Examples with DetailedLibrary uk.ac.bbsrc.tgac.miso.core.data.DetailedLibrary used on opensource projects

Example 1 with DetailedLibrary

use of uk.ac.bbsrc.tgac.miso.core.data.DetailedLibrary in project miso-lims by miso-lims.

the class BulkLibraryIT method testPropagate.

@Test
public void testPropagate() {
    BulkLibraryPage page = BulkLibraryPage.getForPropagate(getDriver(), getBaseUrl(), Arrays.asList(100004L), Arrays.asList(1));
    HandsOnTable table = page.getTable();
    Map<String, String> attrs = Maps.newLinkedHashMap();
    attrs.put(LibColumns.ID_BARCODE, "LIBT_PROP1");
    attrs.put(LibColumns.DESCRIPTION, "LIBT propagate test");
    attrs.put(LibColumns.SOP, "Library SOP 1 v.2.0");
    attrs.put(LibColumns.DESIGN, "WG");
    attrs.put(LibColumns.PLATFORM, "Illumina");
    attrs.put(LibColumns.LIBRARY_TYPE, "Paired End");
    attrs.put(LibColumns.INDEX_FAMILY, "Dual Index 6bp");
    attrs.put(LibColumns.INDEX_1, "A01 (AAACCC)");
    attrs.put(LibColumns.INDEX_2, "B01 (AAATTT)");
    attrs.put(LibColumns.KIT_DESCRIPTOR, "Test Kit");
    attrs.put(LibColumns.KIT_LOT, "20200728");
    attrs.put(LibColumns.QC_STATUS, "Ready");
    attrs.put(LibColumns.SIZE, "123");
    attrs.put(LibColumns.VOLUME, "6.66");
    attrs.put(LibColumns.CONCENTRATION, "12.57");
    fillRow(table, 0, attrs);
    // should be set by selecting Design
    attrs.put(LibColumns.CODE, "WG (Whole Genome)");
    attrs.put(LibColumns.SELECTION, "PCR");
    attrs.put(LibColumns.STRATEGY, "WGS");
    assertColumnValues(table, 0, attrs, "pre-save");
    assertTrue(page.save(false));
    HandsOnTable savedTable = page.getTable();
    Long newId = getSavedId(savedTable, 0);
    DetailedLibrary saved = (DetailedLibrary) getSession().get(LibraryImpl.class, newId);
    assertDetailedLibraryAttributes(attrs, saved);
}

Example 2 with DetailedLibrary

use of uk.ac.bbsrc.tgac.miso.core.data.DetailedLibrary in project miso-lims by miso-lims.

the class BulkLibraryIT method testRemoveFromBox.

@Test
public void testRemoveFromBox() {
    Long libId = 100006L;
    DetailedLibrary before = (DetailedLibrary) getSession().get(LibraryImpl.class, libId);
    assertNotNull(before.getBox());
    assertEquals("BOX100001", before.getBox().getName());
    assertEquals("A02", before.getBoxPosition());
    BulkLibraryPage page = BulkLibraryPage.getForEdit(getDriver(), getBaseUrl(), Sets.newHashSet(libId));
    HandsOnTable table = page.getTable();
    table.clearField(LibColumns.BOX_ALIAS, 0);
    assertTrue(page.save(false));
    DetailedLibrary after = (DetailedLibrary) getSession().get(LibraryImpl.class, libId);
    assertNull(after.getBox());
    assertNull(after.getBoxPosition());
}

Example 3 with DetailedLibrary

use of uk.ac.bbsrc.tgac.miso.core.data.DetailedLibrary in project miso-lims by miso-lims.

the class BulkLibraryIT method testEditChangeValues.

@Test
public void testEditChangeValues() {
    BulkLibraryPage page = BulkLibraryPage.getForEdit(getDriver(), getBaseUrl(), Sets.newHashSet(100001L));
    HandsOnTable table = page.getTable();
    // test initial values
    Map<String, String> attrs = Maps.newLinkedHashMap();
    attrs.put(LibColumns.NAME, "LIB100001");
    attrs.put(LibColumns.ALIAS, "LIBT_0001_Ly_P_PE_251_WG");
    attrs.put(LibColumns.ID_BARCODE, "libbar100001");
    attrs.put(LibColumns.DESCRIPTION, "libdesc100001");
    attrs.put(LibColumns.DESIGN, "");
    attrs.put(LibColumns.CODE, "WG (Whole Genome)");
    attrs.put(LibColumns.PLATFORM, "Illumina");
    attrs.put(LibColumns.LIBRARY_TYPE, "Paired End");
    attrs.put(LibColumns.SELECTION, "PCR");
    attrs.put(LibColumns.STRATEGY, "WGS");
    attrs.put(LibColumns.INDEX_FAMILY, "Dual Index 6bp");
    attrs.put(LibColumns.INDEX_1, "A01 (AAACCC)");
    attrs.put(LibColumns.INDEX_2, "B01 (AAATTT)");
    attrs.put(LibColumns.KIT_DESCRIPTOR, "Test Kit");
    attrs.put(LibColumns.QC_STATUS, "Failed: QC");
    attrs.put(LibColumns.SIZE, "251");
    attrs.put(LibColumns.VOLUME, "2.5");
    attrs.put(LibColumns.CONCENTRATION, "10.0");
    attrs.put(LibColumns.SPIKE_IN, "Spike-In One");
    attrs.put(LibColumns.SPIKE_IN_DILUTION, "1:10");
    attrs.put(LibColumns.SPIKE_IN_VOL, "12.34");
    assertColumnValues(table, 0, attrs, "loaded");
    Map<String, String> changes = Maps.newLinkedHashMap();
    changes.put(LibColumns.ALIAS, "LIBT_0001_Ly_P_PE_241_WG");
    changes.put(LibColumns.ID_BARCODE, "changed100001");
    changes.put(LibColumns.DESCRIPTION, "changed100001");
    changes.put(LibColumns.DESIGN, "EX");
    changes.put(LibColumns.LIBRARY_TYPE, "Single End");
    changes.put(LibColumns.INDEX_FAMILY, "Single Index 6bp");
    changes.put(LibColumns.INDEX_1, "Index 01 (AAAAAA)");
    changes.put(LibColumns.KIT_DESCRIPTOR, "Test Kit Two");
    changes.put(LibColumns.QC_STATUS, "Ready");
    changes.put(LibColumns.SIZE, "241");
    changes.put(LibColumns.VOLUME, "1.88");
    changes.put(LibColumns.CONCENTRATION, "12.34");
    fillRow(table, 0, changes);
    // unchanged
    changes.put(LibColumns.NAME, "LIB100001");
    changes.put(LibColumns.PLATFORM, "Illumina");
    // set based on other changes
    changes.put(LibColumns.CODE, "EX (Exome)");
    changes.put(LibColumns.SELECTION, "Hybrid Selection");
    changes.put(LibColumns.STRATEGY, "WXS");
    changes.put(LibColumns.INDEX_2, "");
    assertColumnValues(table, 0, changes, "changes pre-save");
    assertTrue(page.save(false));
    DetailedLibrary lib = (DetailedLibrary) getSession().get(LibraryImpl.class, 100001L);
    assertDetailedLibraryAttributes(changes, lib);
}

Example 4 with DetailedLibrary

use of uk.ac.bbsrc.tgac.miso.core.data.DetailedLibrary in project miso-lims by miso-lims.

the class BulkLibraryIT method testReceipt.

@Test
public void testReceipt() {
    BulkLibraryPage page = BulkLibraryPage.getForReceive(getDriver(), getBaseUrl(), 1, null, 15L);
    HandsOnTable table = page.getTable();
    Map<String, String> attrs = Maps.newLinkedHashMap();
    attrs.put(SamColumns.SAMPLE_TYPE, "GENOMIC");
    attrs.put(SamColumns.SCIENTIFIC_NAME, "Homo sapiens");
    attrs.put(SamColumns.PROJECT, "LIBT");
    attrs.put(SamColumns.EXTERNAL_NAME, "lkjh");
    attrs.put(SamColumns.DONOR_SEX, "Unknown");
    attrs.put(SamColumns.TISSUE_ORIGIN, "Bn (Brain)");
    attrs.put(SamColumns.TISSUE_TYPE, "P (Primary tumour)");
    attrs.put(SamColumns.TIMES_RECEIVED, "3");
    attrs.put(SamColumns.TUBE_NUMBER, "4");
    attrs.put(LibColumns.ID_BARCODE, "LIBT_RCV1");
    attrs.put(LibColumns.DESCRIPTION, "LIBT receive test");
    attrs.put(LibColumns.RECEIVE_DATE, "2017-10-12");
    attrs.put(LibColumns.RECEIVE_TIME, "3:00 pm");
    attrs.put(LibColumns.RECEIVED_FROM, "University Health Network - BioBank");
    attrs.put(LibColumns.RECEIVED_BY, "TestGroupOne");
    attrs.put(LibColumns.RECEIPT_CONFIRMED, "True");
    attrs.put(LibColumns.RECEIPT_QC_PASSED, "True");
    attrs.put(LibColumns.RECEIPT_QC_NOTE, "");
    attrs.put(LibColumns.DESIGN, "WG");
    attrs.put(LibColumns.PLATFORM, "Illumina");
    attrs.put(LibColumns.LIBRARY_TYPE, "Paired End");
    attrs.put(LibColumns.INDEX_FAMILY, "Dual Index 6bp");
    attrs.put(LibColumns.INDEX_1, "A01 (AAACCC)");
    attrs.put(LibColumns.INDEX_2, "B01 (AAATTT)");
    attrs.put(LibColumns.KIT_DESCRIPTOR, "Test Kit");
    attrs.put(LibColumns.QC_STATUS, "Ready");
    attrs.put(LibColumns.SIZE, "123");
    attrs.put(LibColumns.VOLUME, "6.66");
    attrs.put(LibColumns.CONCENTRATION, "12.57");
    fillRow(table, 0, attrs);
    // should be set by selecting Design
    attrs.put(LibColumns.CODE, "WG (Whole Genome)");
    attrs.put(LibColumns.SELECTION, "PCR");
    attrs.put(LibColumns.STRATEGY, "WGS");
    assertColumnValues(table, 0, attrs, "pre-save");
    assertTrue(page.save(false));
    HandsOnTable savedTable = page.getTable();
    Long newId = getSavedId(savedTable, 0);
    DetailedLibrary saved = (DetailedLibrary) getSession().get(LibraryImpl.class, newId);
    assertDetailedLibraryAttributes(attrs, saved);
    assertParentSampleAttributes(attrs, saved);
}

Example 5 with DetailedLibrary

use of uk.ac.bbsrc.tgac.miso.core.data.DetailedLibrary in project miso-lims by miso-lims.

the class BulkLibraryIT method testEditValueAdditions.

@Test
public void testEditValueAdditions() {
    BulkLibraryPage page = BulkLibraryPage.getForEdit(getDriver(), getBaseUrl(), Sets.newHashSet(100003L));
    HandsOnTable table = page.getTable();
    Map<String, String> attrs = Maps.newLinkedHashMap();
    attrs.put(LibColumns.NAME, "LIB100003");
    attrs.put(LibColumns.ALIAS, "LIBT_0001_Ly_P_PE_253_WG");
    attrs.put(LibColumns.ID_BARCODE, null);
    attrs.put(LibColumns.DESCRIPTION, null);
    attrs.put(LibColumns.DESIGN, "");
    attrs.put(LibColumns.CODE, "WG (Whole Genome)");
    attrs.put(LibColumns.PLATFORM, "Illumina");
    attrs.put(LibColumns.LIBRARY_TYPE, "Paired End");
    attrs.put(LibColumns.SELECTION, "PCR");
    attrs.put(LibColumns.STRATEGY, "WGS");
    attrs.put(LibColumns.INDEX_FAMILY, NO_INDEX_FAMILY);
    attrs.put(LibColumns.INDEX_1, "");
    attrs.put(LibColumns.INDEX_2, "");
    attrs.put(LibColumns.KIT_DESCRIPTOR, "Test Kit");
    attrs.put(LibColumns.QC_STATUS, "Not Ready");
    attrs.put(LibColumns.SIZE, null);
    attrs.put(LibColumns.VOLUME, null);
    attrs.put(LibColumns.CONCENTRATION, null);
    attrs.put(LibColumns.SPIKE_IN, null);
    attrs.put(LibColumns.SPIKE_IN_DILUTION, null);
    attrs.put(LibColumns.SPIKE_IN_VOL, null);
    assertColumnValues(table, 0, attrs, "loaded");
    Map<String, String> changes = Maps.newLinkedHashMap();
    changes.put(LibColumns.ID_BARCODE, "changed_bar_100003");
    changes.put(LibColumns.DESCRIPTION, "changed_desc_100003");
    changes.put(LibColumns.DESIGN, "TS (PCR)");
    changes.put(LibColumns.INDEX_FAMILY, "Dual Index 6bp");
    changes.put(LibColumns.INDEX_1, "A04 (TTTGGG)");
    changes.put(LibColumns.INDEX_2, "B04 (TTTAAA)");
    changes.put(LibColumns.QC_STATUS, "Ready");
    changes.put(LibColumns.SIZE, "253");
    changes.put(LibColumns.VOLUME, "18.0");
    changes.put(LibColumns.CONCENTRATION, "7.6");
    fillRow(table, 0, changes);
    // changed because of design
    changes.put(LibColumns.CODE, "TS (Targeted Sequencing)");
    changes.put(LibColumns.SELECTION, "PCR");
    changes.put(LibColumns.STRATEGY, "AMPLICON");
    // unchanged
    attrs.forEach((key, val) -> {
        if (!changes.containsKey(key)) {
            changes.put(key, val);
        }
    });
    assertColumnValues(table, 0, changes, "changes pre-save");
    assertTrue(page.save(false));
    DetailedLibrary lib = (DetailedLibrary) getSession().get(LibraryImpl.class, 100003L);
    assertDetailedLibraryAttributes(changes, lib);
}