/converters/base.py,sha256=K6Zwfj6VHC_aEnuflqjGf0xF5kX24v_smTAQiyE0pzs,35892
-psdi_data_conversion/converters/c2x.py,sha256=9eSg85-FEhZ4Xj_yEAmbmq75Zg8woaplSfvDygZVbb0,1539
-psdi_data_conversion/converters/openbabel.py,sha256=Y0PN5BwlZaekUrt8dM6IuEtrvpmXYgvwnkLFlENDNoE,13223
+psdi_data_conversion/converters/base.py,sha256=gYZ-2f693_YBgJdlXFUZOpjVhB8PAbkbLFkOS9BFg9Q,36022
+psdi_data_conversion/converters/c2x.py,sha256=jDA84H8Jpz--ajTWNWX6K6oMfOMMbMxkA31-VnGi0gU,2019
+psdi_data_conversion/converters/openbabel.py,sha256=OYppOMfnvxmVgRY5vUkcVokWn-bQSSeG8MOFqN1MCIY,13224
 psdi_data_conversion/scripts/atomsk.sh,sha256=N_NMO5q8sI3Lt1TerC-xcKbMI0kfscAudy5UAbY0uR0,804
 psdi_data_conversion/scripts/c2x.sh,sha256=F48jhgtgouKKZDQ9p6tCCNBN5bPuidBq2GcTurdWzQc,770
 psdi_data_conversion/static/content/accessibility.htm,sha256=5mzlPM-d5KBoOuvuBTmer5QEI9lWQSd7FPH1KFn_7B0,14187
@@ -29,13 +29,13 @@ psdi_data_conversion/static/content/documentation.htm,sha256=1GiEjlDCP0kJ3CKkx3l
 psdi_data_conversion/static/content/download.htm,sha256=DQKWEuq_Bjv2TyV6DnPXnHrSOBvGYRHOU-m6YOwfsh4,4727
 psdi_data_conversion/static/content/feedback.htm,sha256=fZrhn4Egs9g6ygqPzV6ZG9ndYK02VdALNVNXRsZ716k,1788
 psdi_data_conversion/static/content/header-links.html,sha256=7B2bHa7dLfSZ4hPMvVJ3kR0niVAOO3FtHJo0K6m1oP4,693
-psdi_data_conversion/static/content/psdi-common-footer.html,sha256=CM9F6AXM1LVMLvTP51xTzOicEelSXlyXQyN-BjrQAJk,3933
+psdi_data_conversion/static/content/psdi-common-footer.html,sha256=Qo6ecItnjqngIu1Kyg8YOptqjraMFxyJTYu3wiW5Wuw,4080
 psdi_data_conversion/static/content/psdi-common-header.html,sha256=vRAgLGKE_RhXgBUQnarxnpkGl9j2Qeedqqo3VNDVGdk,1825
 psdi_data_conversion/static/content/report.htm,sha256=CRwlF7a7QvAjHsajuehWOtLxbo-JAjqrS_Q-I4BWxzs,4549
 psdi_data_conversion/static/content/index-versions/header-links.html,sha256=WN9oZL7hLtH_yv5PvX3Ky7_YGrNvQL_RQ5eU8DB50Rg,764
-psdi_data_conversion/static/content/index-versions/psdi-common-footer.html,sha256=zzizo_YEPhvH3_jNPFkFoKZA0TnIG6EXzQOsgooU1K8,3989
+psdi_data_conversion/static/content/index-versions/psdi-common-footer.html,sha256=nFZtEObp-X73p95oTOAvqzoPwjsEJD5dKUDhUPDCcj4,4136
 psdi_data_conversion/static/content/index-versions/psdi-common-header.html,sha256=IXmvdlArY-60b7HgvKjcNF3eSmEmTImX7Hdasswyi5s,1907
-psdi_data_conversion/static/data/data.json,sha256=_3o3BFEmnWGhoGMaviJsu-U9dJnk_tH9Wf0g-eDVWuU,3630027
+psdi_data_conversion/static/data/data.json,sha256=1nljosxtwbLRfIIIa6-GHJnhvzhB759oEGvVQ18QP_4,3647095
 psdi_data_conversion/static/img/colormode-toggle-dm.svg,sha256=Q85ODwU67chZ77lyT9gITtnmqzJEycFmz35dJuqaPXE,502
 psdi_data_conversion/static/img/colormode-toggle-lm.svg,sha256=sIKXsNmLIXU4fSuuqrN0r-J4Hd3NIqoiXNT3mdq5-Fo,1155
 psdi_data_conversion/static/img/psdi-icon-dark.svg,sha256=-hYXxegsw67i0qqAOYCx-I-ZPyG04wG0aBVTKoZQlL0,69747
@@ -62,26 +62,26 @@ psdi_data_conversion/static/img/ukri-logo-darktext.png,sha256=3UgghERAmFdnre0Ffc
 psdi_data_conversion/static/img/ukri-logo-lighttext.png,sha256=ptIQwIGGdVsO2rTximo9QjtJFH9DpkJcAs1glwKFjwo,25579
 psdi_data_conversion/static/javascript/accessibility.js,sha256=kbnWHeBNPrTLrnYRjMEUmiOcCXM2bORYIRfzUB03TAE,7208
 psdi_data_conversion/static/javascript/common.js,sha256=3YZdwfq54OPl-xIImTwjbXqxKqlrAaEbeac0cAHvScU,1720
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