DAOTHER-8197: Add em_map display to review page.

wwpdb/apps/ann_tasks_v2/report/PdbxReport.py

@@ -20,13 +20,14 @@
 import sys
 import traceback
 
-from wwpdb.apps.ann_tasks_v2.report.styles.PdbxIo import PdbxReportIo, PdbxGeometryReportIo, PdbxXrayExpReportIo, PdbxLinksReportIo
+from wwpdb.apps.ann_tasks_v2.report.styles.PdbxIo import PdbxReportIo, PdbxGeometryReportIo, PdbxXrayExpReportIo, PdbxLinksReportIo, EmInfoReportIo
 from mmcif_utils.style.PdbxGeometryReportCategoryStyle import PdbxGeometryReportCategoryStyle
 
 from wwpdb.apps.ann_tasks_v2.report.PdbxReportDepictBootstrap import PdbxReportDepictBootstrap
 from wwpdb.apps.ann_tasks_v2.report.styles.DCCReport import PdbxXrayExpReportCategoryStyle
 from wwpdb.apps.ann_tasks_v2.report.styles.ModelReport import PdbxReportCategoryStyle
 from wwpdb.apps.ann_tasks_v2.report.styles.LinksReport import PdbxLinksReportCategoryStyle
+from wwpdb.apps.ann_tasks_v2.report.styles.PdbxEmExtensionCategoryStyle import PdbxEmExtensionCategoryStyle
 
 
 class PdbxReport(object):
@@ -117,6 +118,12 @@ def makeTabularReport(self, filePath=None, contentType=None, idCode=None, layout
                 rdd = PdbxReportDepictBootstrap(styleObject=PdbxLinksReportCategoryStyle(), includePath=includePath, verbose=self.__verbose, log=self.__lfh)
                 oL = rdd.render(dd, style=layout, leadingHtmlL=leadingHtmlL, trailingHtmlL=trailingHtmlL)
 
+            if contentType in ["em-map-info-report"]:
+                self.setFilePath(filePath, fileFormat=fileFormat, idCode=idCode)
+                dd = self.doReport(contentType)
+                rdd = PdbxReportDepictBootstrap(styleObject=PdbxEmExtensionCategoryStyle(), includePath=includePath, verbose=self.__verbose, log=self.__lfh)
+                oL = rdd.render(dd, style=layout, leadingHtmlL=leadingHtmlL, trailingHtmlL=trailingHtmlL)
+
             if self.__debug:
                 self.__lfh.write("+PdbxReport.makeTabularReport - generated HTML \n%s\n" % "\n".join(oL))
 
@@ -182,6 +189,8 @@ def doReport(self, contentType="model"):
                 pdbxR = PdbxXrayExpReportIo(verbose=self.__verbose, log=self.__lfh)
             elif contentType == "links-report":
                 pdbxR = PdbxLinksReportIo(verbose=self.__verbose, log=self.__lfh)
+            elif contentType == "em-map-info-report":
+                pdbxR = EmInfoReportIo(verbose=self.__verbose, log=self.__lfh)
 
             pdbxR.setFilePath(localPath, idCode=None)
             pdbxR.get()

wwpdb/apps/ann_tasks_v2/report/PdbxReportDepictBootstrap.py

@@ -137,6 +137,12 @@ def __setup(self):
             self.__reportCategories = [
                 ("struct_conn", "", "row-wise"),
             ]
+        elif self.__st.getStyleId() in ["PDBX_STYLE_EmExtension_V1"]:
+            self.__reportCategories = [
+                ("em_map", "", "row-wise"),
+            ]
+        else:
+            self.__lfh.write("Error: PdbxReportDepict.__setup unknown style %s\n" % self.__st.getStyleId())
 
     def render(self, eD, style="tabs", leadingHtmlL=None, trailingHtmlL=None):
         """ """

wwpdb/apps/ann_tasks_v2/report/styles/PdbxIo.py

@@ -45,6 +45,7 @@
 # from mmcif_utils.style.PdbxReportCategoryStyle import PdbxReportCategoryStyle
 from wwpdb.apps.ann_tasks_v2.report.styles.ModelReport import PdbxReportCategoryStyle
 from wwpdb.apps.ann_tasks_v2.report.styles.LinksReport import PdbxLinksReportCategoryStyle
+from wwpdb.apps.ann_tasks_v2.report.styles.PdbxEmExtensionCategoryStyle import PdbxEmExtensionCategoryStyle
 
 logger = logging.getLogger()
 
@@ -872,3 +873,57 @@ def update(self, catName, attributeName, value, iRow=0):
 
     def write(self, filePath):
         return self.writeFile(filePath)
+
+class EmInfoReportIo(PdbxStyleIoUtil):
+    """Methods for reading EM information details."""
+
+    def __init__(self, verbose=True, log=sys.stderr):
+        super(EmInfoReportIo, self).__init__(styleObject=PdbxEmExtensionCategoryStyle(), verbose=verbose, log=log)
+
+        # self.__verbose = verbose
+        # self.__debug = False
+        self.__lfh = log
+        #
+        self.__filePath = None
+
+        self.__idCode = None
+
+    def getCategory(self, catName="entity"):
+        return self.getItemDictList(catName)
+
+    def setFilePath(self, filePath, idCode=None):
+        """Specify the file path for the target and optionally provide an identifier
+        for the data section within the file.
+        """
+        self.__filePath = filePath
+        self.__idCode = idCode
+        if self.readFile(self.__filePath):
+            if self.__idCode is not None:
+                return self.setContainer(containerName=self.__idCode)
+            else:
+                return self.setContainer(containerIndex=0)
+        else:
+            return False
+
+    def get(self):
+        """
+        Check for a valid current data container.
+
+        Returns True for success or False otherwise.
+        """
+        return self.getCurrentContainerId() is not None
+
+    def complyStyle(self):
+        return self.testStyleComplete(self.__lfh)
+
+    def setBlock(self, blockId):
+        return self.setContainer(containerName=blockId)
+
+    def newBlock(self, blockId):
+        return self.newContainer(containerName=blockId)
+
+    def update(self, catName, attributeName, value, iRow=0):
+        return self.updateAttribute(catName, attributeName, value, iRow=iRow)
+
+    def write(self, filePath):
+        return self.writeFile(filePath)

wwpdb/apps/ann_tasks_v2/webapp/CommonTasksWebAppWorker.py

@@ -2114,6 +2114,7 @@ def _renderCheckReports(self, entryId, fileSource="archive", instance=None, cont
             "special-position-report",
             "emd-xml-header-report",
             "em-map-check-report",
+            "em-map-info-report",
             "downloads",
         ]:
             myD[ky] = None
@@ -2297,6 +2298,29 @@ def _renderCheckReports(self, entryId, fileSource="archive", instance=None, cont
                     myD[cT] = self.__getFileTextWithMarkup(downloadPath)
                 else:
                     myD[cT] = self.__getMessageTextWithMarkup("")
+            elif cT == "em-map-info-report":
+                if useModelFileVersion:
+                    versionId = "latest"
+                else:
+                    versionId = "none"
+
+                # Try to avoid fetch if not needed
+                downloadPath = du.getFilePath(entryId, contentType="model", formatType="pdbx", fileSource=fileSource, instance=instance, versionId=versionId)
+                if downloadPath is None or not os.path.exists(downloadPath):
+                    ok = du.fetchId(entryId, contentType="model", formatType="pdbx", fileSource=fileSource, instance=instance, versionId=versionId)
+                    downloadPath = du.getDownloadPath()
+                else:
+                    ok = True
+                if ok:
+                    aTagList.append(du.getAnchorTag())
+                    myD[cT] = "\n".join(pR.makeTabularReport(filePath=downloadPath, contentType="em-map-info-report", idCode=entryId, layout=layout))
+                else:
+                    myD[cT] = self.__getMessageTextWithMarkup("None")
+            elif cT == "downloads":
+                # We call this a "report type" - might not be correct...
+                pass
+            else:
+                self._lfh.write("+CommonTasksWebAppWorker._renderCheckReports() unknown report %r\n" % cT)
 
         # downloads
 
@@ -2700,7 +2724,7 @@ def _generateCheckReportsJson(self, entryId, operation, fileSource="wf-archive",
                 "check-em-map",
             ]
             aTagList = self._makeCheckReports([entryId], operationList=opList, fileSource=fileSource, useFileVersions=useFileVersions)
-            cTList = ["model"]
+            cTList = ["model", "em-map-info-report"]
             cTList.extend(sorted(opCtD.values()))
             if self._verbose:
                 self._lfh.write("+ReviewDataWebAppWorker._reviewDataInlineIdOps() content type list %r\n" % cTList)

wwpdb/apps/ann_tasks_v2/webapp/ReviewDataWebAppWorker.py

@@ -340,6 +340,7 @@ def _generateFullCheckReportHtml(self, idCode, fileSource="wf-archive", instance
             # 'model-pdb',
             "emd-xml-header-report",
             "em-map-check-report",
+            "em-map-info-report",
             "downloads",
         ]
         reportD = self._renderCheckReports(idCode, fileSource=fileSource, instance=instance, contentTypeList=cTL)